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- PDB-6p1g: Copper-bound PCuAC domain from PmoF2 -

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Basic information

Entry
Database: PDB / ID: 6p1g
TitleCopper-bound PCuAC domain from PmoF2
ComponentsCopper chaperone PCu(A)C
KeywordsMETAL BINDING PROTEIN / copper binding protein / chaperone
Function / homologyCopper chaperone PCuAC / Copper chaperone PCuAC superfamily / Copper chaperone PCu(A)C / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / metal ion binding / COPPER (II) ION / Copper chaperone PCu(A)C
Function and homology information
Biological speciesMethylosinus trichosporium OB3b (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsFisher, O.S. / Rosenzweig, A.C.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)F32GM119191 United States
Department of Energy (DOE, United States)DE-SC0016284 United States
CitationJournal: J.Biol.Chem. / Year: 2019
Title: PCuAC domains from methane-oxidizing bacteria use a histidine brace to bind copper.
Authors: Fisher, O.S. / Sendzik, M.R. / Ross, M.O. / Lawton, T.J. / Hoffman, B.M. / Rosenzweig, A.C.
History
DepositionMay 19, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 2, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Nov 13, 2019Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 11, 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_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.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_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: Copper chaperone PCu(A)C
B: Copper chaperone PCu(A)C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5156
Polymers29,2582
Non-polymers2584
Water1,44180
1
A: Copper chaperone PCu(A)C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,7583
Polymers14,6291
Non-polymers1292
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Copper chaperone PCu(A)C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,7583
Polymers14,6291
Non-polymers1292
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.350, 89.350, 60.070
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Copper chaperone PCu(A)C / PmoF2


Mass: 14628.765 Da / Num. of mol.: 2 / Fragment: UNP residues 29-159
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methylosinus trichosporium OB3b (bacteria)
Gene: CQW49_04640 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2D2CWX5
#2: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / 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: 2.4 Å3/Da / Density % sol: 48.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M magnesium acetate, 0.1 M sodium cacodylate, 20% PEG8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.37 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Aug 8, 2018
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.37 Å / Relative weight: 1
ReflectionResolution: 2.05→35.848 Å / Num. obs: 33483 / % possible obs: 99.5 % / Redundancy: 5.233 % / Biso Wilson estimate: 40.36 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.085 / Rrim(I) all: 0.094 / Χ2: 1.211 / Net I/σ(I): 10.55 / Num. measured all: 175231
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.05-2.15.1610.8351.8512439247724100.5740.92797.3
2.1-2.165.3430.7362.2612908242724160.6560.81499.5
2.16-2.225.2940.7042.512552238123710.6740.78199.6
2.22-2.295.3160.6142.9112105228422770.7490.68199.7
2.29-2.375.2160.4823.7711445220321940.860.53699.6
2.37-2.455.1640.3794.6411144216321580.9180.42399.8
2.45-2.545.150.2995.6910697208020770.9390.33499.9
2.54-2.655.1120.2466.7810071197519700.9650.27599.7
2.65-2.764.6340.1877.678935193419280.9730.21299.7
2.76-2.95.3150.13410.969621181018100.9910.149100
2.9-3.065.5450.11113.69698175117490.9910.12399.9
3.06-3.245.4720.08617.178925163216310.9930.09699.9
3.24-3.475.4360.07419.338398154615450.9950.08299.9
3.47-3.745.3590.06820.947765145014490.9960.07699.9
3.74-4.15.3260.05923.356998131513140.9960.06599.9
4.1-4.585.080.05225.396060119411930.9970.05999.9
4.58-5.294.4220.05324.24617106710440.9950.0697.8
5.29-6.485.6130.05127.0649568838830.9970.056100
6.48-9.175.6340.04528.2738996926920.9980.049100
9.17-35.8485.3710.04629.7219983803720.9930.05197.9

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Processing

Software
NameVersionClassification
PHENIX1.8.3_1479refinement
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6P1E

6p1e


Resolution: 2.05→35.848 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.21
RfactorNum. reflection% reflection
Rfree0.2293 3362 10.04 %
Rwork0.1862 --
obs0.1906 33482 99.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 122.66 Å2 / Biso mean: 46.41 Å2 / Biso min: 24.65 Å2
Refinement stepCycle: final / Resolution: 2.05→35.848 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1884 0 4 80 1968
Biso mean--51.27 48.05 -
Num. residues----244
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031929
X-RAY DIFFRACTIONf_angle_d0.8672624
X-RAY DIFFRACTIONf_chiral_restr0.031296
X-RAY DIFFRACTIONf_plane_restr0.003340
X-RAY DIFFRACTIONf_dihedral_angle_d11.246706
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 24

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0505-2.07980.32861330.28981218135196
2.0798-2.11080.31171350.27861234136999
2.1108-2.14380.27511430.27341249139299
2.1438-2.17890.34351360.27851268140499
2.1789-2.21650.32551340.251712481382100
2.2165-2.25680.32541350.2691243137899
2.2568-2.30020.28381520.273812881440100
2.3002-2.34710.30041380.27351248138699
2.3471-2.39820.34051400.246112571397100
2.3982-2.45390.28551330.23912761409100
2.4539-2.51530.25281480.226412581406100
2.5153-2.58330.27081460.212712451391100
2.5833-2.65930.27951350.222712151350100
2.6593-2.74510.25981450.225112731418100
2.7451-2.84320.23411400.206612721412100
2.8432-2.95690.20541370.20612481385100
2.9569-3.09140.2491440.194812931437100
3.0914-3.25430.21081420.186712501392100
3.2543-3.45810.23821420.186812531395100
3.4581-3.72480.23591460.166612671413100
3.7248-4.09920.20221360.156912521388100
4.0992-4.69120.1631410.13112761417100
4.6912-5.90620.22271430.14061228137198
5.9062-35.85330.18171380.165812611399100

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