4K2H | pdb_00004k2h

Crystal structure of C103A mutant of DJ-1 superfamily protein STM1931 from Salmonella typhimurium

PDB DOI: https://doi.org/10.2210/pdb4K2H/pdb

Classification: UNKNOWN FUNCTION
Organism(s): Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2013-04-09 Released: 2013-04-24
Deposition Author(s): Shumilin, I.A., Niedzialkowska, E., Domagalski, M.J., Stam, J., Anderson, W.F., Minor, W., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.205 (Depositor), 0.208 (DCC)
R-Value Work:
0.172 (Depositor), 0.179 (DCC)
R-Value Observed:
0.173 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of C103A mutant of DJ-1 superfamily protein STM1931 from Salmonella typhimurium

Shumilin, I.A., Niedzialkowska, E., Domagalski, M.J., Stam, J., Anderson, W.F., Minor, W., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Macromolecule Content

Total Structure Weight: 280.12 kDa
Atom Count: 20,792
Modeled Residue Count: 2,592
Deposited Residue Count: 2,632
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Intracellular protease/amidase	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N	188	Salmonella enterica subsp. enterica serovar Typhimurium str. LT2	Mutation(s): 1 Gene Names: araH, STM1931
UniProt
Find proteins for Q8ZNU7 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore Q8ZNU7 Go to UniProtKB: Q8ZNU7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8ZNU7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain BA [auth N] SDF format, chain Q [auth C] SDF format, chain V [auth H] SDF format, chain W [auth I] SDF format, chain Y [auth K] SDF format, chain Z [auth L] SDF format, chain X [auth J] SDF format, chain U [auth G] SDF format, chain T [auth F] SDF format, chain S [auth E] SDF format, chain R [auth D] SDF format, chain P [auth B] SDF format, chain O [auth A] SDF format, chain AA [auth M] MOL2 format, chain BA [auth N] MOL2 format, chain Q [auth C] MOL2 format, chain V [auth H] MOL2 format, chain W [auth I] MOL2 format, chain Y [auth K] MOL2 format, chain Z [auth L] MOL2 format, chain X [auth J] MOL2 format, chain U [auth G] MOL2 format, chain T [auth F] MOL2 format, chain S [auth E] MOL2 format, chain R [auth D] MOL2 format, chain P [auth B] MOL2 format, chain O [auth A] MOL2 format, chain AA [auth M] mmCIF format, chain BA [auth N] mmCIF format, chain Q [auth C] mmCIF format, chain V [auth H] mmCIF format, chain W [auth I] mmCIF format, chain Y [auth K] mmCIF format, chain Z [auth L] mmCIF format, chain X [auth J] mmCIF format, chain U [auth G] mmCIF format, chain T [auth F] mmCIF format, chain S [auth E] mmCIF format, chain R [auth D] mmCIF format, chain P [auth B] mmCIF format, chain O [auth A] mmCIF format, chain AA [auth M]	AA [auth M] BA [auth N] O [auth A] P [auth B] Q [auth C] AA [auth M], BA [auth N], O [auth A], P [auth B], Q [auth C], R [auth D], S [auth E], T [auth F], U [auth G], V [auth H], W [auth I], X [auth J], Y [auth K], Z [auth L]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain AA [auth M] Focus chain BA [auth N] Focus chain O [auth A] Focus chain P [auth B] Focus chain Q [auth C] Focus chain R [auth D] Focus chain S [auth E] Focus chain T [auth F] Focus chain U [auth G] Focus chain V [auth H] Focus chain W [auth I] Focus chain X [auth J] Focus chain Y [auth K] Focus chain Z [auth L] Interactions & Density Focus chain AA [auth M] Focus chain BA [auth N] Focus chain O [auth A] Focus chain P [auth B] Focus chain Q [auth C] Focus chain R [auth D] Focus chain S [auth E] Focus chain T [auth F] Focus chain U [auth G] Focus chain V [auth H] Focus chain W [auth I] Focus chain X [auth J] Focus chain Y [auth K] Focus chain Z [auth L]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.205 (Depositor), 0.208 (DCC)
R-Value Work: 0.172 (Depositor), 0.179 (DCC)
R-Value Observed: 0.173 (Depositor)

Diffraction Data:

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 179.662	α = 90
b = 113.751	β = 109.33
c = 175.71	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data collection
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2013-04-24

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2013-04-24
Type: Initial release
Version 1.1: 2017-11-15
Changes: Refinement description
Version 1.2: 2022-04-13
Changes: Database references, Derived calculations, Structure summary
Version 1.3: 2023-09-20
Changes: Data collection, Refinement description