6VBS | pdb_00006vbs

The C2 Crystal form of SodCI Superoxide Dismutase at 1.7 A resolution with 6 molecules in the asymmetric unit.

PDB DOI: https://doi.org/10.2210/pdb6VBS/pdb

Classification: OXYGEN BINDING
Organism(s): Salmonella enterica subsp. enterica serovar Typhimurium
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2019-12-19 Released: 2020-12-30
Deposition Author(s): Satyshur, K.A., Forest, K.T., Newhouse, P.W.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.219 (Depositor), 0.219 (DCC)
R-Value Work:
0.178 (Depositor), 0.188 (DCC)
R-Value Observed:
0.179 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Structure and Muropeptide Binding of the Virulence Factor Superoxide Dismutase C1 from Salmonella Typhimurium

Newhouse, P.W., Satyshur, K.A., Slauch, J.M., Forest, K.T.

To be published.

Macromolecule Content

Total Structure Weight: 105.78 kDa
Atom Count: 7,725
Modeled Residue Count: 934
Deposited Residue Count: 990
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Superoxide dismutase [Cu-Zn]	A, B, C, D, E A, B, C, D, E, F	165	Salmonella enterica subsp. enterica serovar Typhimurium	Mutation(s): 0 Gene Names: sodC1, AAP89_24585, ABO94_13165, AF480_24525, AF488_17800, AF489_22535, AIC76_23135, AU613_25900, AXR84_22600, AXU58_25005... sodC1, AAP89_24585, ABO94_13165, AF480_24525, AF488_17800, AF489_22535, AIC76_23135, AU613_25900, AXR84_22600, AXU58_25005, C2253_23510, CD48_19550, CE87_24875, CET98_19490, CQG18_24025, CVR97_00185, D4369_24860, D4380_23405, D4401_24550, D4E62_23815, D6360_24640, D7F20_18080, D7H43_24310, DD95_21320, DJ388_22940, DKJ11_15870, DKU57_23325, DLM31_21285, DO698_19845, DOJ90_22365, DOQ88_23710, DQ848_24435, DRM14_23695, DSF69_10260, DSR36_22945, DUW48_23400, EBO41_23675, EBP31_23480, EGU67_12495, EHB24_23490, EHC98_23755, EIW53_22710, F0A00_10055, F0A01_03930, F0A02_16630, F0A03_14260, F0A04_11295, F0A05_20695, F0A06_10485, F0U66_16995, FKA80_23505, FKA81_22545, FKA82_23465, FKA83_23450, FKA84_23540, FKA85_22415, FKA86_23320, FKA87_22565, FKA88_23655, FKA89_19440, FKA90_23025, FKA91_22685, FKA92_23550, FKA93_23530, FKA94_23705, FKA95_23590, FKA96_23695, FKA97_23460, FKA98_23465, FKA99_23670, FKB00_23595, FKB01_23750, FKB02_23725, FKB03_23595, FKB12_23280, FKB15_23500, FKB18_22510, FKB19_23085, FYL57_20425, FYL66_21285, FYL68_13470, FYL69_02095, FYL71_08605, FYL73_12165, FYL74_21170, FYL75_22020, FYL77_03645, FYL81_07750, FYL84_20475, FYL90_20575, FYL92_04365, FYL93_18435, FYL94_21135, FYL96_21895, FYM06_15765, FYM08_18765, FYM09_02430, FYM54_04305, FZ992_22195, FZ993_21050, FZ994_04265, FZ995_00435, FZ996_12505, FZ997_14980, FZ998_14695, FZ999_05915, GW08_24555, JO10_24570, LZ63_20420, NCTC13348_01621, NG18_23390, NU83_09530, QA89_23615, QD15_24180, RJ78_24990, SAMEA4398682_02945, Y934_24990, YG50_23900, YI33_24375, YR17_24730, ZB89_24710, ZC54_24870 EC: 1.15.1.1
UniProt
Find proteins for P0CW86 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore P0CW86 Go to UniProtKB: P0CW86
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0CW86
