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- PDB-5ffe: CopM in the Ag-bound form (by soaking) -

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Basic information

Entry
Database: PDB / ID: 5ffe
TitleCopM in the Ag-bound form (by soaking)
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
SILVER ION / CopM / Slr6039 protein
Similarity search - Component
Biological speciesSynechocystis sp. PCC 6803 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.096 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CopM
B: CopM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,05714
Polymers40,7632
Non-polymers1,29412
Water4,396244
1
A: CopM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,0297
Polymers20,3811
Non-polymers6476
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area120 Å2
ΔGint-6 kcal/mol
Surface area7540 Å2
MethodPISA
2
B: CopM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,0297
Polymers20,3811
Non-polymers6476
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area120 Å2
ΔGint-6 kcal/mol
Surface area7600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.984, 67.035, 85.614
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein CopM


Mass: 20381.482 Da / Num. of mol.: 2
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 / Silver


Mass: 107.868 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Ag
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 244 / 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: 35.27 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: 0.1M MES 6.0, 20% PEG 2000MME

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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: 2.09→50 Å / Num. obs: 18184 / % possible obs: 96.3 % / Redundancy: 4 % / Net I/σ(I): 11.1
Reflection shellResolution: 2.09→2.18 Å / Redundancy: 4 % / Rmerge(I) obs: 0.309 / Mean I/σ(I) obs: 2.9 / % 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: 3BT5

3bt5


Resolution: 2.096→37.74 Å / FOM work R set: 0.7733 / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2566 821 5.12 %
Rwork0.214 15207 -
obs0.2161 16028 85.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 59.43 Å2 / Biso mean: 21.3 Å2 / Biso min: 11.7 Å2
Refinement stepCycle: final / Resolution: 2.096→37.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2227 0 12 244 2483
Biso mean--31.36 25.21 -
Num. residues----271
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052328
X-RAY DIFFRACTIONf_angle_d0.833131
X-RAY DIFFRACTIONf_chiral_restr0.061322
X-RAY DIFFRACTIONf_plane_restr0.003407
X-RAY DIFFRACTIONf_dihedral_angle_d14.924887
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0955-2.22680.29261200.26781969208968
2.2268-2.39870.30111300.26762226235676
2.3987-2.640.24581370.20752591272888
2.64-3.02190.24641500.20972903305397
3.0219-3.80670.28771450.20372680282590
3.8067-37.74590.221390.20322838297790

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