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- PDB-6e0y: A131Q mutant of cyt P460 of Nitrosomonas sp. AL212 with bound NH2OH -

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Basic information

Entry
Database: PDB / ID: 6e0y
TitleA131Q mutant of cyt P460 of Nitrosomonas sp. AL212 with bound NH2OH
ComponentsCytochrome P460
KeywordsMETAL BINDING PROTEIN / nitrification / ammonia-oxidizing bacteria
Function / homology
Function and homology information


Cytochrome P460 / Cytochrome P460 / Cytochrome P460 superfamily / Cytochrome P460 / Chalcone isomerase / 3-Layer(bba) Sandwich / Alpha Beta
Similarity search - Domain/homology
HEME C / HYDROXYAMINE / Cytochrome P460
Similarity search - Component
Biological speciesNitrosomonas sp. AL212 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.257 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_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

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)78,19012
Polymers75,5844
Non-polymers2,6068
Water3,009167
1
A: Cytochrome P460
B: Cytochrome P460
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,0956
Polymers37,7922
Non-polymers1,3034
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6270 Å2
ΔGint-68 kcal/mol
Surface area13830 Å2
MethodPISA
2
C: Cytochrome P460
D: Cytochrome P460
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,0956
Polymers37,7922
Non-polymers1,3034
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6230 Å2
ΔGint-67 kcal/mol
Surface area13910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.031, 80.941, 120.598
Angle α, β, γ (deg.)90.00, 96.03, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Cytochrome P460


Mass: 18896.076 Da / Num. of mol.: 4 / Mutation: A131Q
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


Mass: 618.503 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#3: Chemical
ChemComp-HOA / HYDROXYAMINE


Mass: 33.030 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: H3NO
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 167 / 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: 2.69 Å3/Da / Density % sol: 54.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 0.2 M sodium chloride, 0.1 M sodium acetate, and PEG 6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 4, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.25→29.43 Å / Num. obs: 41097 / % possible obs: 94.8 % / Redundancy: 1.9 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 13.6
Reflection shellResolution: 2.2572→2.3136 Å / Rmerge(I) obs: 1.65 / Num. unique obs: 41095

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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: 2.257→29.186 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.42
RfactorNum. reflection% reflection
Rfree0.2417 1992 4.85 %
Rwork0.1928 --
obs0.1953 41095 94.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.257→29.186 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5066 0 180 167 5413
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085449
X-RAY DIFFRACTIONf_angle_d1.0177418
X-RAY DIFFRACTIONf_dihedral_angle_d6.3823034
X-RAY DIFFRACTIONf_chiral_restr0.056696
X-RAY DIFFRACTIONf_plane_restr0.006956
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2572-2.31360.4004770.3491467X-RAY DIFFRACTION50
2.3136-2.37610.34241280.33392532X-RAY DIFFRACTION87
2.3761-2.4460.32711440.3022837X-RAY DIFFRACTION97
2.446-2.52490.34671500.2722938X-RAY DIFFRACTION100
2.5249-2.61510.30091470.24672910X-RAY DIFFRACTION100
2.6151-2.71970.3381480.23082888X-RAY DIFFRACTION99
2.7197-2.84340.25421500.22132960X-RAY DIFFRACTION100
2.8434-2.99320.2981490.21922920X-RAY DIFFRACTION100
2.9932-3.18050.26161490.21892919X-RAY DIFFRACTION100
3.1805-3.42570.26441490.21532935X-RAY DIFFRACTION100
3.4257-3.76980.27681490.19452935X-RAY DIFFRACTION100
3.7698-4.31380.19711510.16162941X-RAY DIFFRACTION100
4.3138-5.42920.17261490.14012958X-RAY DIFFRACTION100
5.4292-29.18830.20581520.15912963X-RAY DIFFRACTION98

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