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- PDB-4dnj: The crystal structures of 4-methoxybenzoate bound CYP199A2 -

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Basic information

Entry
Database: PDB / ID: 4dnj
TitleThe crystal structures of 4-methoxybenzoate bound CYP199A2
ComponentsPutative cytochrome P450
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


4-methoxybenzoate monooxygenase (O-demethylating) / 4-methoxybenzoate monooxygenase (O-demethylating) activity / xenobiotic metabolic process / iron ion binding / heme binding / cytoplasm
Similarity search - Function
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
4-METHOXYBENZOIC ACID / PROTOPORPHYRIN IX CONTAINING FE / Cytochrome p450 CYP199A2
Similarity search - Component
Biological speciesRhodopseudomonas palustris (phototrophic)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsZhou, W. / Bell, S.G. / Yang, W. / Tan, A.B.H. / Zhou, R. / Johnson, E.O.D. / Zhang, A. / Rao, Z. / Wong, L.-L.
CitationJournal: Dalton Trans / Year: 2012
Title: The crystal structures of 4-methoxybenzoate bound CYP199A2 and CYP199A4: structural changes on substrate binding and the identification of an anion binding site
Authors: Bell, S.G. / Yang, W. / Tan, A.B.H. / Zhou, R. / Johnson, E.O.D. / Zhang, A. / Zhou, W. / Rao, Z. / Wong, L.-L.
History
DepositionFeb 8, 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_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: Putative cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4774
Polymers44,6731
Non-polymers8043
Water9,926551
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.917, 73.884, 96.876
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Putative cytochrome P450


Mass: 44672.625 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodopseudomonas palustris (phototrophic)
Strain: CGA009 / Gene: RPA1871 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q6N8N2, 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: Chemical ChemComp-ANN / 4-METHOXYBENZOIC ACID / P-ANISIC ACID


Mass: 152.147 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H8O3
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 551 / 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: 2.16 Å3/Da / Density % sol: 43.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.4
Details: 0.1M Tris, 26% PEG 4000, 10% isopropanol, pH 8.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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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
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 36699 / Num. obs: 36209 / % possible obs: 98.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5 % / Biso Wilson estimate: 15.577 Å2 / Rmerge(I) obs: 0.077 / Rsym value: 0.063 / Net I/σ(I): 25.2
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.264 / Mean I/σ(I) obs: 6.64 / Num. unique all: 3521 / Rsym value: 0.248 / % possible all: 97.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2RF7

2rf7


Resolution: 1.8→29.07 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.936 / SU B: 2.342 / SU ML: 0.074 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.128 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20537 1792 5 %RANDOM
Rwork0.158 ---
obs0.16041 33863 97.34 %-
all-34788 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.577 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20 Å20 Å2
2--0.01 Å20 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.8→29.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3058 0 55 551 3664
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0223195
X-RAY DIFFRACTIONr_angle_refined_deg1.9282.0214362
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.145400
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.6222.867143
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.39715484
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.21531
X-RAY DIFFRACTIONr_chiral_restr0.1360.2469
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0212512
X-RAY DIFFRACTIONr_mcbond_it1.1541.51996
X-RAY DIFFRACTIONr_mcangle_it1.94123197
X-RAY DIFFRACTIONr_scbond_it3.38831199
X-RAY DIFFRACTIONr_scangle_it5.1324.51164
LS refinement shellResolution: 1.799→1.846 Å / Rfactor Rfree error: 0.125 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 120 -
Rwork0.242 2446 -
obs-2446 96.68 %

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