[English] 日本語
Yorodumi
- PDB-4wwd: High-resolution structure of the Co-bound form of the Y135F mutan... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4wwd
TitleHigh-resolution structure of the Co-bound form of the Y135F mutant of C. metallidurans CnrXs
ComponentsNickel and cobalt resistance protein CnrR
KeywordsMETAL BINDING PROTEIN / Nickel sensor
Function / homologyHeavy-metal resistance protein / Heavy-metal resistance / periplasmic space / : / CARBON DIOXIDE / FORMIC ACID / : / Nickel and cobalt resistance protein CnrR
Function and homology information
Biological speciesRalstonia metallidurans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsVolbeda, A. / Coves, J. / Maillard, A.P. / Kuennemann, S. / Grosse, C. / Schleuder, G. / Petit-Haertlein, I. / de Rosny, E. / Nies, D.H.
CitationJournal: Metallomics / Year: 2015
Title: Response of CnrX from Cupriavidus metallidurans CH34 to nickel binding.
Authors: Maillard, A.P. / Kunnemann, S. / Groe, C. / Volbeda, A. / Schleuder, G. / Petit-Hartlein, I. / de Rosny, E. / Nies, D.H. / Coves, J.
History
DepositionNov 10, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Feb 11, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 15, 2015Group: Database references
Revision 1.2Nov 20, 2019Group: Derived calculations / Category: pdbx_struct_conn_angle / struct_conn
Revision 1.3May 8, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Nickel and cobalt resistance protein CnrR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,5557
Polymers13,2961
Non-polymers2596
Water4,216234
1
A: Nickel and cobalt resistance protein CnrR
hetero molecules

A: Nickel and cobalt resistance protein CnrR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,11014
Polymers26,5922
Non-polymers51812
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area4170 Å2
ΔGint-57 kcal/mol
Surface area12010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.420, 32.420, 196.100
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-318-

HOH

Detailsbiological unit is the same as asym.

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Nickel and cobalt resistance protein CnrR


Mass: 13295.874 Da / Num. of mol.: 1 / Fragment: Metal-sensor domain of CnrX, UNP residues 31-148 / Mutation: Y135F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ralstonia metallidurans (bacteria) / Strain: CH34 / ATCC 43123 / DSM 2839 / Gene: cnrR, cnrX, Rmet_6206, RMe0087 / Plasmid: pET30b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P37975

-
Non-polymers , 6 types, 240 molecules

#2: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-CO2 / CARBON DIOXIDE / Carbon dioxide


Mass: 44.010 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO2
#5: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#6: Chemical ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 234 / 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: 1.94 Å3/Da / Density % sol: 36.52 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: PEG 3350, HEPES, NaH2P04/KH2PO4

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.979725 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 13, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979725 Å / Relative weight: 1
ReflectionResolution: 1.11→20 Å / Num. obs: 78323 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 7.9 % / Biso Wilson estimate: 11.253 Å2 / Rmerge F obs: 0.998 / Rmerge(I) obs: 0.103 / Rrim(I) all: 0.11 / Χ2: 1.035 / Net I/σ(I): 12.29 / Num. measured all: 618117
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
1.11-1.180.8280.5963.779703913241126590.63995.6
1.18-1.260.9020.4225.349363811716117160.452100
1.26-1.360.9450.3047.28920611073110730.325100
1.36-1.490.980.19610.228311210277102740.21100
1.49-1.660.9890.13313.8872247900990090.142100
1.66-1.920.9920.09917.865789838683860.106100
1.92-2.350.9940.07622.2351733692969280.082100
2.35-3.30.9970.06526.8441476532253220.069100
3.30.9980.0532.5523877299129560.05498.8

-
Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XSCALEdata scaling
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→19.79 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.959 / WRfactor Rfree: 0.1783 / WRfactor Rwork: 0.134 / FOM work R set: 0.9244 / SU B: 1.638 / SU ML: 0.032 / SU R Cruickshank DPI: 0.0514 / SU Rfree: 0.0505 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.051 / ESU R Free: 0.05 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1716 1430 5.3 %RANDOM
Rwork0.1304 25670 --
obs0.1326 40322 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 88.13 Å2 / Biso mean: 12.327 Å2 / Biso min: 3.59 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å20 Å20 Å2
2---0.06 Å20 Å2
3---0.13 Å2
Refinement stepCycle: final / Resolution: 1.3→19.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms882 0 12 260 1154
Biso mean--13.04 24.55 -
Num. residues----112
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0191029
X-RAY DIFFRACTIONr_bond_other_d0.0010.021013
X-RAY DIFFRACTIONr_angle_refined_deg1.4571.9711408
X-RAY DIFFRACTIONr_angle_other_deg0.85332327
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.1375139
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.22922.29561
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.43215192
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1911519
X-RAY DIFFRACTIONr_chiral_restr0.0860.2151
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211217
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02255
X-RAY DIFFRACTIONr_mcbond_it1.4840.847484
X-RAY DIFFRACTIONr_mcbond_other1.4830.848485
X-RAY DIFFRACTIONr_mcangle_it1.7391.608611
X-RAY DIFFRACTIONr_rigid_bond_restr1.96632042
X-RAY DIFFRACTIONr_sphericity_free36.251551
X-RAY DIFFRACTIONr_sphericity_bonded10.67652228
LS refinement shellResolution: 1.3→1.334 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.248 107 -
Rwork0.155 1809 -
all-1916 -
obs--100 %

+
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