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- PDB-5fej: CopM in the Cu(I)-bound form -

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Basic information

Entry
Database: PDB / ID: 5fej
TitleCopM in the Cu(I)-bound form
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
COPPER (I) ION / CopM / Slr6039 protein
Similarity search - Component
Biological speciesSynechocystis sp. PCC 6803 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 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 17, 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
B: CopM
C: CopM
D: CopM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,03412
Polymers81,5264
Non-polymers5088
Water2,522140
1
A: CopM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,5093
Polymers20,3811
Non-polymers1272
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: CopM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,5093
Polymers20,3811
Non-polymers1272
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: CopM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,5093
Polymers20,3811
Non-polymers1272
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: CopM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,5093
Polymers20,3811
Non-polymers1272
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.824, 86.082, 74.971
Angle α, β, γ (deg.)90.000, 106.260, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
CopM


Mass: 20381.482 Da / Num. of mol.: 4
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-CU1 / COPPER (I) ION


Mass: 63.546 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cu
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / 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: 2.01 Å3/Da / Density % sol: 38.72 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.1M MES 6.0, 20% PEG 2000 MME, 1mM CuSO4, 10mM Vitamin C

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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: 2.5→50 Å / Num. obs: 22448 / % possible obs: 99.6 % / Redundancy: 3.1 % / Net I/σ(I): 10.1
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.521 / Mean I/σ(I) obs: 2.2 / % possible all: 99.6

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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: 2.5→36.939 Å / FOM work R set: 0.7758 / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 29.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2586 916 5 %
Rwork0.2109 17399 -
obs0.2133 18315 81.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 68.59 Å2 / Biso mean: 16.62 Å2 / Biso min: 6.07 Å2
Refinement stepCycle: final / Resolution: 2.5→36.939 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4544 0 8 140 4692
Biso mean--12.38 16.19 -
Num. residues----554
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044682
X-RAY DIFFRACTIONf_angle_d0.7036297
X-RAY DIFFRACTIONf_chiral_restr0.052652
X-RAY DIFFRACTIONf_plane_restr0.002821
X-RAY DIFFRACTIONf_dihedral_angle_d14.9751767
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4934-2.62480.33821020.26381564166652
2.6248-2.78920.335770.25261882195961
2.7892-3.00450.29491210.25272212233373
3.0045-3.30670.30191380.26152649278787
3.3067-3.78470.27771620.21213011317398
3.7847-4.76670.2431610.18033023318499
4.7667-36.94340.19731550.18323058321398

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