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- PDB-4rm4: The crystal structure of the versatile cytochrome P450 enzyme CYP... -

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Basic information

Entry
Database: PDB / ID: 4rm4
TitleThe crystal structure of the versatile cytochrome P450 enzyme CYP109B1 from Bacillus subtilis
ComponentsCytochrome P450
KeywordsELECTRON TRANSPORT / Cytochrome P450 / Secondary metabolites biosynthesis / transport / catabolism
Function / homology
Function and homology information


Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / monooxygenase activity / iron ion binding / heme binding
Similarity search - Function
Cytochrome P450, B-class / Cytochrome p450 / Cytochrome P450 / Cytochrome P450, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Putative cytochrome P450 YjiB
Similarity search - Component
Biological speciesBacillus subtilis subsp. subtilis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.771 Å
AuthorsZhouw, W.H. / Zhang, A.L. / Zhang, T. / Hall, E.A. / Hutchinson, S. / Cryle, M.J. / Wong, L.-L. / Bell, S.G.
CitationJournal: Mol Biosyst / Year: 2015
Title: The crystal structure of the versatile cytochrome P450 enzyme CYP109B1 from Bacillus subtilis.
Authors: Zhang, A. / Zhang, T. / Hall, E.A. / Hutchinson, S. / Cryle, M.J. / Wong, L.L. / Zhou, W. / Bell, S.G.
History
DepositionOct 18, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 4, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 4, 2015Group: Database references
Revision 1.2Sep 20, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,6652
Polymers45,0481
Non-polymers6161
Water4,234235
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.996, 67.573, 56.406
Angle α, β, γ (deg.)90.00, 113.04, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Cytochrome P450


Mass: 45048.484 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis (bacteria)
Strain: strain W23 / Gene: BSU12210, genomic DNA, yjiB / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: O34374, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 235 / 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: 2.1 Å3/Da / Density % sol: 41.49 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 16% w/v PEG 1000, 10% w/v PEG 8000, 0.625% w/v PEG 3350, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Details: mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.77→50 Å / Num. all: 36543 / Num. obs: 31135 / % possible obs: 85.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 2.5 % / Biso Wilson estimate: 23.01 Å2 / Rmerge(I) obs: 0.037 / Rsym value: 0.031 / Net I/σ(I): 21.7
Reflection shellResolution: 1.77→1.83 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.229 / Mean I/σ(I) obs: 3.65 / Num. unique all: 2286 / Rsym value: 0.21 / % possible all: 93.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
PHENIX(phenix.refine: 1.6.2_432)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2WHW

2whw


Resolution: 1.771→27.939 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Phase error: 23.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2529 1512 5.02 %RANDOM
Rwork0.202 ---
obs0.2046 30135 82.73 %-
all-36426 --
Solvent computationShrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 27.606 Å2 / ksol: 0.321 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.6192 Å2-0 Å22.3686 Å2
2---0.061 Å2-0 Å2
3---1.6802 Å2
Refinement stepCycle: LAST / Resolution: 1.771→27.939 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2892 0 43 235 3170
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073020
X-RAY DIFFRACTIONf_angle_d1.0684109
X-RAY DIFFRACTIONf_dihedral_angle_d12.7911124
X-RAY DIFFRACTIONf_chiral_restr0.071444
X-RAY DIFFRACTIONf_plane_restr0.005533
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7706-1.82780.30051490.24962809X-RAY DIFFRACTION90
1.8278-1.89310.30271420.23832861X-RAY DIFFRACTION91
1.8931-1.96880.3658860.2711623X-RAY DIFFRACTION52
1.9688-2.05840.26981450.21362923X-RAY DIFFRACTION93
2.0584-2.16690.24391590.19792866X-RAY DIFFRACTION91
2.1669-2.30260.2684840.19561658X-RAY DIFFRACTION53
2.3026-2.48030.24041360.19943040X-RAY DIFFRACTION95
2.4803-2.72970.26731790.20742923X-RAY DIFFRACTION94
2.7297-3.12430.22521560.2052948X-RAY DIFFRACTION93
3.1243-3.93450.25491370.20272320X-RAY DIFFRACTION75
3.9345-27.94260.2361390.17882652X-RAY DIFFRACTION82

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