5HPA | pdb_00005hpa

The crystal of rhodanese domain of YgaP treated with sodium thiosulfate

PDB DOI: https://doi.org/10.2210/pdb5HPA/pdb

Classification: TRANSFERASE
Organism(s): Escherichia coli K-12
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2016-01-20 Released: 2017-02-01
Deposition Author(s): Eichmann, C., Tzitzilonis, C., Kwiatkowski, W., Riek, R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.66 Å
R-Value Free:
0.197 (Depositor), 0.208 (DCC)
R-Value Work:
0.167 (Depositor), 0.179 (DCC)
R-Value Observed:
0.168 (Depositor)

Starting Model: experimental
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This is version 1.2 of the entry. See complete history.

Literature

S-Sulfhydration of the Catalytic Cysteine in the Rhodanese Domain of YgaP is a Complex Dynamical Process.

Eichmann, C., Tzitzilonis, C., Kwiatkowski, W., Riek, R.

To be published.

Macromolecule Content

Total Structure Weight: 14.08 kDa
Atom Count: 998
Modeled Residue Count: 104
Deposited Residue Count: 128
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Inner membrane protein YgaP	A	127	Escherichia coli K-12	Mutation(s): 0 Gene Names: ygaP, b2668, JW2643 EC: 2.8.1.1
UniProt
Find proteins for P55734 (Escherichia coli (strain K12)) Explore P55734 Go to UniProtKB: P55734
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P55734
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSS Query on CSS	A	L-PEPTIDE LINKING	C₃ H₇ N O₂ S₂		CYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.66 Å
R-Value Free: 0.197 (Depositor), 0.208 (DCC)
R-Value Work: 0.167 (Depositor), 0.179 (DCC)
R-Value Observed: 0.168 (Depositor)

Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.699	α = 90
b = 43.699	β = 90
c = 52.28	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2017-02-01

Deposition Author(s):

Tzitzilonis, C.

Kwiatkowski, W.

Revision History (Full details and data files)

Version 1.0: 2017-02-01
Type: Initial release
Version 1.1: 2024-01-10
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.2: 2024-11-13
Changes: Structure summary

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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.