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- PDB-6p17: Apo PCuAC domain from PmoF1 -

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Basic information

Entry
Database: PDB / ID: 6p17
TitleApo PCuAC domain from PmoF1
ComponentsPmoF1
KeywordsMETAL BINDING PROTEIN / copper binding protein / chaperone
Biological speciesMethylocystis sp. ATCC 49242 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.851 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: PmoF1
A: PmoF1


Theoretical massNumber of molelcules
Total (without water)26,5162
Polymers26,5162
Non-polymers00
Water4,882271
1
B: PmoF1


Theoretical massNumber of molelcules
Total (without water)13,2581
Polymers13,2581
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: PmoF1


Theoretical massNumber of molelcules
Total (without water)13,2581
Polymers13,2581
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.642, 60.579, 85.100
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: 13258.194 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 271 / 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: 2.36 Å3/Da / Density % sol: 47.96 %
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.1 M sodium acetate, 0.2 M ammonium acetate, 34% PEG4000

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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: Aug 8, 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: 1.7→37.448 Å / Num. obs: 21609 / % possible obs: 96.8 % / Redundancy: 3.451 % / Biso Wilson estimate: 30.678 Å2 / CC1/2: 0.985 / Rmerge(I) obs: 0.129 / Rrim(I) all: 0.153 / Χ2: 1.014 / Net I/σ(I): 5.29 / Num. measured all: 174487
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
1.7-1.753.4071.0431.1411658387234220.6511.2488.4
1.75-1.793.4530.8671.4312407376535930.781.0395.4
1.79-1.853.4440.6741.8211978364834780.8580.80295.3
1.85-1.93.3890.5262.2911644356634360.90.62896.4
1.9-1.963.2950.4013.0411046346033520.9240.48196.9
1.96-2.032.9980.3183.449472332131590.9360.38895.1
2.03-2.113.410.2594.3910671320231290.9550.30997.7
2.11-2.23.6110.2225.1911068312030650.970.26398.2
2.2-2.293.6040.2015.4510471295029050.9750.23898.5
2.29-2.413.5760.1656.1710102285528250.9750.19698.9
2.41-2.543.5720.1566.549486268326560.9720.18699
2.54-2.693.5450.14678947255025240.9770.17399
2.69-2.883.4810.1297.768379242424070.9760.15399.3
2.88-3.113.3960.1118.557496223022070.9820.13499
3.11-3.43.1430.1088.976336205920160.9790.13197.9
3.4-3.83.2050.1049.495525183617240.9810.12493.9
3.8-4.393.7910.10511.326232165016440.9780.12299.6
4.39-5.383.8270.09111.645297138813840.9870.10699.7
5.38-7.613.8430.08911.24108107110690.9870.10399.8
7.61-37.4483.790.08211.7521645785710.9870.09898.8

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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: 1.851→37.448 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 33.94
RfactorNum. reflection% reflection
Rfree0.2772 1996 9.44 %
Rwork0.2271 --
obs0.2317 21136 97.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 104.49 Å2 / Biso mean: 30.8719 Å2 / Biso min: 10.67 Å2
Refinement stepCycle: final / Resolution: 1.851→37.448 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1826 0 0 271 2097
Biso mean---35.97 -
Num. residues----240
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8515-1.89780.43771300.37381248137891
1.8978-1.94910.33811400.29281336147698
1.9491-2.00640.28881390.25331333147298
2.0064-2.07120.30131390.23371334147396
2.0712-2.14520.29251420.23141352149499
2.1452-2.23110.25341410.22941357149899
2.2311-2.33260.25191430.22851368151199
2.3326-2.45560.28341450.22851374151999
2.4556-2.60940.31321440.23931388153299
2.6094-2.81080.32571440.24881386153099
2.8108-3.09360.30471460.24091391153799
3.0936-3.54090.26191410.20871354149595
3.5409-4.460.24511470.19351420156799
4.46-37.45610.23871550.2081499165499

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