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- PDB-3tkt: Crystal structure of CYP108D1 from Novosphingobium aromaticivoran... -

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Basic information

Entry
Database: PDB / ID: 3tkt
TitleCrystal structure of CYP108D1 from Novosphingobium aromaticivorans DSM12444
ComponentsCytochrome P450
KeywordsOXIDOREDUCTASE / Cytochrome P450 fold / aromatic hydrocarbon binding of P450 enzyme
Function / homology
Function and homology information


cholest-4-en-3-one 26-monooxygenase activity / steroid hydroxylase activity / cholesterol catabolic process / 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
Similarity search - Component
Biological speciesNovosphingobium aromaticivorans (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsYang, W. / Bell, S.G. / Wang, H. / Zhou, W. / Bartlam, M. / Wong, L.-L. / Rao, Z.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2012
Title: Structure and function of CYP108D1 from Novosphingobium aromaticivorans DSM12444: an aromatic hydrocarbon-binding P450 enzyme
Authors: Bell, S.G. / Yang, W. / Yorke, J.A. / Zhou, W. / Wang, H. / Harmer, J. / Copley, R. / Zhang, A. / Zhou, R. / Bartlam, M. / Rao, Z. / Wong, L.-L.
History
DepositionAug 29, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 29, 2012Provider: repository / Type: Initial release
Revision 1.1May 2, 2012Group: Database references
Revision 1.2Nov 1, 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

Downloads & links

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Assembly

Deposited unit
A: Cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,9652
Polymers49,3481
Non-polymers6161
Water4,810267
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)93.979, 93.979, 299.366
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-531-

HOH

21A-618-

HOH

31A-648-

HOH

41A-691-

HOH

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Components

#1: Protein Cytochrome P450


Mass: 49348.137 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Novosphingobium aromaticivorans (bacteria)
Strain: DSM 12444 / Gene: Saro_3162 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q2G3H6
#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.: 267 / 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: 2.58 Å3/Da / Density % sol: 52.28 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.3
Details: 0.2M lithium sulfate, 0.1M Tris, 27% PEG 4000, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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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 IV++ / Detector: IMAGE PLATE / Date: Oct 3, 2008 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 26342 / Num. obs: 26332 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 24.3
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.401 / Mean I/σ(I) obs: 4.5 / Num. unique all: 2582 / % possible all: 100

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
REFMAC5.5.0044refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY: 1CPT

1cpt


Resolution: 2.2→50 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.929 / SU B: 5.226 / SU ML: 0.133 / Cross valid method: THROUGHOUT / σ(I): 0 / ESU R Free: 0.196 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23424 1337 5.1 %RANDOM
Rwork0.18691 ---
obs0.18935 24989 99.9 %-
all-25014 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.721 Å2
Baniso -1Baniso -2Baniso -3
1--0.28 Å2-0.14 Å2-0 Å2
2---0.28 Å20 Å2
3---0.43 Å2
Refinement stepCycle: LAST / Resolution: 2.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3164 0 43 267 3474
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0223287
X-RAY DIFFRACTIONr_angle_refined_deg1.7432.0074480
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1455409
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.43323.427143
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.72215526
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.7431527
X-RAY DIFFRACTIONr_chiral_restr0.1170.2488
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212533
X-RAY DIFFRACTIONr_mcbond_it0.7531.52055
X-RAY DIFFRACTIONr_mcangle_it1.42523299
X-RAY DIFFRACTIONr_scbond_it2.61331232
X-RAY DIFFRACTIONr_scangle_it4.1544.51181
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 83 -
Rwork0.197 1819 -
obs--99.42 %

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