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- PDB-7n60: The crystal structure of 4-methoxybenzoate-bound CYP199A S244D mutant -

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Basic information

Entry
Database: PDB / ID: 7n60
TitleThe crystal structure of 4-methoxybenzoate-bound CYP199A S244D mutant
ComponentsCytochrome P450
KeywordsOXIDOREDUCTASE / P450
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, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450
Similarity search - Domain/homology
4-METHOXYBENZOIC ACID / PROTOPORPHYRIN IX CONTAINING FE / Cytochrome P450
Similarity search - Component
Biological speciesRhodopseudomonas palustris (phototrophic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.892 Å
AuthorsLau, I.C.K. / Coleman, T. / Bell, S.G. / Bruning, J.B.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC)DP140103229 Australia
CitationJournal: To Be Published
Title: The crystal structure of 4-methoxybenzoate-bound CYP199A S244D mutant
Authors: Lau, I.C.K. / Coleman, T. / Bell, S.G. / Bruning, J.B.
History
DepositionJun 7, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 15, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)43,7555
Polymers42,9271
Non-polymers8284
Water10,196566
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1830 Å2
ΔGint-34 kcal/mol
Surface area15090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.291, 51.220, 79.181
Angle α, β, γ (deg.)90.000, 92.140, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Cytochrome P450


Mass: 42926.668 Da / Num. of mol.: 1 / Fragment: UNP residues 18-410 / Mutation: S244D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodopseudomonas palustris (strain HaA2) (phototrophic)
Strain: HaA2 / Gene: RPB_3613 / Production host: Escherichia coli (E. coli)
References: UniProt: Q2IU02, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen

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Non-polymers , 5 types, 570 molecules

#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 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 566 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 1.95 Å3/Da / Density % sol: 36.9 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.25
Details: 0.1 M Bis-Tris, pH 5.25, 22% PEG3350, 0.2 M magnesium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Apr 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.89→43 Å / Num. obs: 25827 / % possible obs: 96.1 % / Redundancy: 6.2 % / Biso Wilson estimate: 12.73 Å2 / CC1/2: 0.975 / Rmerge(I) obs: 0.304 / Rpim(I) all: 0.13 / Rrim(I) all: 0.331 / Net I/σ(I): 5.7 / Num. measured all: 160287 / Scaling rejects: 398
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Diffraction-ID% possible all
1.89-1.934.81.24611250.454166.1
9.04-436.10.0732710.996199.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.89 Å43 Å
Translation1.89 Å43 Å

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
Aimless0.5.21data scaling
PHASER2.6.1phasing
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4DO1

4do1


Resolution: 1.892→42.998 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.36
RfactorNum. reflection% reflectionSelection details
Rfree0.2643 1996 7.81 %Random selection
Rwork0.1742 ---
obs0.181 25546 96.03 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 57.78 Å2 / Biso mean: 13.8643 Å2 / Biso min: 2.35 Å2
Refinement stepCycle: final / Resolution: 1.892→42.998 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3023 0 56 566 3645
Biso mean--9.07 21.69 -
Num. residues----393
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073161
X-RAY DIFFRACTIONf_angle_d14318
X-RAY DIFFRACTIONf_chiral_restr0.05469
X-RAY DIFFRACTIONf_plane_restr0.006573
X-RAY DIFFRACTIONf_dihedral_angle_d18.4051887
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.892-1.93890.4029980.28941198X-RAY DIFFRACTION70
1.9389-1.99130.33211490.25371694X-RAY DIFFRACTION96
1.9913-2.04990.35171510.23921662X-RAY DIFFRACTION96
2.0499-2.11610.30341310.22561687X-RAY DIFFRACTION98
2.1161-2.19170.35311440.21391719X-RAY DIFFRACTION98
2.1917-2.27940.28731460.19791687X-RAY DIFFRACTION98
2.2794-2.38320.26991400.18331700X-RAY DIFFRACTION98
2.3832-2.50880.27451460.17681720X-RAY DIFFRACTION98
2.5088-2.6660.2581420.171729X-RAY DIFFRACTION98
2.666-2.87180.29861470.16551722X-RAY DIFFRACTION98
2.8718-3.16070.22741520.15741750X-RAY DIFFRACTION99
3.1607-3.61790.23561480.14211729X-RAY DIFFRACTION99
3.6179-4.55730.21541450.12551745X-RAY DIFFRACTION99
4.5573-42.9980.20191570.14991808X-RAY DIFFRACTION100

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