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- PDB-6wis: Copper resistance protein copG- Form 1 -

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Basic information

Entry
Database: PDB / ID: 6wis
TitleCopper resistance protein copG- Form 1
ComponentsDUF411 domain-containing protein
KeywordsMETAL BINDING PROTEIN / metal resistance copper-binding protein
Function / homologyProtein of unknown function DUF411 / Protein of unknown function, DUF / ACETATE ION / COPPER (II) ION / : / Metal-binding protein
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsHausrath, A.C. / Ly, A. / McEvoy, M.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM079192 United States
CitationJournal: J.Biol.Chem. / Year: 2020
Title: The bacterial copper resistance protein CopG contains a cysteine-bridged tetranuclear copper cluster.
Authors: Hausrath, A.C. / Ramirez, N.A. / Ly, A.T. / McEvoy, M.M.
History
DepositionApr 10, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 8, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Aug 19, 2020Group: Database references / Derived calculations
Category: citation / pdbx_struct_conn_angle ...citation / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.ptnr1_symmetry / _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_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DUF411 domain-containing protein
B: DUF411 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,26131
Polymers27,2852
Non-polymers1,97629
Water1,63991
1
A: DUF411 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,53314
Polymers13,6431
Non-polymers89013
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: DUF411 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,72917
Polymers13,6431
Non-polymers1,08616
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)86.130, 86.130, 58.560
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein DUF411 domain-containing protein


Mass: 13642.728 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: FQ758_25220 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A5C0YHL7, UniProt: Q9HV84*PLUS

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Non-polymers , 5 types, 120 molecules

#2: Chemical
ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 91 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.34 Å3/Da / Density % sol: 47.4 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 100 mM Na Cacodylate 200 mM Zn Acetate 17% ethanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 14, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2→74.6 Å / Num. obs: 32888 / % possible obs: 99.9 % / Redundancy: 7.1 % / CC1/2: 0.996 / Rmerge(I) obs: 0.133 / Net I/σ(I): 10.7
Reflection shellResolution: 2→2.05 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.928 / Num. unique obs: 2437 / CC1/2: 0.594 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XSCALEdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2→46.061 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 2 / Phase error: 23.51
RfactorNum. reflection% reflection
Rfree0.2204 3303 10.08 %
Rwork0.1721 --
obs0.177 32776 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 96.07 Å2 / Biso mean: 35.7801 Å2 / Biso min: 19.21 Å2
Refinement stepCycle: final / Resolution: 2→46.061 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1832 0 55 91 1978
Biso mean--51.52 44.43 -
Num. residues----249
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.0001-2.02870.2661460.23811211100
2.0287-2.0590.25671380.23391223100
2.059-2.09120.32381380.24551229100
2.0912-2.12540.30331260.2471226100
2.1254-2.16210.31151480.25171218100
2.1621-2.20140.31531420.27991235100
2.2014-2.24380.26361340.24041228100
2.2438-2.28960.29651250.21961239100
2.2896-2.33930.28611340.20131219100
2.3393-2.39370.24541470.18621260100
2.3937-2.45360.22321340.17221227100
2.4536-2.51990.2071340.16031213100
2.5199-2.59410.23041490.15441239100
2.5941-2.67780.19311380.14891247100
2.6778-2.77350.191260.13981208100
2.7735-2.88450.21551300.14511248100
2.8845-3.01580.18131360.14221213100
3.0158-3.17480.1911380.1571238100
3.1748-3.37360.20651340.15511246100
3.3736-3.6340.20031500.16191221100
3.634-3.99950.22511400.14271221100
3.9995-4.57780.20221460.16491211100
4.5778-5.76580.20481380.17341248100
5.7658-8.940.20751320.1706120599

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