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- PDB-6p16: Cu-bound PCuAC domain from PmoF1 -

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Basic information

Entry
Database: PDB / ID: 6p16
TitleCu-bound PCuAC domain from PmoF1
ComponentsPmoF1
KeywordsMETAL BINDING PROTEIN / copper binding protein / chaperone
Function / homologyCOPPER (II) ION
Function and homology information
Biological speciesMethylocystis sp. ATCC 49242 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.913 Å
AuthorsSendzik, M.R. / Fisher, 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: PmoF1
A: PmoF1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2074
Polymers26,0802
Non-polymers1272
Water2,396133
1
B: PmoF1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,1032
Polymers13,0401
Non-polymers641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: PmoF1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,1032
Polymers13,0401
Non-polymers641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.285, 65.818, 77.952
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 PmoF1


Mass: 13039.921 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methylocystis sp. ATCC 49242 (bacteria)
Gene: Met49242_1449 / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 133 / 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: 2.68 Å3/Da / Density % sol: 54.13 %
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop / pH: 6.7 / Details: 0.1 M MES, 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: 1.373 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 1, 2018
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.373 Å / Relative weight: 1
ReflectionResolution: 1.91→33.537 Å / Num. obs: 40709 / % possible obs: 97.7 % / Redundancy: 3.468 % / Biso Wilson estimate: 39.758 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.098 / Rrim(I) all: 0.116 / Χ2: 1.207 / Net I/σ(I): 7.14 / Num. measured all: 141162 / Scaling rejects: 6
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
1.91-1.963.3761.3990.769935308429430.3141.66595.4
1.96-2.023.4621.0611.0710489303930300.4931.2699.7
2.02-2.083.4140.8081.529907292329020.6690.96399.3
2.08-2.143.3980.6471.939436282727770.7720.77298.2
2.14-2.213.4010.542.379156275126920.8140.64497.9
2.21-2.293.270.4472.988300266525380.860.53595.2
2.29-2.373.3020.3543.697661259323200.9330.42189.5
2.37-2.473.5840.2714.568663242424170.950.32199.7
2.47-2.583.6120.2155.48600238623810.9710.25599.8
2.58-2.713.6050.1776.588133226822560.9730.2199.5
2.71-2.853.5660.1467.897596214321300.980.17499.4
2.85-3.033.5730.1099.977182202420100.9890.12999.3
3.03-3.233.5220.0912.226684191918980.990.10798.9
3.23-3.493.4740.07514.656051177317420.9910.08998.3
3.49-3.833.3460.06116.655306163115860.9950.07397.2
3.83-4.282.9610.05616.864139150913980.9940.06892.6
4.28-4.943.7380.04920.924818129412890.9970.05799.6
4.94-6.053.7970.04721.394203111011070.9970.05599.7
6.05-8.563.8360.04420.9932268448410.9970.05199.6
8.56-33.5373.710.04123.2216774594520.9920.04898.5

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6P1E

6p1e


Resolution: 1.913→33.537 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.91
RfactorNum. reflection% reflection
Rfree0.2373 3720 9.15 %
Rwork0.1949 --
obs0.1988 40664 97.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 132.34 Å2 / Biso mean: 47.5445 Å2 / Biso min: 22.05 Å2
Refinement stepCycle: final / Resolution: 1.913→33.537 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1826 0 2 133 1961
Biso mean--37.61 48.81 -
Num. residues----240
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9135-1.93770.44111330.42351332146591
1.9377-1.96320.46651320.389213391471100
1.9632-1.99010.38071460.384614381584100
1.9901-2.01850.35791430.34581376151999
2.0185-2.04870.36151410.33321389153099
2.0487-2.08070.32181400.34571374151499
2.0807-2.11480.37891420.31481377151998
2.1148-2.15120.34721390.29731350148998
2.1512-2.19030.31851400.29551405154598
2.1903-2.23250.28871360.2731343147997
2.2325-2.2780.31171360.25911325146195
2.278-2.32750.28331230.25071224134788
2.3275-2.38170.28411290.23461306143593
2.3817-2.44120.2651400.223314121552100
2.4412-2.50720.26991410.217413971538100
2.5072-2.58090.28141450.227213841529100
2.5809-2.66420.2431390.205813951534100
2.6642-2.75940.26161360.20621402153899
2.7594-2.86980.2431400.183413941534100
2.8698-3.00040.21171390.17741387152699
3.0004-3.15840.28391360.1811382151899
3.1584-3.35610.21431310.16951374150598
3.3561-3.6150.20231350.17791397153298
3.615-3.97830.22081340.14811339147397
3.9783-4.55270.18281350.13941313144894
4.5527-5.73130.16791460.127614011547100
5.7313-33.54190.1651430.15761389153299

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