[English] 日本語
Yorodumi
- PDB-6vbt: The P212121 Crystal structure of SodCI Superoxide Dismutase with ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6vbt
TitleThe P212121 Crystal structure of SodCI Superoxide Dismutase with 2 molecules in the asymmetric unit at 1.7 A resolution
ComponentsSuperoxide dismutase [Cu-Zn]
KeywordsOXYGEN BINDING / Superoxide Dismutase / enzyme / peptidoglycan binding
Function / homology
Function and homology information


superoxide dismutase / superoxide dismutase activity / removal of superoxide radicals / periplasmic space / copper ion binding / identical protein binding / metal ion binding
Similarity search - Function
Superoxide dismutase, copper/zinc, binding site / Copper/Zinc superoxide dismutase signature 2. / Superoxide dismutase, copper/zinc binding domain / Superoxide dismutase (Cu/Zn) / superoxide dismutase copper chaperone / Copper/zinc superoxide dismutase (SODC) / Superoxide dismutase-like, copper/zinc binding domain superfamily
Similarity search - Domain/homology
COPPER (II) ION / Superoxide dismutase [Cu-Zn] / Superoxide dismutase [Cu-Zn] 1
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsSatyshur, K.A. / Forest, K.T. / Newhouse, P.W.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32GM007215 United States
CitationJournal: To Be Published
Title: Structure and Muropeptide Binding of the Virulence Factor Superoxide Dismutase C1 from Salmonella Typhimurium
Authors: Newhouse, P.W. / Satyshur, K.A. / Slauch, J.M. / Forest, K.T.
History
DepositionDec 19, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 30, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 16, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Superoxide dismutase [Cu-Zn]
B: Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1336
Polymers34,8752
Non-polymers2584
Water7,458414
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis, Light Scattering SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1520 Å2
ΔGint-14 kcal/mol
Surface area13550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.052, 57.428, 120.548
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

#1: Protein Superoxide dismutase [Cu-Zn]


Mass: 17437.734 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria)
Gene: 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_ ...Gene: 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
Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS
References: UniProt: A0A0D6GQL3, UniProt: P0CW86*PLUS, superoxide dismutase
#2: Chemical ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 414 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.19 Å3/Da / Density % sol: 43.74 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop
Details: 20 mg/ml SODC1 plus 1.2 mM trachaeal cytotoxin in 20 mM Tris pH 6.6 150 mM NaCl set up as hanging drop with mother liquor 0.1M KCN, 30% polyethylene glycol monomethyl ether 2000 (unbuffered)

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.07812 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: May 30, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07812 Å / Relative weight: 1
ReflectionResolution: 1.487→60.274 Å / Num. obs: 36880 / % possible obs: 72.1 % / Redundancy: 12.4 % / Biso Wilson estimate: 15.46 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.028 / Rrim(I) all: 0.098 / Net I/σ(I): 13.7
Reflection shellResolution: 1.487→1.631 Å / Redundancy: 8.3 % / Rmerge(I) obs: 0.611 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 1844 / CC1/2: 0.866 / Rpim(I) all: 0.218 / Rrim(I) all: 0.651 / % possible all: 15.1
Serial crystallography sample deliveryMethod: fixed target

-
Processing

Software
NameVersionClassification
autoPROCv1.0.5data processing
XDSVERSION Mar 15, 2019 BUILT=20190606data reduction
STARANISOVersion 2.2.19 (11-May-2019data scaling
AutoSol1.17.1phasing
PHENIX1.17.1refinement
RefinementMethod to determine structure: SAD / Resolution: 1.7→33.57 Å / SU ML: 0.1767 / Cross valid method: FREE R-VALUE / Phase error: 20.0265
RfactorNum. reflection% reflection
Rfree0.2123 3392 5.41 %
Rwork0.1748 --
obs0.1768 62649 96.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 21.85 Å2
Refinement stepCycle: LAST / Resolution: 1.7→33.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2256 0 4 414 2674
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00472343
X-RAY DIFFRACTIONf_angle_d0.75193185
X-RAY DIFFRACTIONf_chiral_restr0.0456347
X-RAY DIFFRACTIONf_plane_restr0.0075424
X-RAY DIFFRACTIONf_dihedral_angle_d3.10411913
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.720.28911030.28331754X-RAY DIFFRACTION68.37
1.72-1.750.28481080.24851897X-RAY DIFFRACTION74.87
1.75-1.780.23771290.22942269X-RAY DIFFRACTION87.45
1.78-1.810.26921320.20622339X-RAY DIFFRACTION91.28
1.81-1.840.25391400.20272419X-RAY DIFFRACTION95.02
1.84-1.870.23011440.19832509X-RAY DIFFRACTION99.62
1.87-1.910.24581450.19772632X-RAY DIFFRACTION99.96
1.91-1.950.22841470.19282518X-RAY DIFFRACTION99.89
1.95-1.990.26811450.20012574X-RAY DIFFRACTION100
1.99-2.030.24551420.1922546X-RAY DIFFRACTION100
2.03-2.090.22751500.2022577X-RAY DIFFRACTION100
2.09-2.140.19991490.18352534X-RAY DIFFRACTION99.89
2.14-2.20.24551470.18392589X-RAY DIFFRACTION100
2.2-2.280.20071430.17192543X-RAY DIFFRACTION100
2.28-2.360.21171460.1652551X-RAY DIFFRACTION100
2.36-2.450.23581520.1682557X-RAY DIFFRACTION98.29
2.45-2.560.22631480.16692552X-RAY DIFFRACTION100
2.56-2.70.20881430.17092541X-RAY DIFFRACTION100
2.7-2.870.21981470.16572564X-RAY DIFFRACTION100
2.87-3.090.18521480.16222549X-RAY DIFFRACTION100
3.09-3.40.20921490.16642574X-RAY DIFFRACTION99.71
3.4-3.890.19831430.162560X-RAY DIFFRACTION100
3.89-4.90.14351460.13782551X-RAY DIFFRACTION99.59
4.9-33.570.21551460.182558X-RAY DIFFRACTION99.82

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more