[English] 日本語
Yorodumi
- PDB-3dsp: Crystal structure of apo copper resistance protein CopK -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3dsp
TitleCrystal structure of apo copper resistance protein CopK
ComponentsPutative uncharacterized protein copK
KeywordsMETAL BINDING PROTEIN / copper binding / copper resistance
Function / homology
Function and homology information


periplasmic space / metal ion binding
Similarity search - Function
Copper resistance protein K / Copper resistance protein K / CopK superfamily / Copper resistance protein K / Thrombin, subunit H / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Copper resistance protein K
Similarity search - Component
Biological speciesRalstonia metallidurans (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsAsh, M.-R. / Maher, M.J.
CitationJournal: J.Am.Chem.Soc. / Year: 2009
Title: Unprecedented binding cooperativity between Cu(I) and Cu(II) in the copper resistance protein CopK from Cupriavidus metallidurans CH34: implications from structural studies by NMR spectroscopy ...Title: Unprecedented binding cooperativity between Cu(I) and Cu(II) in the copper resistance protein CopK from Cupriavidus metallidurans CH34: implications from structural studies by NMR spectroscopy and X-ray crystallography
Authors: Chong, L.X. / Ash, M.-R. / Maher, M.J. / Hinds, M.G. / Xiao, Z. / Wedd, A.G.
History
DepositionJul 13, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Nov 1, 2023Group: 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
A: Putative uncharacterized protein copK


Theoretical massNumber of molelcules
Total (without water)8,2951
Polymers8,2951
Non-polymers00
Water1086
1
A: Putative uncharacterized protein copK

A: Putative uncharacterized protein copK


Theoretical massNumber of molelcules
Total (without water)16,5892
Polymers16,5892
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area1630 Å2
ΔGint-7 kcal/mol
Surface area7940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.760, 37.510, 27.650
Angle α, β, γ (deg.)90.000, 103.690, 90.000
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Putative uncharacterized protein copK / Putative uncharacterized protein precursor


Mass: 8294.567 Da / Num. of mol.: 1 / Fragment: UNP residues 21-74
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ralstonia metallidurans (bacteria) / Strain: CH34 / Gene: copK / Plasmid: pCX07 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q58AD3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 2.57 Å3/Da / Density % sol: 52.22 % / Mosaicity: 1.771 °
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: 1.4M Sodium citrate, 0.1M Na-HEPES, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54179 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 22, 2007 / Details: Osmic mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 4293 / Num. obs: 4293 / % possible obs: 97.7 % / Redundancy: 8.6 % / Biso Wilson estimate: 42 Å2 / Rmerge(I) obs: 0.05 / Χ2: 1.158 / Net I/σ(I): 26.1
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.252 / Mean I/σ(I) obs: 5.35 / Num. unique all: 405 / Χ2: 0.969 / % possible all: 94.8

-
Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 44.75 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å34.14 Å
Translation2.5 Å34.14 Å

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3DSO

3dso


Resolution: 2.2→34.14 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.922 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.796 / SU B: 15.744 / SU ML: 0.172 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic with TLS / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.256 / ESU R Free: 0.2 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.248 193 4.5 %RANDOM
Rwork0.221 ---
obs0.223 4269 97.4 %-
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: 59.06 Å2 / Biso mean: 40.037 Å2 / Biso min: 24.95 Å2
Baniso -1Baniso -2Baniso -3
1--1.39 Å20 Å20.27 Å2
2--0.44 Å20 Å2
3---1.08 Å2
Refinement stepCycle: LAST / Resolution: 2.2→34.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms517 0 0 6 523
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.022522
X-RAY DIFFRACTIONr_bond_other_d0.0030.02373
X-RAY DIFFRACTIONr_angle_refined_deg1.5211.977691
X-RAY DIFFRACTIONr_angle_other_deg0.8353918
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.245565
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.92526.08723
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.65515114
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3152
X-RAY DIFFRACTIONr_chiral_restr0.0710.274
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02565
X-RAY DIFFRACTIONr_gen_planes_other0.0010.0293
X-RAY DIFFRACTIONr_nbd_refined0.210.277
X-RAY DIFFRACTIONr_nbd_other0.1850.2336
X-RAY DIFFRACTIONr_nbtor_refined0.1690.2248
X-RAY DIFFRACTIONr_nbtor_other0.0880.2309
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1880.216
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1090.24
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1960.213
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1730.28
X-RAY DIFFRACTIONr_mcbond_it1.3892416
X-RAY DIFFRACTIONr_mcbond_other0.1972137
X-RAY DIFFRACTIONr_mcangle_it1.7533518
X-RAY DIFFRACTIONr_scbond_it1.2032225
X-RAY DIFFRACTIONr_scangle_it1.7643173
LS refinement shellResolution: 2.199→2.256 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.528 11 -
Rwork0.278 268 -
all-279 -
obs-279 93.31 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
19.47330.1798-0.6889.86633.76843.3351-0.13590.20530.0195-0.37080.10290.3162-0.3121-0.46780.033-0.1907-0.0007-0.0121-0.20820.1461-0.2057-17.212815.8729-0.8846
228.0220.7024-5.04084.7982-1.13798.78580.0097-0.8487-0.2397-0.02510.32990.43660.2186-0.2194-0.3396-0.19-0.0071-0.0403-0.371-0.0089-0.4015-3.995816.04762.3969
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 391 - 39
2X-RAY DIFFRACTION2AA40 - 6640 - 66

+
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