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- PDB-6wje: Copper resistance protein copG- Form 2 -

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Basic information

Entry
Database: PDB / ID: 6wje
TitleCopper resistance protein copG- Form 2
Components(DUF411 domain-containing ...) x 2
KeywordsMETAL BINDING PROTEIN / metal resistance copper-binding protein
Function / homologyProtein of unknown function DUF411 / Protein of unknown function, DUF411 / metal ion binding / ACETATE ION / COPPER (II) ION / : / DUF411 domain-containing protein
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsHausrath, A.C. / Ly, A.T. / 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
Citation
Journal: 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.
#1: Journal: To Be Published
Title: Copper resistance protein copG- Form 2
Authors: Hausrath, A.C. / Ly, A.T. / McEvoy, M.M.
History
DepositionApr 13, 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_alt_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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_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_alt_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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _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
Revision 1.3Oct 18, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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
C: DUF411 domain-containing protein
D: DUF411 domain-containing protein
E: DUF411 domain-containing protein
F: DUF411 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,25164
Polymers80,5146
Non-polymers3,73758
Water2,288127
1
A: DUF411 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,11612
Polymers13,4081
Non-polymers70811
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DUF411 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9269
Polymers13,4081
Non-polymers5188
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: DUF411 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,20913
Polymers13,4401
Non-polymers76912
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: DUF411 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,08211
Polymers13,4401
Non-polymers64210
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: DUF411 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,05711
Polymers13,4081
Non-polymers64910
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: DUF411 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,8618
Polymers13,4081
Non-polymers4527
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.700, 87.460, 143.270
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and ((resid 1 and (name N or name...
21(chain B and ((resid 1 and (name N or name...
31(chain C and ((resid 1 and (name N or name...
41(chain D and ((resid 1 and (name N or name...
51(chain E and (resid 1 through 12 or resid 14...
61(chain F and ((resid 1 and (name N or name...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLUGLUGLU(chain A and ((resid 1 and (name N or name...AA11
12GLUGLUHOHHOH(chain A and ((resid 1 and (name N or name...AA - MB1 - 3061
13GLUGLUHOHHOH(chain A and ((resid 1 and (name N or name...AA - MB1 - 3061
14GLUGLUHOHHOH(chain A and ((resid 1 and (name N or name...AA - MB1 - 3061
15GLUGLUHOHHOH(chain A and ((resid 1 and (name N or name...AA - MB1 - 3061
21GLUGLUGLUGLU(chain B and ((resid 1 and (name N or name...BB11
22GLUGLUHOHHOH(chain B and ((resid 1 and (name N or name...BB - NB1 - 3061
23GLUGLUHOHHOH(chain B and ((resid 1 and (name N or name...BB - NB1 - 3061
24GLUGLUHOHHOH(chain B and ((resid 1 and (name N or name...BB - NB1 - 3061
25GLUGLUHOHHOH(chain B and ((resid 1 and (name N or name...BB - NB1 - 3061
31GLUGLUGLUGLU(chain C and ((resid 1 and (name N or name...CC11
32GLUGLUHOHHOH(chain C and ((resid 1 and (name N or name...CC - OB1 - 3061
33GLUGLUHOHHOH(chain C and ((resid 1 and (name N or name...CC - OB1 - 3061
34GLUGLUHOHHOH(chain C and ((resid 1 and (name N or name...CC - OB1 - 3061
35GLUGLUHOHHOH(chain C and ((resid 1 and (name N or name...CC - OB1 - 3061
41GLUGLUGLUGLU(chain D and ((resid 1 and (name N or name...DD11
42GLUGLUHOHHOH(chain D and ((resid 1 and (name N or name...DD - PB1 - 3061
43GLUGLUHOHHOH(chain D and ((resid 1 and (name N or name...DD - PB1 - 3061
44GLUGLUHOHHOH(chain D and ((resid 1 and (name N or name...DD - PB1 - 3061
45GLUGLUHOHHOH(chain D and ((resid 1 and (name N or name...DD - PB1 - 3061
51GLUGLUASNASN(chain E and (resid 1 through 12 or resid 14...EE1 - 121 - 12
52GLYGLYCYSCYS(chain E and (resid 1 through 12 or resid 14...EE14 - 1514 - 15
53LYSLYSLYSLYS(chain E and (resid 1 through 12 or resid 14...EE1717
54GLUGLUHOHHOH(chain E and (resid 1 through 12 or resid 14...EE - QB1 - 3061
55GLUGLUHOHHOH(chain E and (resid 1 through 12 or resid 14...EE - QB1 - 3061
56GLUGLUHOHHOH(chain E and (resid 1 through 12 or resid 14...EE - QB1 - 3061
57GLUGLUHOHHOH(chain E and (resid 1 through 12 or resid 14...EE - QB1 - 3061
61GLUGLUGLUGLU(chain F and ((resid 1 and (name N or name...FF11
62GLUGLUHOHHOH(chain F and ((resid 1 and (name N or name...FF - RB1 - 3061
63GLUGLUHOHHOH(chain F and ((resid 1 and (name N or name...FF - RB1 - 3061
64GLUGLUHOHHOH(chain F and ((resid 1 and (name N or name...FF - RB1 - 3061
65GLUGLUHOHHOH(chain F and ((resid 1 and (name N or name...FF - RB1 - 3061

