9EWK | pdb_00009ewk

Solvent organization in ultrahigh-resolution protein crystal structure at room temperature

PDB DOI: https://doi.org/10.2210/pdb9EWK/pdb

Classification: PLANT PROTEIN
Organism(s): Crambe hispanica subsp. abyssinica
Mutation(s): Yes

Deposited: 2024-04-04 Released: 2024-09-04
Deposition Author(s): Chen, J.C.-H., Gilski, M., Chang, C., Borek, D., Rosenbaum, G., Lavens, A., Otwinowski, Z., Kubicki, M., Dauter, Z., Jaskolski, M., Joachimiak, A.
Funding Organization(s): Department of Energy (DOE, United States), National Institutes of Health/National Cancer Institute (NIH/NCI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 0.70 Å
R-Value Work:
0.076 (Depositor), 0.068 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Solvent organization in the ultrahigh-resolution crystal structure of crambin at room temperature.

Chen, J.C.H., Gilski, M., Chang, C., Borek, D., Rosenbaum, G., Lavens, A., Otwinowski, Z., Kubicki, M., Dauter, Z., Jaskolski, M., Joachimiak, A.

(2024) IUCrJ 11: 649-663

PubMed: 39190507 Search on PubMed
DOI: https://doi.org/10.1107/S2052252524007784
Primary Citation of Related Structures:
9EWK

PubMed Abstract:
Ultrahigh-resolution structures provide unprecedented details about protein dynamics, hydrogen bonding and solvent networks. The reported 0.70 Å, room-temperature crystal structure of crambin is the highest-resolution ambient-temperature structure of a protein achieved to date. Sufficient data were collected to enable unrestrained refinement of the protein and associated solvent networks using SHELXL. Dynamic solvent networks resulting from alternative side-chain conformations and shifts in water positions are revealed, demonstrating that polypeptide flexibility and formation of clathrate-type structures at hydrophobic surfaces are the key features endowing crambin crystals with extraordinary diffraction power.

Organizational Affiliation

Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Lemont, IL 60439, USA.

Macromolecule Content

Total Structure Weight: 4.82 kDa
Atom Count: 546
Modelled Residue Count: 48
Deposited Residue Count: 48
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Crambin	A	46	Crambe hispanica subsp. abyssinica	Mutation(s): 2
UniProt
Find proteins for P01542 (Crambe hispanica subsp. abyssinica) Explore P01542 Go to UniProtKB: P01542
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P01542
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EOH Query on EOH Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A]	B [auth A], C [auth A]	ETHANOL C₂ H₆ O LFQSCWFLJHTTHZ-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 0.70 Å
R-Value Work: 0.076 (Depositor), 0.068 (DCC)

Diffraction Data: https://doi.org/10.18150/1RI4XW

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 22.725	α = 90
b = 18.767	β = 90.55
c = 41.059	γ = 90

Software Package:

Software Name	Purpose
SHELX	refinement
SCALEPACK	data scaling
HKL-2000	data reduction
PHENIX	phasing

Structure Validation

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Entry History & Funding Information

Deposition Data

Released Date: 2024-09-04

Deposition Author(s):

Funding Organization	Location	Grant Number
Department of Energy (DOE, United States)	United States	DE-AC02-06CH11357
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	R35GM145365