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- PDB-5ffa: CopM (with an N-terminal His-tag) in the apo form -

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Basic information

Entry
Database: PDB / ID: 5ffa
TitleCopM (with an N-terminal His-tag) in the apo form
ComponentsCopM
KeywordsMETAL BINDING PROTEIN / copper binding protein
Function / homology
Function and homology information


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: 1.501 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


Theoretical massNumber of molelcules
Total (without water)23,7901
Polymers23,7901
Non-polymers00
Water4,125229
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.133, 86.019, 32.042
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: 23790.307 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 / Water


Mass: 18.015 Da / Num. of mol.: 229 / 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: 1.57 Å3/Da / Density % sol: 21.55 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.1 M HEPES 7.0, 0.1 M 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: Jul 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 23853 / % possible obs: 96.8 % / Redundancy: 9.3 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 30.4
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 9.7 % / Rmerge(I) obs: 0.441 / Mean I/σ(I) obs: 5.2 / % possible all: 100

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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: 3B5T

3b5t


Resolution: 1.501→27.574 Å / FOM work R set: 0.8138 / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2179 1210 5.14 %
Rwork0.1893 22330 -
obs0.1908 23540 95.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 54.28 Å2 / Biso mean: 22.5 Å2 / Biso min: 11.97 Å2
Refinement stepCycle: final / Resolution: 1.501→27.574 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1124 0 0 229 1353
Biso mean---34.51 -
Num. residues----135
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081190
X-RAY DIFFRACTIONf_angle_d1.0811614
X-RAY DIFFRACTIONf_chiral_restr0.078166
X-RAY DIFFRACTIONf_plane_restr0.006212
X-RAY DIFFRACTIONf_dihedral_angle_d14.051468
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 (%)
1.5014-1.56150.26521210.23512471259298
1.5615-1.63260.26521270.185225602687100
1.6326-1.71870.1971360.172625622698100
1.7187-1.82630.24561390.176525542693100
1.8263-1.96730.29361190.25752473259295
1.9673-2.16520.22451520.189925672719100
2.1652-2.47830.20781250.19492160228583
2.4783-3.12170.21421580.178926002758100
3.1217-27.57830.18631330.17382383251686
Refinement TLS params.Method: refined / Origin x: -13.3343 Å / Origin y: 5.6535 Å / Origin z: -7.1996 Å
111213212223313233
T0.1237 Å20.0092 Å2-0.0034 Å2-0.1554 Å2-0.0039 Å2--0.1192 Å2
L0.8677 °2-0.4177 °20.1085 °2-3.4331 °2-0.109 °2--0.2628 °2
S0.0486 Å °0.0436 Å °-0.0017 Å °-0.1474 Å °-0.0609 Å °0.0792 Å °-0.0115 Å °-0.0023 Å °0.011 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA44 - 195
2X-RAY DIFFRACTION1allA201 - 429

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