[English] 日本語
Yorodumi
- PDB-5um7: Crystal structure of the reduced state of the thiol-disulfide red... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5um7
TitleCrystal structure of the reduced state of the thiol-disulfide reductase SdbA from Streptococcus gordonii
ComponentsThioredoxin signature protein
KeywordsOXIDOREDUCTASE / THIOREDOXIN-LIKE DOMAIN / ALPHA-BETA PROTEIN / structural genomics / Center for Structural Genomics of Infectious Diseases / CSGID / National Institute of Allergy and Infectious Diseases / NIAID
Function / homology
Function and homology information


antioxidant activity / oxidoreductase activity / membrane
Similarity search - Function
: / Alkyl hydroperoxide reductase subunit C/ Thiol specific antioxidant / AhpC/TSA family / Thioredoxin domain profile. / Thioredoxin domain / Thioredoxin-like superfamily
Similarity search - Domain/homology
ACETATE ION / Thioredoxin signature protein
Similarity search - Component
Biological speciesStreptococcus gordonii (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.62 Å
AuthorsStogios, P.J. / Evdokimova, E. / Wawrzak, Z. / Yim, V. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSCN27220120026C United States
CitationJournal: To Be Published
Title: Crystal structure of the reduced state of the thiol-disulfide reductase SdbA from Streptococcus gordonii
Authors: Stogios, P.J.
History
DepositionJan 26, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Dec 11, 2019Group: Author supporting evidence / Database references / Category: citation / pdbx_audit_support
Item: _citation.title / _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Thioredoxin signature protein
B: Thioredoxin signature protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,9693
Polymers43,9102
Non-polymers591
Water7,188399
1
A: Thioredoxin signature protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0142
Polymers21,9551
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Thioredoxin signature protein


Theoretical massNumber of molelcules
Total (without water)21,9551
Polymers21,9551
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.250, 49.320, 196.540
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-388-

HOH

21B-386-

HOH

-
Components

#1: Protein Thioredoxin signature protein


Mass: 21955.070 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus gordonii (strain Challis / ATCC 35105 / BCRC 15272 / CH1 / DL1 / V288) (bacteria)
Strain: Challis / ATCC 35105 / BCRC 15272 / CH1 / DL1 / V288
Gene: SGO_2006 / Plasmid: pMCSG53 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Gold / References: UniProt: A8AZP5
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 399 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.44 Å3/Da / Density % sol: 64 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 2.5 M ammonium sulfate, 0.1 M sodium acetate pH 4.6

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Aug 28, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.62→28.43 Å / Num. obs: 30533 / % possible obs: 98.6 % / Redundancy: 4.9 % / CC1/2: 0.992 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.065 / Net I/σ(I): 14.9
Reflection shellResolution: 1.62→1.66 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.102 / Mean I/σ(I) obs: 10.2 / Num. unique all: 2076 / Num. unique obs: 2076 / CC1/2: 0.958 / Rpim(I) all: 0.082 / % possible all: 90.2

-
Processing

Software
NameVersionClassification
PHENIX(dev_2481: ???)refinement
XDSdata reduction
Aimlessdata scaling
BALBESphasing
PHENIXmodel building
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2F9S

2f9s


Resolution: 1.62→28.426 Å / Cross valid method: FREE R-VALUE / σ(F): 1.44 / Phase error: 30.86
RfactorNum. reflection% reflectionSelection details
Rfree0.292 1537 5.04 %RANDOM
Rwork0.2377 ---
obs0.2465 30503 98.35 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.62→28.426 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2367 0 4 399 2770
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042452
X-RAY DIFFRACTIONf_angle_d0.563310
X-RAY DIFFRACTIONf_dihedral_angle_d18.183953
X-RAY DIFFRACTIONf_chiral_restr0.042343
X-RAY DIFFRACTIONf_plane_restr0.004428
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6227-1.6750.33361250.34152519X-RAY DIFFRACTION91
1.675-1.73490.30991300.33112591X-RAY DIFFRACTION93
1.7349-1.80430.33691260.31512571X-RAY DIFFRACTION94
1.8043-1.88640.3521680.30652571X-RAY DIFFRACTION93
1.8864-1.98580.34261390.2922596X-RAY DIFFRACTION94
1.9858-2.11010.32291230.28422654X-RAY DIFFRACTION95
2.1101-2.27280.30951250.27782649X-RAY DIFFRACTION95
2.2728-2.50130.28531190.25672719X-RAY DIFFRACTION96
2.5013-2.86250.30611740.232619X-RAY DIFFRACTION94
2.8625-3.60390.2551610.19452663X-RAY DIFFRACTION94
3.6039-21.8660.27271260.17742795X-RAY DIFFRACTION94
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.1167-0.2077-0.41420.73520.34590.719-0.0064-0.1130.0622-0.00020.0293-0.0819-0.03040.0141-0.03370.08230.05520.03060.1538-0.00740.1702-13.3607-11.3994-0.5534
20.51741.2507-1.51973.0723-3.53724.9533-0.13670.1674-0.1812-0.21030.00950.03820.1114-0.21760.11190.12860.01310.01490.2609-0.03650.1957-12.3271-9.3421-20.0908
30.03880.0081-0.00740.1515-0.02070.106-0.01710.027-0.007-0.0263-0.01710.03970.0286-0.00580.00080.0465-0.007-0.00550.01120.03250.2233-0.5149-8.077-17.0036
40.1061-0.08140.02760.1334-0.03150.06920.030.014-0.00610.01190.03670.03060.0155-0.01630.0290.03850.0216-0.01050.0350.02650.1445-9.603-6.6753-9.799
50.8340.398-0.12350.22970.06580.40860.02790.0184-0.14520.007-0.0642-0.00040.0399-0.0791-0.01520.0367-0.022-0.03410.09510.03120.18290.1271-15.9266-3.889
61.85590.20930.35891.511.38571.7735-0.05170.10030.1469-0.25110.0685-0.1596-0.23750.0726-0.00520.09040.0004-0.03080.02270.00090.1142-11.9674-38.6019-46.3902
70.27070.09010.00110.072-0.08140.1830.02110.0431-0.04590.0203-0.01540.0739-0.00030.0181-0.00220.0223-0.00480.0030.04590.01380.147-10.379-27.659-32.9168
80.1313-0.2577-0.14122.77470.36631.48770.03370.01710.0343-0.0298-0.05480.2492-0.1399-0.14810.04450.20940.05830.01550.0902-0.06330.1974-17.113-27.6432-33.191
90.0762-0.144-0.08920.29570.1120.25130.06560.0389-0.11820.0245-0.0216-0.10460.13670.0421-0.04190.08460.0182-0.02250.0502-0.01890.1477-4.9561-29.0001-34.7302
100.23480.3348-0.42291.7382-0.17151.286-0.1208-0.0444-0.13940.04020.09350.16010.268-0.1213-0.0070.2021-0.0222-0.01320.12750.09640.2203-16.0573-21.0362-45.3147
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 5:10)
2X-RAY DIFFRACTION2(chain A and resid 11:23)
3X-RAY DIFFRACTION3(chain A and resid 24:98)
4X-RAY DIFFRACTION4(chain A and resid 99:122)
5X-RAY DIFFRACTION5(chain A and resid 123:144)
6X-RAY DIFFRACTION6(chain B and resid 4:13)
7X-RAY DIFFRACTION7(chain B and resid 14:62)
8X-RAY DIFFRACTION8(chain B and resid 63:71)
9X-RAY DIFFRACTION9(chain B and resid 72:129)
10X-RAY DIFFRACTION10(chain B and resid 130:145)

+
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