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain R [auth D] SDF format, chain O [auth C] SDF format, chain N [auth C] SDF format, chain K [auth B] MOL2 format, chain R [auth D] MOL2 format, chain O [auth C] MOL2 format, chain N [auth C] MOL2 format, chain K [auth B] mmCIF format, chain R [auth D] mmCIF format, chain O [auth C] mmCIF format, chain N [auth C] mmCIF format, chain K [auth B]	K [auth B], N [auth C], O [auth C], R [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain K [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain R [auth D] Interactions & Density Focus chain K [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain R [auth D]
ZN (Subject of Investigation/LOI) Query on ZN Download:Ideal Coordinates CCD File SDF format, chain U [auth F] SDF format, chain T [auth E] SDF format, chain P [auth D] SDF format, chain L [auth C] SDF format, chain I [auth B] SDF format, chain H [auth A] MOL2 format, chain U [auth F] MOL2 format, chain T [auth E] MOL2 format, chain P [auth D] MOL2 format, chain L [auth C] MOL2 format, chain I [auth B] MOL2 format, chain H [auth A] mmCIF format, chain U [auth F] mmCIF format, chain T [auth E] mmCIF format, chain P [auth D] mmCIF format, chain L [auth C] mmCIF format, chain I [auth B] mmCIF format, chain H [auth A]	H [auth A] I [auth B] L [auth C] P [auth D] T [auth E] H [auth A], I [auth B], L [auth C], P [auth D], T [auth E], U [auth F]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth B] Focus chain L [auth C] Focus chain P [auth D] Focus chain T [auth E] Focus chain U [auth F] Interactions & Density Focus chain H [auth A] Focus chain I [auth B] Focus chain L [auth C] Focus chain P [auth D] Focus chain T [auth E] Focus chain U [auth F]
CU (Subject of Investigation/LOI) Query on CU Download:Ideal Coordinates CCD File SDF format, chain V [auth F] SDF format, chain S [auth E] SDF format, chain Q [auth D] SDF format, chain M [auth C] SDF format, chain J [auth B] SDF format, chain G [auth A] MOL2 format, chain V [auth F] MOL2 format, chain S [auth E] MOL2 format, chain Q [auth D] MOL2 format, chain M [auth C] MOL2 format, chain J [auth B] MOL2 format, chain G [auth A] mmCIF format, chain V [auth F] mmCIF format, chain S [auth E] mmCIF format, chain Q [auth D] mmCIF format, chain M [auth C] mmCIF format, chain J [auth B] mmCIF format, chain G [auth A]	G [auth A] J [auth B] M [auth C] Q [auth D] S [auth E] G [auth A], J [auth B], M [auth C], Q [auth D], S [auth E], V [auth F]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain Q [auth D] Focus chain S [auth E] Focus chain V [auth F] Interactions & Density Focus chain G [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain Q [auth D] Focus chain S [auth E] Focus chain V [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.219 (Depositor), 0.219 (DCC)
R-Value Work: 0.178 (Depositor), 0.188 (DCC)
R-Value Observed: 0.179 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 152.838	α = 90
b = 69.474	β = 116.888
c = 95.288	γ = 90

Software Package:

Software Name	Purpose
autoPROC	data processing
XDS	data reduction
STARANISO	data scaling
PHENIX	phasing
PHENIX	refinement

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2020-12-30

Deposition Author(s):

Satyshur, K.A.

Forest, K.T.

Newhouse, P.W.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	T32GM007215

Revision History (Full details and data files)

Version 1.0: 2020-12-30
Type: Initial release
Version 1.1: 2022-03-16
Changes: Author supporting evidence, Database references
Version 1.2: 2023-10-11
Changes: Data collection, Refinement description
Version 1.3: 2024-10-16
Changes: Structure summary