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- PDB-3rwl: Structure of P450pyr hydroxylase -

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Basic information

Entry
Database: PDB / ID: 3rwl
TitleStructure of P450pyr hydroxylase
ComponentsCytochrome P450 alkane hydroxylase 1 CYP153A7
KeywordsOXIDOREDUCTASE / P450 monooxygenase
Function / homology
Function and homology information


alkane 1-monooxygenase / 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 / Cytochrome P450 alkane hydroxylase 1 CYP153A7
Similarity search - Component
Biological speciesSphingopyxis macrogoltabida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsPompidor, G.
CitationJournal: Chem.Commun.(Camb.) / Year: 2012
Title: Evolving P450pyr hydroxylase for highly enantioselective hydroxylation at non-activated carbon atom.
Authors: Pham, S.Q. / Pompidor, G. / Liu, J. / Li, X.D. / Li, Z.
History
DepositionMay 9, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 18, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 25, 2012Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: Cytochrome P450 alkane hydroxylase 1 CYP153A7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8752
Polymers48,2591
Non-polymers6161
Water5,008278
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)112.604, 112.604, 41.964
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31

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Components

#1: Protein Cytochrome P450 alkane hydroxylase 1 CYP153A7


Mass: 48258.559 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sphingopyxis macrogoltabida (bacteria) / Gene: ahpG1, Sphingomonas sp. / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q5F4D9, alkane 1-monooxygenase
#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.: 278 / 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: 3.18 Å3/Da / Density % sol: 61.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% PEG 4000, 10% ISOPROPANOL, 100 mM TRIS, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.736 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 20, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.736 Å / Relative weight: 1
ReflectionResolution: 2→48.759 Å / Num. all: 38307 / Num. obs: 38307 / % possible obs: 95.3 % / Redundancy: 5.1 % / Rsym value: 0.071 / Net I/σ(I): 14.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2-2.114.80.5221.42398050460.52285.8
2.11-2.2450.3740.12625152270.37494.6
2.24-2.395.20.1983.82586349820.19895.3
2.39-2.585.10.1454.92385046600.14596
2.58-2.835.30.0947.82309743550.09497
2.83-3.165.20.071102082039900.07198.3
3.16-3.655.30.0513.81848234720.0598.1
3.65-4.475.20.0416.91559929900.0499
4.47-6.325.40.03618.31255023180.03699.4
6.32-48.7595.30.03418671112670.03499.5

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
SCALA3.3.9data scaling
SHELXphasing
DMphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
XSCALEdata scaling
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 2→48.759 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.947 / WRfactor Rfree: 0.188 / WRfactor Rwork: 0.154 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8974 / SU B: 2.754 / SU ML: 0.078 / SU R Cruickshank DPI: 0.1346 / SU Rfree: 0.1279 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.135 / ESU R Free: 0.128 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1962 1913 5 %RANDOM
Rwork0.1603 ---
obs0.1621 38304 95.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 70.13 Å2 / Biso mean: 27.3493 Å2 / Biso min: 2.84 Å2
Baniso -1Baniso -2Baniso -3
1-0.17 Å20.09 Å20 Å2
2--0.17 Å20 Å2
3----0.26 Å2
Refinement stepCycle: LAST / Resolution: 2→48.759 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3229 0 43 278 3550
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0223430
X-RAY DIFFRACTIONr_bond_other_d0.0010.022379
X-RAY DIFFRACTIONr_angle_refined_deg2.0851.9944679
X-RAY DIFFRACTIONr_angle_other_deg1.14935753
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6695422
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.41323.036168
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.02215590
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4011536
X-RAY DIFFRACTIONr_chiral_restr0.1490.2502
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0213829
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02719
X-RAY DIFFRACTIONr_mcbond_it1.3411.52048
X-RAY DIFFRACTIONr_mcbond_other0.4041.5822
X-RAY DIFFRACTIONr_mcangle_it2.30723333
X-RAY DIFFRACTIONr_scbond_it3.64831382
X-RAY DIFFRACTIONr_scangle_it5.7214.51335
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 121 -
Rwork0.305 2266 -
all-2387 -
obs--81.86 %

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