[English] 日本語
Yorodumi
- PDB-4ar6: X-ray crystallographic structure of the reduced form perdeuterate... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4ar6
TitleX-ray crystallographic structure of the reduced form perdeuterated Pyrococcus furiosus rubredoxin at 295 K (in quartz capillary) to 0.92 Angstroms resolution.
ComponentsRUBREDOXIN
KeywordsELECTRON TRANSPORT
Function / homology
Function and homology information


alkane catabolic process / electron transfer activity / iron ion binding
Similarity search - Function
Rubredoxin / Rubredoxin, iron-binding site / Rubredoxin signature. / Rubrerythrin, domain 2 - #10 / Rubredoxin domain / Rubredoxin / Rubredoxin-like domain / Rubredoxin-like domain profile. / Rubrerythrin, domain 2 / Single Sheet / Mainly Beta
Similarity search - Domain/homology
DEUTERATED WATER / : / Rubredoxin
Similarity search - Component
Biological speciesPYROCOCCUS FURIOSUS (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 0.92 Å
AuthorsCuypers, M.G. / Mason, S.A. / Blakeley, M.P. / Mitchell, E.P. / Haertlein, M. / Forsyth, V.T.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2013
Title: Near-Atomic Resolution Neutron Crystallography on Perdeuterated Pyrococcus Furiosus Rubredoxin: Implication of Hydronium Ions and Protonation Equilibria and Hydronium Ions in Redox Changes
Authors: Cuypers, M.G. / Mason, S.A. / Blakeley, M.P. / Mitchell, E.P. / Haertlein, M. / Forsyth, V.T.
History
DepositionApr 20, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 19, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 30, 2013Group: Database references
Revision 1.2May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: RUBREDOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,0882
Polymers6,0321
Non-polymers561
Water2,576143
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)34.375, 35.183, 43.944
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein RUBREDOXIN / RD


Mass: 6031.728 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: REDUCED STATE (FE II) / Source: (gene. exp.) PYROCOCCUS FURIOSUS (archaea) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P24297
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-DOD / water


Mass: 18.015 Da / Num. of mol.: 143 / Source method: isolated from a natural source / Formula: D2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.46 Å3/Da / Density % sol: 14.97 %
Description: SOLVED BY RIGID BODY FIT FROM 100 K 0.75 A RESOLUTION REDUCED PF RUBREDOXIN STRUCTURE.
Crystal growpH: 6.2 / Details: pH 6.2

-
Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.77
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 7, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.77 Å / Relative weight: 1
ReflectionResolution: 0.92→43.94 Å / Num. obs: 37464 / % possible obs: 99.2 % / Observed criterion σ(I): 2 / Redundancy: 6.06 % / Biso Wilson estimate: 11.4 Å2 / Rmerge(I) obs: 0.03 / Net I/σ(I): 21.4
Reflection shellResolution: 0.92→0.97 Å / Redundancy: 4.22 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 2.1 / % possible all: 94.8

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: OTHER / Resolution: 0.92→27.465 Å / SU ML: 0.06 / σ(F): 1.34 / Phase error: 9.92 / Stereochemistry target values: ML
Details: CRYSTAL WAS REDUCED WITH SODIUM DITHIONITE IN D2O AND THEN SEALED IN A QUARTZ CAPILLARY FOR 295 K DATA COLLECTION. 8 DIFFERENT ZONES OF THE SAME CRYSTAL (VOLUME 0.012 MM3) WERE EXPOSED TO X- ...Details: CRYSTAL WAS REDUCED WITH SODIUM DITHIONITE IN D2O AND THEN SEALED IN A QUARTZ CAPILLARY FOR 295 K DATA COLLECTION. 8 DIFFERENT ZONES OF THE SAME CRYSTAL (VOLUME 0.012 MM3) WERE EXPOSED TO X-RAYS OVER 180 DEGREES OSCILLATION ROTATION. DATA WAS SCALED AND MERGED.
RfactorNum. reflection% reflection
Rfree0.1361 1864 5 %
Rwork0.1285 --
obs0.1288 37395 99.18 %
Solvent computationShrinkage radii: 0.47 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 121.734 Å2 / ksol: 0.591 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 0.92→27.465 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms421 0 1 143 565
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007479
X-RAY DIFFRACTIONf_angle_d1.247657
X-RAY DIFFRACTIONf_dihedral_angle_d11.275186
X-RAY DIFFRACTIONf_chiral_restr0.08564
X-RAY DIFFRACTIONf_plane_restr0.00790
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.92-0.94490.25611270.232509X-RAY DIFFRACTION92
0.9449-0.97270.18041320.17092648X-RAY DIFFRACTION98
0.9727-1.00410.14621370.12372748X-RAY DIFFRACTION100
1.0041-1.040.11721290.10472710X-RAY DIFFRACTION100
1.04-1.08160.1061500.0922714X-RAY DIFFRACTION100
1.0816-1.13080.0911370.08422717X-RAY DIFFRACTION100
1.1308-1.19050.10031340.08252753X-RAY DIFFRACTION100
1.1905-1.2650.10121600.08922730X-RAY DIFFRACTION100
1.265-1.36270.11541240.09512771X-RAY DIFFRACTION100
1.3627-1.49980.10281630.10122739X-RAY DIFFRACTION100
1.4998-1.71690.12411490.10812765X-RAY DIFFRACTION100
1.7169-2.16290.13181660.12442797X-RAY DIFFRACTION100
2.1629-27.4770.16191560.15692930X-RAY DIFFRACTION100

+
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://pdbjlvh1.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