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- PDB-6hiu: Cytochrome P460 from Methylococcus capsulatus (Bath) -

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Basic information

Entry
Database: PDB / ID: 6hiu
TitleCytochrome P460 from Methylococcus capsulatus (Bath)
ComponentsCytochrome P460
KeywordsOXIDOREDUCTASE / cytochrome / NO / CO / methanotroph
Function / homologyCytochrome P460 / Cytochrome P460 superfamily / Cytochrome P460 / HEME C / Cytochrome P460
Function and homology information
Biological speciesMethylococcus capsulatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.36 Å
AuthorsAdams, H. / Chicano, T.M. / Hough, M.A.
CitationJournal: Chem Sci / Year: 2019
Title: One fold, two functions: cytochrome P460 and cytochromec'-beta from the methanotrophMethylococcus capsulatus(Bath).
Authors: Adams, H.R. / Krewson, C. / Vardanega, J.E. / Fujii, S. / Moreno, T. / Sambongi, Y. / Svistunenko, D. / Paps, J. / Andrew, C.R. / Hough, M.A.
History
DepositionAug 31, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 20, 2019Provider: repository / Type: Initial release
Revision 1.1May 1, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
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_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)36,1596
Polymers34,7342
Non-polymers1,4254
Water4,468248
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6700 Å2
ΔGint-81 kcal/mol
Surface area12250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.623, 81.647, 85.264
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: 17366.906 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methylococcus capsulatus (strain ATCC 33009 / NCIMB 11132 / Bath) (bacteria)
Strain: ATCC 33009 / NCIMB 11132 / Bath / Gene: MCA0524 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: G1UBD9
#2: Chemical ChemComp-HEC / HEME C / Heme C


Mass: 618.503 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 248 / 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: 2.62 Å3/Da / Density % sol: 53.06 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 8
Details: 2microlitres of 15mg/ml protein in 20mM Tris buffer, pH8, with an equivalent volume of reservoir solution containing 0.1M Tris, 2.4M Ammonium sulfate pH8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.928 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.928 Å / Relative weight: 1
ReflectionResolution: 1.36→46.62 Å / Num. obs: 70585 / % possible obs: 99.9 % / Redundancy: 5.4 % / Biso Wilson estimate: 16 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.043 / Rpim(I) all: 0.02 / Rrim(I) all: 0.048 / Net I/σ(I): 13.7
Reflection shellResolution: 1.36→1.38 Å / Redundancy: 4.4 % / Rmerge(I) obs: 1.048 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 3431 / CC1/2: 0.486 / Rpim(I) all: 0.562 / Rrim(I) all: 1.195 / % possible all: 98.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
PDB_EXTRACT3.22data extraction
xia2data reduction
Aimlessdata scaling
Auto-Rickshawphasing
RefinementMethod to determine structure: SAD / Resolution: 1.36→42.67 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.96 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.057 / ESU R Free: 0.06
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2237 1103 1.6 %RANDOM
Rwork0.1965 ---
obs0.1969 68885 99.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 51.84 Å2 / Biso mean: 19.701 Å2 / Biso min: 9.78 Å2
Baniso -1Baniso -2Baniso -3
1-0.33 Å20 Å20 Å2
2---0.21 Å20 Å2
3----0.12 Å2
Refinement stepCycle: final / Resolution: 1.36→42.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2159 0 97 250 2506
Biso mean--17.72 30.09 -
Num. residues----286
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0142456
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172135
X-RAY DIFFRACTIONr_angle_refined_deg1.841.7243372
X-RAY DIFFRACTIONr_angle_other_deg1.5571.684993
X-RAY DIFFRACTIONr_dihedral_angle_1_deg17.6235.309324
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.65222.547106
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.40415351
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1391510
X-RAY DIFFRACTIONr_chiral_restr0.0840.2297
X-RAY DIFFRACTIONr_gen_planes_refined0.0240.023199
X-RAY DIFFRACTIONr_gen_planes_other0.0660.02501
X-RAY DIFFRACTIONr_mcbond_it1.6991.8481187
X-RAY DIFFRACTIONr_mcbond_other1.6771.8471186
X-RAY DIFFRACTIONr_mcangle_it2.4012.7671494
LS refinement shellResolution: 1.36→1.395 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.385 91 -
Rwork0.397 4910 -
all-5001 -
obs--96.94 %

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