3SWS

Crystal Structure of the Quinone Form of Methylamine Dehydrogenase in Complex with the Diferric Form of MauG

PDB DOI: https://doi.org/10.2210/pdb3SWS/pdb

Classification: OXIDOREDUCTASE/ELECTRON TRANSPORT
Organism(s): Paracoccus denitrificans PD1222
Expression System: Paracoccus denitrificans PD1222, Cereibacter sphaeroides
Mutation(s): No

Deposited: 2011-07-14 Released: 2012-07-25
Deposition Author(s): Jensen, L.M.R., Wilmot, C.M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.86 Å
R-Value Free:
0.178 (Depositor), 0.180 (DCC)
R-Value Work:
0.136 (Depositor), 0.140 (DCC)
R-Value Observed:
0.138 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Crystal Structure of the Quinone Form of Methylamine Dehydrogenase in Complex with the Diferric Form of MauG

Jensen, L.M.R., Wilmot, C.M.

To be published.

Macromolecule Content

Total Structure Weight: 200.79 kDa
Atom Count: 15,667
Modelled Residue Count: 1,711
Deposited Residue Count: 1,792
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Methylamine utilization protein MauG	A, B	373	Paracoccus denitrificans PD1222	Mutation(s): 0 Gene Names: mauG, Pden_4736 EC: 1
UniProt
Find proteins for Q51658 (Paracoccus denitrificans (strain Pd 1222)) Explore Q51658 Go to UniProtKB: Q51658
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q51658
Sequence Annotations Expand
Reference Sequence LOADING

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Methylamine dehydrogenase light chain	C, E	137	Paracoccus denitrificans PD1222	Mutation(s): 0 Gene Names: mauA EC: 1.4.99.3 (PDB Primary Data), 1.4.9.1 (UniProt)
UniProt
Find proteins for A1BBA0 (Paracoccus denitrificans (strain Pd 1222)) Explore A1BBA0 Go to UniProtKB: A1BBA0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A1BBA0
Sequence Annotations Expand
Reference Sequence LOADING

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Methylamine dehydrogenase heavy chain	D, F	386	Paracoccus denitrificans PD1222	Mutation(s): 0 Gene Names: Pden_4730 EC: 1.4.99.3 (PDB Primary Data), 1.4.9.1 (UniProt)
UniProt
Find proteins for A1BB97 (Paracoccus denitrificans (strain Pd 1222)) Explore A1BB97 Go to UniProtKB: A1BB97
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A1BB97
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEC Query on HEC Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain K [auth A]	J [auth A], K [auth A], P [auth B], Q [auth B]	HEME C C₃₄ H₃₄ Fe N₄ O₄ HXQIYSLZKNYNMH-LJNAALQVSA-N		Interactions Focus chain J [auth A] Focus chain K [auth A] Focus chain P [auth B] Focus chain Q [auth B] Interactions & Density Focus chain J [auth A] Focus chain K [auth A] Focus chain P [auth B] Focus chain Q [auth B]
1PE Query on 1PE Download Ideal Coordinates CCD File SDF format, chain V [auth D] MOL2 format, chain V [auth D] mmCIF format, chain V [auth D]	V [auth D]	PENTAETHYLENE GLYCOL C₁₀ H₂₂ O₆ JLFNLZLINWHATN-UHFFFAOYSA-N		Interactions Focus chain V [auth D] Interactions & Density Focus chain V [auth D]
MES Query on MES Download Ideal Coordinates CCD File SDF format, chain S [auth D] MOL2 format, chain S [auth D] mmCIF format, chain S [auth D]	S [auth D]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain S [auth D] Interactions & Density Focus chain S [auth D]
PG4 Query on PG4 Download Ideal Coordinates CCD File SDF format, chain W [auth F] MOL2 format, chain W [auth F] mmCIF format, chain W [auth F]	W [auth F]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain W [auth F] Interactions & Density Focus chain W [auth F]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain R [auth B] SDF format, chain T [auth D] MOL2 format, chain L [auth A] MOL2 format, chain R [auth B] MOL2 format, chain T [auth D] mmCIF format, chain L [auth A] mmCIF format, chain R [auth B] mmCIF format, chain T [auth D]	L [auth A], R [auth B], T [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain L [auth A] Focus chain R [auth B] Focus chain T [auth D] Interactions & Density Focus chain L [auth A] Focus chain R [auth B] Focus chain T [auth D]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain U [auth D] MOL2 format, chain U [auth D] mmCIF format, chain U [auth D]	U [auth D]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain U [auth D] Interactions & Density Focus chain U [auth D]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain M [auth B] MOL2 format, chain G [auth A] MOL2 format, chain M [auth B] mmCIF format, chain G [auth A] mmCIF format, chain M [auth B]	G [auth A], M [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain M [auth B] Interactions & Density Focus chain G [auth A] Focus chain M [auth B]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain H [auth A] SDF format, chain I [auth A] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A]	H [auth A], I [auth A], N [auth B], O [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain N [auth B] Focus chain O [auth B] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain N [auth B] Focus chain O [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
TRQ Query on TRQ	C, E	L-PEPTIDE LINKING	C₁₁ H₁₀ N₂ O₄		TRP

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.86 Å
R-Value Free: 0.178 (Depositor), 0.180 (DCC)
R-Value Work: 0.136 (Depositor), 0.140 (DCC)
R-Value Observed: 0.138 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.222	α = 64.77
b = 99.422	β = 74.77
c = 102.832	γ = 75.14

Software Package:

Software Name	Purpose
Blu-Ice	data collection
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
REFMAC	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2012-07-25

Deposition Author(s):

Jensen, L.M.R.

Wilmot, C.M.

Revision History (Full details and data files)

Version 1.0: 2012-07-25
Type: Initial release
Version 1.1: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description