[English] 日本語
Yorodumi
- PDB-1a8l: PROTEIN DISULFIDE OXIDOREDUCTASE FROM ARCHAEON PYROCOCCUS FURIOSUS -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1a8l
TitlePROTEIN DISULFIDE OXIDOREDUCTASE FROM ARCHAEON PYROCOCCUS FURIOSUS
ComponentsPROTEIN DISULFIDE OXIDOREDUCTASEProtein-disulfide reductase
KeywordsOXIDOREDUCTASE / PDI / THIOREDOXIN FOLD
Function / homology
Function and homology information


protein-disulfide reductase activity / metal ion binding
Similarity search - Function
Glutaredoxin-like, bacteria/archaea / Thioredoxin domain / Thioredoxin-like fold / Glutaredoxin / Glutaredoxin domain profile. / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Glutaredoxin-like protein
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / MIRAS / Resolution: 1.9 Å
AuthorsRen, B. / Tibbelin, G. / Pascale, D. / Rossi, M. / Bartolucci, S. / Ladenstein, R.
Citation
Journal: Nat.Struct.Biol. / Year: 1998
Title: A protein disulfide oxidoreductase from the archaeon Pyrococcus furiosus contains two thioredoxin fold units.
Authors: Ren, B. / Tibbelin, G. / de Pascale, D. / Rossi, M. / Bartolucci, S. / Ladenstein, R.
#1: Journal: Nat.Struct.Biol. / Year: 1998
Title: Erratum. A Protein Disulfide Oxidoreductase from the Archaeon Pyrococcus Furiosus Contains Two Thioredoxin Fold Units
Authors: Ren, B. / Tibbelin, G. / De Pascale, D. / Rossi, M. / Bartolucci, S. / Ladenstein, R.
#2: Journal: J.Struct.Biol. / Year: 1997
Title: Crystallization and Preliminary X-Ray Structure Analysis of a Hyperthermostable Thioltransferase from the Archaeon Pyrococcus Furiosus
Authors: Ren, B. / Tibbelin, G. / Pascale, D. / Rossi, M. / Bartolucci, S. / Ladenstein, R.
History
DepositionMar 26, 1998Processing site: BNL
Revision 1.0Mar 30, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PROTEIN DISULFIDE OXIDOREDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8782
Polymers25,8131
Non-polymers651
Water2,504139
1
A: PROTEIN DISULFIDE OXIDOREDUCTASE
hetero molecules

A: PROTEIN DISULFIDE OXIDOREDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,7564
Polymers51,6252
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z+2/31
Buried area1810 Å2
ΔGint-59 kcal/mol
Surface area19560 Å2
MethodPISA, PQS
2
A: PROTEIN DISULFIDE OXIDOREDUCTASE
hetero molecules

A: PROTEIN DISULFIDE OXIDOREDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,7564
Polymers51,6252
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_666-y+1,-x+1,-z+7/61
Buried area2140 Å2
ΔGint-73 kcal/mol
Surface area19230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.291, 110.291, 68.514
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-347-

HOH

21A-424-

HOH

31A-425-

HOH

-
Components

#1: Protein PROTEIN DISULFIDE OXIDOREDUCTASE / Protein-disulfide reductase


Mass: 25812.666 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Production host: Escherichia coli (E. coli) / References: UniProt: Q51760
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 139 / 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: 2.4 Å3/Da / Density % sol: 49 %
Crystal growpH: 6 / Details: pH 6.0
Crystal grow
*PLUS
Temperature: 293 K / Method: vapor diffusion, sitting drop
Details: drop consists of equal volume of protein and reservoir solutions
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
17 mg/mlprotein1drop
210 mMTris-HCl1drop
30.01 %sodium azide1drop
425 %mPEG5501reservoir
50.2 Mzinc chloride1reservoir
60.1 Mbis-Tris1reservoir

-
Data collection

DiffractionMean temperature: 288 K
Diffraction sourceSource: ROTATING ANODE / Type: MACSCIENCE / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 1, 1997 / Details: COLLIMATOR
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 1.9 Å / Num. obs: 20703 / % possible obs: 99 % / Observed criterion σ(I): 2 / Redundancy: 16 % / Biso Wilson estimate: 30 Å2 / Rmerge(I) obs: 0.069 / Rsym value: 0.12 / Net I/σ(I): 27
Reflection shellResolution: 1.9→2 Å / Redundancy: 7 % / Rmerge(I) obs: 0.05 / Mean I/σ(I) obs: 7 / Rsym value: 0.3 / % possible all: 96

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.851model building
X-PLOR3.851refinement
X-PLOR3.851phasing
RefinementMethod to determine structure: MIRAS / Resolution: 1.9→8 Å / Rfactor Rfree error: 0.0049 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.217 1906 10 %RANDOM
Rwork0.192 ---
obs0.192 19064 97.5 %-
Displacement parametersBiso mean: 28.6 Å2
Baniso -1Baniso -2Baniso -3
1-0.731 Å20.35 Å20 Å2
2--0.731 Å20 Å2
3---1.736 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.25 Å
Luzzati d res low-5 Å
Refinement stepCycle: LAST / Resolution: 1.9→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1811 0 1 139 1951
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.2
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.8
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.6
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 1.9→1.99 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.2354 233 10.1 %
Rwork0.1984 2061 -
obs--96 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM19X.PROTOPH19X.PRO
X-RAY DIFFRACTION2PARHCSDX.PROTOPHCSDX.PRO
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.8
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.6
LS refinement shell
*PLUS
Rfactor obs: 0.1984

+
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