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Components

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DUF411 domain-containing ... , 2 types, 6 molecules ABEFCD

#1: Protein
DUF411 domain-containing protein


Mass: 13408.251 Da / Num. of mol.: 4
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
#2: Protein DUF411 domain-containing protein


Mass: 13440.250 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 , 4 types, 185 molecules

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


Mass: 63.546 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical...
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 35 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 127 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.48 Å3/Da / Density % sol: 50.37 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 100 mM Na Cacodylate pH 6.8 200 mM Zn Acetate 19% ethanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.5→55.42 Å / Num. obs: 28435 / % possible obs: 99.8 % / Redundancy: 6.62 % / CC1/2: 0.996 / Rrim(I) all: 0.148 / Net I/σ(I): 8.93
Reflection shellResolution: 2.5→2.57 Å / Mean I/σ(I) obs: 1.9 / Num. unique obs: 2067 / CC1/2: 0.566

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Processing

Software
NameVersionClassification
PHENIXdev_3724refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6WIS

6wis


Resolution: 2.5→55.42 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 24.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2454 2842 10.02 %
Rwork0.1881 25532 -
obs0.1938 28374 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 119.91 Å2 / Biso mean: 53.5931 Å2 / Biso min: 24.92 Å2
Refinement stepCycle: final / Resolution: 2.5→55.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5450 0 67 127 5644
Biso mean--65.08 53.26 -
Num. residues----754
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2088X-RAY DIFFRACTION3.142TORSIONAL
12B2088X-RAY DIFFRACTION3.142TORSIONAL
13C2088X-RAY DIFFRACTION3.142TORSIONAL
14D2088X-RAY DIFFRACTION3.142TORSIONAL
15E2088X-RAY DIFFRACTION3.142TORSIONAL
16F2088X-RAY DIFFRACTION3.142TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5-2.540.29571390.24371252139199
2.54-2.590.34981400.24212511391100
2.59-2.640.29221400.232512591399100
2.64-2.690.30371390.224612511390100
2.69-2.750.30241410.223212681409100
2.75-2.820.3041390.21412491388100
2.82-2.890.25341410.212661407100
2.89-2.960.26591390.194112491388100
2.96-3.050.31491410.212801421100
3.05-3.150.27831400.199712581398100
3.15-3.260.2761410.19712631404100
3.26-3.390.25781400.202512701410100
3.39-3.550.2211410.182312641405100
3.55-3.730.24911430.17071291143499
3.73-3.970.21141430.171212781421100
3.97-4.270.23971410.160112711412100
4.27-4.70.20121440.1612941438100
4.7-5.380.2291460.182113101456100
5.39-6.780.26031470.20713141461100
6.78-55.420.21491570.186713941551100

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