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- PDB-4dxy: Crystal structures of CYP101D2 Y96A mutant -

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Basic information

Entry
Database: PDB / ID: 4dxy
TitleCrystal structures of CYP101D2 Y96A mutant
ComponentsCytochrome P450
KeywordsOXIDOREDUCTASE / Cytochrome P450 mutant / haem-dependent / mono-oxygenases
Function / homology
Function and homology information


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 / DI(HYDROXYETHYL)ETHER / Cytochrome P450
Similarity search - Component
Biological speciesNovosphingobium aromaticivorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsZhou, W. / Bell, S.G. / Yang, W. / Dale, A. / Wong, L.-L.
CitationJournal: Appl.Microbiol.Biotechnol. / Year: 2012
Title: Improving the affinity and activity of CYP101D2 for hydrophobic substrates
Authors: Bell, S.G. / Yang, W. / Dale, A. / Zhou, W. / Wong, L.-L.
History
DepositionFeb 28, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 15, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,9467
Polymers46,7991
Non-polymers1,1476
Water4,630257
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.896, 86.896, 124.828
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Cytochrome P450 / CYP101D2


Mass: 46799.336 Da / Num. of mol.: 1 / Mutation: Y96A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Novosphingobium aromaticivorans (bacteria)
Strain: DSM12444 / Gene: Saro_1478 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q2G8A2
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 257 / 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: 2.91 Å3/Da / Density % sol: 57.69 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.3
Details: 0.1M Tris, pH 8.3, 5% v/v PEG 400, 1.9M ammonium sulphate, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 28, 2009
Details: double crystal monochromator and the K-B mirror system
RadiationMonochromator: flat Si(111) crystals / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 37867 / Num. obs: 37490 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.7 % / Biso Wilson estimate: 34.498 Å2 / Rmerge(I) obs: 0.064 / Rsym value: 0.054 / Net I/σ(I): 48.3
Reflection shellResolution: 2→2.07 Å / Redundancy: 9.4 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 4.37 / Num. unique all: 3697 / Rsym value: 0.361 / % possible all: 99.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3NV5

3nv5


Resolution: 2→41.03 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.934 / SU B: 4.068 / SU ML: 0.114 / Isotropic thermal model: Overall / Cross valid method: THROUGHOUT / ESU R: 0.171 / ESU R Free: 0.161 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24858 1866 5 %RANDOM
Rwork0.20452 ---
all0.234 35619 --
obs0.20675 35480 99.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.498 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0 Å20 Å2
2---0.01 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 2→41.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3207 0 78 257 3542
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0223407
X-RAY DIFFRACTIONr_angle_refined_deg2.042.0114633
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4715419
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.73323.671158
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.45915560
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.121526
X-RAY DIFFRACTIONr_chiral_restr0.1490.2490
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0212622
X-RAY DIFFRACTIONr_mcbond_it1.261.52049
X-RAY DIFFRACTIONr_mcangle_it2.17823316
X-RAY DIFFRACTIONr_scbond_it3.67731358
X-RAY DIFFRACTIONr_scangle_it5.2024.51310
LS refinement shellResolution: 1.999→2.051 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.378 134 -
Rwork0.339 2561 -
obs-2561 99.48 %

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