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- PDB-6w6n: K106L/A131E mutant of cytochrome P460 from Nitrosomonas sp. AL212 -

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Basic information

Entry
Database: PDB / ID: 6w6n
TitleK106L/A131E mutant of cytochrome P460 from Nitrosomonas sp. AL212
ComponentsCytochrome P460
KeywordsMETAL BINDING PROTEIN / Cytochrome c / NH2OH oxidation
Function / homologyCytochrome P460 / Cytochrome P460 / Cytochrome P460 superfamily / Cytochrome P460 / Chalcone isomerase / 3-Layer(bba) Sandwich / Alpha Beta / HEME C / Cytochrome P460
Function and homology information
Biological speciesNitrosomonas sp. AL212 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsColeman, R.E. / Lancaster, K.M.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE-SC0013997 United States
CitationJournal: Biochemistry / Year: 2020
Title: The Heme-Lys Cross-Link in Cytochrome P460 Promotes Catalysis by Enforcing Secondary Coordination Sphere Architecture.
Authors: Coleman, R.E. / Vilbert, A.C. / Lancaster, K.M.
History
DepositionMar 17, 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.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 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.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.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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytochrome P460
B: Cytochrome P460
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0494
Polymers35,8122
Non-polymers1,2372
Water77543
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5880 Å2
ΔGint-73 kcal/mol
Surface area13670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.373, 80.172, 110.767
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 Cytochrome P460


Mass: 17906.016 Da / Num. of mol.: 2 / Mutation: K106L, A131E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nitrosomonas sp. AL212 (bacteria) / Gene: NAL212_0896 / Plasmid: pET22b(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: F9ZFJ0
#2: Chemical ChemComp-HEC / HEME C / Heme C


Mass: 618.503 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H34FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 43 / Source method: isolated from a natural source / Formula: H2O
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: 2.95 Å3/Da / Density % sol: 58.34 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8
Details: Protein in 50 mM MOPS pH 8.0 PEG 6000, 0.1 M sodium acetate pH 5.0, and 0.2 M NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 5, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.25→110.77 Å / Num. obs: 20467 / % possible obs: 98.1 % / Redundancy: 6.5 % / CC1/2: 0.995 / Rmerge(I) obs: 0.1507 / Net I/σ(I): 7.66
Reflection shellResolution: 2.25→2.33 Å / Redundancy: 6 % / Rmerge(I) obs: 1.824 / Mean I/σ(I) obs: 0.99 / Num. unique obs: 1756 / CC1/2: 0.518 / % possible all: 86.45

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Processing

Software
NameVersionClassification
XDSdata scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHENIX1.14_3260phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6amg

6amg


Resolution: 2.25→55.383 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 36.08 / Details: Fe atoms were refined anisotropically
RfactorNum. reflection% reflection
Rfree0.2775 1999 9.85 %
Rwork0.2575 --
obs0.2596 20292 98.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 109.63 Å2 / Biso mean: 63.1606 Å2 / Biso min: 29.9 Å2
Refinement stepCycle: final / Resolution: 2.25→55.383 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2517 0 86 43 2646
Biso mean--59.27 55.35 -
Num. residues----318
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.2503-2.30660.45331160.4312105582
2.3066-2.3690.45451440.4194131499
2.369-2.43870.37711400.40551288100
2.4387-2.51740.39731440.3738131599
2.5174-2.60740.30771420.35251296100
2.6074-2.71180.35721410.3227129299
2.7118-2.83520.34711430.30471316100
2.8352-2.98460.34791450.29861327100
2.9846-3.17160.34311430.30891318100
3.1716-3.41650.30031450.2823131599
3.4165-3.76020.26481450.2623132199
3.7602-4.30410.22611460.2249134699
4.3041-5.4220.23541480.19521355100
5.422-55.3830.23111570.2032143599

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