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- PDB-5ffb: CopM in the apo form -

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Basic information

Entry
Database: PDB / ID: 5ffb
TitleCopM in the apo form
ComponentsCopM
KeywordsMETAL BINDING PROTEIN / Copper binding protein
Function / homology
Function and homology information


membrane / metal ion binding
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
CopM / Slr6039 protein
Similarity search - Component
Biological speciesSynechocystis sp. PCC 6803 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.702 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

Downloads & links

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Assembly

Deposited unit
A: CopM


Theoretical massNumber of molelcules
Total (without water)20,3811
Polymers20,3811
Non-polymers00
Water3,549197
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.867, 86.115, 33.442
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 197 / 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: 1.9 Å3/Da / Density % sol: 35.36 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.1M HEPES 7.0, 0.1M Lithium sulphate, 25% PEG 3350

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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: Oct 9, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 17514 / % possible obs: 98.7 % / Redundancy: 6.5 % / Net I/σ(I): 15
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.484 / Mean I/σ(I) obs: 2.7 / % possible all: 93.9

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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: 1.702→26.981 Å / FOM work R set: 0.8222 / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2185 615 4.87 %
Rwork0.1815 12011 -
obs0.1833 12626 71.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 70.07 Å2 / Biso mean: 19.69 Å2 / Biso min: 5.48 Å2
Refinement stepCycle: final / Resolution: 1.702→26.981 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1124 0 0 197 1321
Biso mean---35.54 -
Num. residues----135
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071185
X-RAY DIFFRACTIONf_angle_d1.0061603
X-RAY DIFFRACTIONf_chiral_restr0.068164
X-RAY DIFFRACTIONf_plane_restr0.004210
X-RAY DIFFRACTIONf_dihedral_angle_d14.202463
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7021-1.87340.2159970.17682014211148
1.8734-2.14430.2221320.17692488262060
2.1443-2.70120.23161760.18633217339377
2.7012-26.98470.21182100.18114292450298
Refinement TLS params.Method: refined / Origin x: -13.4029 Å / Origin y: 5.2518 Å / Origin z: -6.8055 Å
111213212223313233
T0.0913 Å20.0031 Å20.004 Å2-0.095 Å2-0.0082 Å2--0.0225 Å2
L1.6457 °2-0.4701 °20.0509 °2-1.675 °20.0928 °2--0.1553 °2
S0.0343 Å °0.0076 Å °0.0346 Å °-0.095 Å °-0.0116 Å °-0.1457 Å °-0.0302 Å °0.0161 Å °-0.0257 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA44 - 195
2X-RAY DIFFRACTION1allA201 - 397

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