[English] 日本語
Yorodumi
- PDB-3fhk: Crystal structure of APC1446, B.subtilis YphP disulfide isomerase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3fhk
TitleCrystal structure of APC1446, B.subtilis YphP disulfide isomerase
ComponentsUPF0403 protein yphP
Keywordsstructural genomics / unknown function / disulfide isomerase / Thioredoxin superfamily / CXC motif / Surface Entropy Reduction / SER / PSI-2 / Protein structure initiative / ISFI / Integrated Center for Structure and Function Innovation
Function / homology
Function and homology information


response to hydroperoxide / protein disulfide isomerase activity / cell redox homeostasis / response to oxidative stress / oxidoreductase activity
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2150 / Bacilliredoxins BrxB/BrxA / Disulphide isomerase / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special / Glutaredoxin / Glutaredoxin / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsDerewenda, U. / Boczek, T. / Cooper, D.R. / Yu, M. / Hung, L. / Derewenda, Z.S. / Integrated Center for Structure and Function Innovation (ISFI)
CitationJournal: Biochemistry / Year: 2009
Title: Structure and function of Bacillus subtilis YphP, a prokaryotic disulfide isomerase with a CXC catalytic motif .
Authors: Derewenda, U. / Boczek, T. / Gorres, K.L. / Yu, M. / Hung, L.W. / Cooper, D. / Joachimiak, A. / Raines, R.T. / Derewenda, Z.S.
History
DepositionDec 9, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 1, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 24, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: UPF0403 protein yphP
D: UPF0403 protein yphP
E: UPF0403 protein yphP
F: UPF0403 protein yphP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,34916
Polymers64,1974
Non-polymers1,15312
Water4,486249
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6400 Å2
ΔGint-195 kcal/mol
Surface area25890 Å2
MethodPISA
2
A: UPF0403 protein yphP
E: UPF0403 protein yphP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6758
Polymers32,0982
Non-polymers5766
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: UPF0403 protein yphP
D: UPF0403 protein yphP
F: UPF0403 protein yphP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,01212
Polymers48,1483
Non-polymers8659
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: UPF0403 protein yphP
E: UPF0403 protein yphP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6758
Polymers32,0982
Non-polymers5766
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: UPF0403 protein yphP
F: UPF0403 protein yphP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6758
Polymers32,0982
Non-polymers5766
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.161, 68.161, 302.024
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Detailsmonomer

-
Components

#1: Protein
UPF0403 protein yphP


Mass: 16049.176 Da / Num. of mol.: 4 / Mutation: Q100A, E101A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: BSU21860, yphP / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P54170
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 249 / 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: 2.73 Å3/Da / Density % sol: 54.98 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 2M Ammonium Sulfate, 100mM Tris, 5% PEP 629., pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.97950, 0.9796, 0.9393
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 3, 2007 / Details: KOHZU: Double Crystal Si(111)
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97951
20.97961
30.93931
ReflectionResolution: 2.3→30 Å / Num. all: 32111 / Num. obs: 31840 / % possible obs: 97.2 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.119 / Net I/σ(I): 19.7
Reflection shellResolution: 2.3→2.39 Å / Redundancy: 3 % / Rmerge(I) obs: 0.419 / Mean I/σ(I) obs: 2.2 / % possible all: 82.9

-
Processing

Software
NameVersionClassification
PHENIXrefinement
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
SHELXEmodel building
RefinementMethod to determine structure: MAD / Resolution: 2.3→30 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.9 / SU ML: 0.34 / Phase error: 25.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2464 1593 5 %
Rwork0.1899 --
obs0.1928 31840 96.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 58.627 Å2 / ksol: 0.349 e/Å3
Displacement parametersBiso mean: 46.587 Å2
Baniso -1Baniso -2Baniso -3
1--0.37 Å20 Å20 Å2
2---0.37 Å20 Å2
3---0.73 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.253 Å0.312 Å
Refinement stepCycle: LAST / Resolution: 2.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4484 0 60 249 4793
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064616
X-RAY DIFFRACTIONf_angle_d1.0176261
X-RAY DIFFRACTIONf_dihedral_angle_d18.8981692
X-RAY DIFFRACTIONf_chiral_restr0.069705
X-RAY DIFFRACTIONf_plane_restr0.004820
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.37420.37361260.31782461X-RAY DIFFRACTION90
2.3742-2.45910.30131230.26452533X-RAY DIFFRACTION90
2.4591-2.55760.3141370.2312596X-RAY DIFFRACTION93
2.5576-2.6740.30351390.21652663X-RAY DIFFRACTION95
2.674-2.8150.26981450.21082695X-RAY DIFFRACTION97
2.815-2.99130.28141390.20092794X-RAY DIFFRACTION98
2.9913-3.22230.26661540.19742797X-RAY DIFFRACTION100
3.2223-3.54660.25231700.172804X-RAY DIFFRACTION100
3.5466-4.05970.19081410.15352865X-RAY DIFFRACTION100
4.0597-5.11470.20571590.14562912X-RAY DIFFRACTION100
5.1147-75.54670.23341600.20163127X-RAY DIFFRACTION100
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDMethodL11 (°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)
1refined1.7769-0.16861.17371.63720.19212.5303-0.1055-0.2010.2357-0.0260.0101-0.0993-0.1227-0.2580.07150.01430.0113-0.01620.3013-0.06630.211170.001632.2351-28.1221
22.9858-0.25662.18673.1851-0.15864.8037-0.13460.02680.0941-0.47690.08470.2527-0.0656-0.23590.03410.28610.0167-0.05050.09570.0590.2171
32.530.4375-1.20862.3087-0.02894.3693-0.02650.03010.0074-0.0275-0.03390.12940.2572-1.16390.00760.0728-0.1019-0.04550.39980.01150.1241
42.68920.8737-0.38245.9409-1.28382.19880.08180.08620.2502-0.0304-0.2035-0.4845-0.47070.11690.03180.3857-0.01150.04410.0638-0.02180.3645
Refinement TLS groupSelection details: chain F

+
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