9YZW | pdb_00009yzw

Joint Xray/Neutron structure of Escherichia coli YajL at room temperature

PDB DOI: https://doi.org/10.2210/pdb9YZW/pdb

Classification: HYDROLASE
Organism(s): Escherichia coli
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2025-10-30 Released: 2025-11-19
Deposition Author(s): Lin, J., Kovalevsky, A., Walker, A.R., Wilson, M.A.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free:
0.164 (Depositor), 0.163 (DCC)
R-Value Work:
0.137 (Depositor), 0.137 (DCC)
R-Value Observed:
0.139 (Depositor)

Method: NEUTRON DIFFRACTION
Resolution: 1.79 Å
R-Value Free:
0.223 (Depositor)
R-Value Work:
0.177 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Environmental contributions to proton sharing in protein low barrier hydrogen bonds

Lin, J., Gerlits, O., Kneller, D.W., Weiss, K.L., Coates, L., Hix, M.A., Effah, S.Y., Kovalevsky, A., Walker, A.R., Wilson, M.A.

To be published.

Macromolecule Content

Total Structure Weight: 42.16 kDa
Atom Count: 3,275
Modeled Residue Count: 390
Deposited Residue Count: 398
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chaperone YajL	A, B	199	Escherichia coli	Mutation(s): 0 Gene Names: thiJ, ACU57_11870, AM266_04520, ERS085365_02411, ERS085416_01937, ERS139211_01908, ERS150873_01827, PU15_11320, PU38_04800, SK85_00449 EC: 3.5.1.124
UniProt
Find proteins for W8T6D9 (Escherichia coli) Explore W8T6D9 Go to UniProtKB: W8T6D9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	W8T6D9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
D8U (Subject of Investigation/LOI) Query on D8U Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	deuterium(1+) D GPRLSGONYQIRFK-DYCDLGHISA-N		Interactions Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free: 0.164 (Depositor), 0.163 (DCC)
R-Value Work: 0.137 (Depositor), 0.137 (DCC)
R-Value Observed: 0.139 (Depositor)

Method: NEUTRON DIFFRACTION
Resolution: 1.79 Å
R-Value Free: 0.223 (Depositor)
R-Value Work: 0.177 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.289	α = 90
b = 79.303	β = 90
c = 100.183	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement

Structure Validation

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Entry History & Funding Information

Deposition Data

Released Date: 2025-11-19

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35GM153337

Revision History (Full details and data files)

Version 1.0: 2025-11-19
Type: Initial release

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.