[English] 日本語
Yorodumi
- PDB-4wbr: Structure of Bradyrhizobium japonicum ScoI with copper bound -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4wbr
TitleStructure of Bradyrhizobium japonicum ScoI with copper bound
ComponentsBlr1131 protein
KeywordsCHAPERONE / copper / cytochrome oxidase / CuA
Function / homology
Function and homology information


membrane / metal ion binding
Similarity search - Function
Copper chaperone SCO1/SenC / SCO1/SenC / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
COPPER (II) ION / Blr1131 protein
Similarity search - Component
Biological speciesBradyrhizobium diazoefficiens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.4 Å
AuthorsQuade, N. / Abicht, H.K. / Hennecke, H. / Glockshuber, R.
CitationJournal: To Be Published
Title: Structure of Bradyrhizobium japonicum ScoI with copper bound
Authors: Quade, N. / Abicht, H.K. / Hennecke, H. / Glockshuber, R.
History
DepositionSep 3, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 23, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: 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
D: Blr1131 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,4972
Polymers17,4341
Non-polymers641
Water4,234235
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-12 kcal/mol
Surface area8020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.860, 44.760, 40.000
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11D-376-

HOH

21D-414-

HOH

-
Components

#1: Protein Blr1131 protein


Mass: 17433.846 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bradyrhizobium diazoefficiens (bacteria)
Strain: JCM 10833 / IAM 13628 / NBRC 14792 / USDA 110 / Gene: blr1131 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q89VB6
#2: Chemical ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 235 / 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: 2.38 Å3/Da / Density % sol: 48.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 0.1 M Na-citrate, 20% PEG 6000

-
Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 25, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→46 Å / Num. obs: 30788 / % possible obs: 91.2 % / Observed criterion σ(I): -3 / Redundancy: 12 % / Biso Wilson estimate: 19.097 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.099 / Rrim(I) all: 0.103 / Χ2: 0.958 / Net I/σ(I): 17.04 / Num. measured all: 378601
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.4-1.430.7760.7632.3312200246713800.80955.9
1.43-1.470.8630.6563.1718023237416040.68667.6
1.47-1.520.9010.5713.8823618232019640.59684.7
1.52-1.560.9470.4884.9228191225320910.50792.8
1.56-1.610.9680.4056.0127813222421020.42194.5
1.61-1.670.9720.3467.0826247213120520.3696.3
1.67-1.730.9750.2988.0624256204319650.31196.2
1.73-1.810.9820.25610.2325975199919460.26697.3
1.81-1.890.9920.19612.924094189818540.20497.7
1.89-1.980.9930.15616.1422665183418010.16298.2
1.98-2.080.9950.12818.520153172916870.13497.6
2.08-2.210.9960.11123.4721272166516400.11698.5
2.21-2.360.9970.09726.1319087155715280.10298.1
2.36-2.550.9970.09827.9417275144314270.10298.9
2.55-2.80.9980.08531.7415994135713230.08897.5
2.8-3.130.9990.0737.3215270121812130.07399.6
3.13-3.610.9990.05342.5112910110010950.05599.5
3.61-4.420.9990.04646.2105289459340.04898.8
4.42-6.250.9990.04347.9784797347320.04599.7
6.250.9990.03546.6245514564500.03798.7

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.4 Å46.43 Å
Translation1.4 Å46.43 Å

-
Processing

Software
NameVersionClassification
XDSdata reduction
REFMAC5.8.0073refinement
PDB_EXTRACT3.15data extraction
XSCALEdata scaling
PHASERphasing
XSCALEdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4txo

4txo


Resolution: 1.4→42 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.96 / WRfactor Rfree: 0.1672 / WRfactor Rwork: 0.1197 / FOM work R set: 0.8892 / SU B: 2.144 / SU ML: 0.037 / SU R Cruickshank DPI: 0.0571 / SU Rfree: 0.0582 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.057 / ESU R Free: 0.058 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1753 1494 4.9 %RANDOM
Rwork0.126 29294 --
obs0.1283 30788 91.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 121.95 Å2 / Biso mean: 18.926 Å2 / Biso min: 6.26 Å2
Baniso -1Baniso -2Baniso -3
1-0.47 Å20 Å2-0 Å2
2---0.27 Å20 Å2
3----0.2 Å2
Refinement stepCycle: final / Resolution: 1.4→42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1225 0 1 235 1461
Biso mean--18.5 35.07 -
Num. residues----157
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0191305
X-RAY DIFFRACTIONr_bond_other_d0.0010.021254
X-RAY DIFFRACTIONr_angle_refined_deg2.0121.9891780
X-RAY DIFFRACTIONr_angle_other_deg0.98932922
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7935174
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.43624.18255
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.45915234
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.667157
X-RAY DIFFRACTIONr_chiral_restr0.1460.2199
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0211469
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02276
X-RAY DIFFRACTIONr_mcbond_it3.7291.404645
X-RAY DIFFRACTIONr_mcbond_other3.7211.4644
X-RAY DIFFRACTIONr_mcangle_it3.7792.114809
X-RAY DIFFRACTIONr_rigid_bond_restr5.40532557
X-RAY DIFFRACTIONr_sphericity_free49.923561
X-RAY DIFFRACTIONr_sphericity_bonded14.63252697
LS refinement shellResolution: 1.398→1.435 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 62 -
Rwork0.256 1315 -
all-1377 -
obs--55.91 %

+
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