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- PDB-6e0x: A131E mutant of cyt P460 of Nitrosomonas sp. AL212 -

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Basic information

Entry
Database: PDB / ID: 6e0x
TitleA131E mutant of cyt P460 of Nitrosomonas sp. AL212
ComponentsCytochrome P460
KeywordsMETAL BINDING PROTEIN / nitrification / ammonia-oxidizing bacteria
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: 1.974 Å
AuthorsSmith, M. / Lancaster, K.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Energy (DOE, United States) United States
CitationJournal: Chem Sci / Year: 2019
Title: Controlling a burn: outer-sphere gating of hydroxylamine oxidation by a distal base in cytochrome P460.
Authors: Smith, M.A. / Majer, S.H. / Vilbert, A.C. / Lancaster, K.M.
History
DepositionJul 7, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 27, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2019Group: Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 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.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_label_asym_id / _struct_conn.ptnr2_label_atom_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)78,0628
Polymers75,5884
Non-polymers2,4744
Water3,243180
1
A: Cytochrome P460
D: Cytochrome P460
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,0314
Polymers37,7942
Non-polymers1,2372
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5790 Å2
ΔGint-70 kcal/mol
Surface area13870 Å2
MethodPISA
2
B: Cytochrome P460
C: Cytochrome P460
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,0314
Polymers37,7942
Non-polymers1,2372
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5810 Å2
ΔGint-69 kcal/mol
Surface area14160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.152, 80.356, 120.033
Angle α, β, γ (deg.)90.00, 95.85, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Cytochrome P460


Mass: 18897.061 Da / Num. of mol.: 4 / Mutation: A131E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nitrosomonas sp. AL212 (bacteria) / Gene: NAL212_0896 / Production host: Escherichia coli (E. coli) / References: UniProt: F9ZFJ0
#2: Chemical
ChemComp-HEC / HEME C / Heme C


Mass: 618.503 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H34FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 180 / 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: 3.06 Å3/Da / Density % sol: 53.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 0.2 M sodium chloride, 0.1 M sodium acetate, PEG 6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 6, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.97→119.63 Å / Num. obs: 62608 / % possible obs: 96.1 % / Redundancy: 1.9 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 32
Reflection shellResolution: 1.9736→2.0045 Å / Rmerge(I) obs: 1.11 / Num. unique obs: 62608

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Processing

Software
NameVersionClassification
PHENIX(dev_3126)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6AMG

6amg


Resolution: 1.974→47.924 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.63
RfactorNum. reflection% reflection
Rfree0.2486 3073 4.91 %
Rwork0.2057 --
obs0.2077 62531 97.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.974→47.924 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5064 0 172 180 5416
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085444
X-RAY DIFFRACTIONf_angle_d1.0387416
X-RAY DIFFRACTIONf_dihedral_angle_d6.4263036
X-RAY DIFFRACTIONf_chiral_restr0.056697
X-RAY DIFFRACTIONf_plane_restr0.006955
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9736-2.00450.48351430.43412365X-RAY DIFFRACTION85
2.0045-2.03730.37981530.40182645X-RAY DIFFRACTION98
2.0373-2.07240.41591400.37642732X-RAY DIFFRACTION99
2.0724-2.11010.41681370.352713X-RAY DIFFRACTION99
2.1101-2.15070.36381650.32882714X-RAY DIFFRACTION99
2.1507-2.19460.41951280.322756X-RAY DIFFRACTION99
2.1946-2.24230.38761460.29442705X-RAY DIFFRACTION99
2.2423-2.29450.28861430.27332761X-RAY DIFFRACTION99
2.2945-2.35190.33011270.262722X-RAY DIFFRACTION99
2.3519-2.41550.29021600.25182685X-RAY DIFFRACTION98
2.4155-2.48650.36831290.24152690X-RAY DIFFRACTION98
2.4865-2.56680.28071400.23172680X-RAY DIFFRACTION97
2.5668-2.65850.29951560.2182757X-RAY DIFFRACTION99
2.6585-2.7650.26631280.21642731X-RAY DIFFRACTION99
2.765-2.89080.28341280.21442768X-RAY DIFFRACTION99
2.8908-3.04320.26561370.21592763X-RAY DIFFRACTION99
3.0432-3.23380.2471420.21632749X-RAY DIFFRACTION99
3.2338-3.48340.23371450.21522731X-RAY DIFFRACTION98
3.4834-3.83380.22331370.19712691X-RAY DIFFRACTION98
3.8338-4.38830.20261290.16372719X-RAY DIFFRACTION96
4.3883-5.52740.1851330.15492608X-RAY DIFFRACTION93
5.5274-47.9380.20771270.16782773X-RAY DIFFRACTION96

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