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- PDB-5ffd: CopM in the Ag-bound form (by co-crystallization) -

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Basic information

Entry
Database: PDB / ID: 5ffd
TitleCopM in the Ag-bound form (by co-crystallization)
ComponentsCopM
KeywordsMETAL BINDING PROTEIN / Copper binding protein
Function / homology
Function and homology information


metal ion binding / membrane
Similarity search - Function
Domain of unknown function DUF305, CopM-like / Domain of unknown function (DUF305) / Ferritin, core subunit, four-helix bundle / Ferritin / Ferritin-like / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
SILVER ION / CopM / Slr6039 protein
Similarity search - Component
Biological speciesSynechocystis sp. PCC 6803 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.451 Å
AuthorsZhao, S. / Wang, X. / Liu, L.
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2016
Title: Structural basis for copper/silver binding by the Synechocystis metallochaperone CopM.
Authors: Zhao, S. / Wang, X. / Niu, G. / Dong, W. / Wang, J. / Fang, Y. / Lin, Y. / Liu, L.
History
DepositionDec 18, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 7, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2019Group: Database references / Derived calculations / Category: citation / pdbx_struct_oper_list
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 8, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CopM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7054
Polymers20,3811
Non-polymers3243
Water3,927218
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area250 Å2
ΔGint-12 kcal/mol
Surface area7380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.872, 85.959, 31.729
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein CopM


Mass: 20381.482 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. PCC 6803 (bacteria) / Gene: pcopM / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0F6QDN6, UniProt: Q6YRW5*PLUS
#2: Chemical ChemComp-AG / SILVER ION


Mass: 107.868 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ag
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 218 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 1.8 Å3/Da / Density % sol: 31.75 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: 0.1M MES 6.0, 20% PEG 2000 MME, 1mM AgNO3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 6, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.45→50 Å / Num. obs: 26798 / % possible obs: 99.6 % / Redundancy: 4.2 % / Net I/σ(I): 13.5
Reflection shellResolution: 1.45→1.5 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.474 / Mean I/σ(I) obs: 2.6 / % possible all: 98.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
PHASERphasing
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3BT5

3bt5


Resolution: 1.451→33.597 Å / FOM work R set: 0.8757 / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1926 1263 5.03 %
Rwork0.1562 23845 -
obs0.158 25108 93.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 51.19 Å2 / Biso mean: 17.32 Å2 / Biso min: 7.7 Å2
Refinement stepCycle: final / Resolution: 1.451→33.597 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1138 0 3 218 1359
Biso mean--16.34 31.8 -
Num. residues----137
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081217
X-RAY DIFFRACTIONf_angle_d0.8161641
X-RAY DIFFRACTIONf_chiral_restr0.06167
X-RAY DIFFRACTIONf_plane_restr0.004216
X-RAY DIFFRACTIONf_dihedral_angle_d13.416475
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4506-1.50860.2197770.1681810188764
1.5086-1.57730.23221140.15032347246184
1.5773-1.66040.2281500.15052667281796
1.6604-1.76450.20661610.15022771293299
1.7645-1.90070.19591540.143227832937100
1.9007-2.09190.19451560.151628212977100
2.0919-2.39460.18341510.139428252976100
2.3946-3.01660.18621510.15852847299899
3.0166-33.60620.1841490.16892974312398

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