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- PDB-6prr: The crystal structure of 3-methylaminobenzoate-bound CYP199A4 -

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Basic information

Entry
Database: PDB / ID: 6prr
TitleThe crystal structure of 3-methylaminobenzoate-bound CYP199A4
ComponentsCytochrome P450
KeywordsOXIDOREDUCTASE / Cytochrome P450 / 3-methylaminobenzoic acid
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 / 3-(methylamino)benzoic acid / Cytochrome P450
Similarity search - Component
Biological speciesRhodopseudomonas palustris (phototrophic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.67 Å
AuthorsPodgorski, M.N. / Bruning, J.B. / Bell, S.G.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC)DP140103229 and ANSTO Australian Synchrotron Collaborative Access Program (CAP) grant MXCAP12393/13630 Australia
CitationJournal: J.Inorg.Biochem. / Year: 2019
Title: Investigation of the requirements for efficient and selective cytochrome P450 monooxygenase catalysis across different reactions.
Authors: Podgorski, M.N. / Coleman, T. / Chao, R.R. / De Voss, J.J. / Bruning, J.B. / Bell, S.G.
History
DepositionJul 11, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2019Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)45,3914
Polymers44,5871
Non-polymers8033
Water10,683593
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1380 Å2
ΔGint-37 kcal/mol
Surface area15050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.354, 51.430, 79.460
Angle α, β, γ (deg.)90.000, 92.130, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Cytochrome P450 / CYP199A4


Mass: 44587.430 Da / Num. of mol.: 1
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 BL21(DE3) (bacteria) / References: UniProt: Q2IU02
#2: Chemical ChemComp-OW4 / 3-(methylamino)benzoic acid


Mass: 151.163 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H9NO2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#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.: 593 / Source method: isolated from a natural source / Formula: H2O
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: 2.11 Å3/Da / Density % sol: 41.74 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 1:1 35-40 mg/mL protein (in 50 mM Tris-HCl, pH 7.4) + reservoir (0.2 M magnesium acetate, 100 mM Bis-Tris adjusted with acetic acid to pH 5.0-5.75, 20-32% w/v PEG3350)
PH range: 5.0-5.75

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 14, 2018
RadiationMonochromator: Double-crystal Si(111) liquid nitrogen cooled (DC) or channel-cut Si(111) liquid nitrogen cooled (CC)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.67→44.323 Å / Num. obs: 40980 / % possible obs: 98 % / Redundancy: 6.7 % / Biso Wilson estimate: 13.06 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.026 / Rrim(I) all: 0.067 / Net I/σ(I): 16.7
Reflection shell

Diffraction-ID: 1 / Redundancy: 6.3 %

Resolution (Å)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.67-1.70.349856913510.9170.150.3814.162.9
8.99-44.320.03718552960.9980.0160.0438.799.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.84 Å44.32 Å
Translation5.84 Å44.32 Å

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.7.1data scaling
PHASER2.8.2phasing
PHENIXrefinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5UVB

5uvb


Resolution: 1.67→44.323 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 18.53
RfactorNum. reflection% reflection
Rfree0.1836 2000 4.88 %
Rwork0.1457 --
obs0.1476 40950 98.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 76.78 Å2 / Biso mean: 15.4939 Å2 / Biso min: 4.88 Å2
Refinement stepCycle: final / Resolution: 1.67→44.323 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3021 0 55 593 3669
Biso mean--8.57 25.92 -
Num. residues----393
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073213
X-RAY DIFFRACTIONf_angle_d0.9014396
X-RAY DIFFRACTIONf_chiral_restr0.055476
X-RAY DIFFRACTIONf_plane_restr0.006587
X-RAY DIFFRACTIONf_dihedral_angle_d8.7783334
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.6705-1.71220.29841190.2234217077
1.7122-1.75850.21941340.17682774100
1.7585-1.81030.19551530.15562805100
1.8103-1.86870.22251460.15382797100
1.8687-1.93550.19691400.14962846100
1.9355-2.0130.19161450.15532799100
2.013-2.10460.21091470.14962816100
2.1046-2.21560.18071370.14872821100
2.2156-2.35440.19121460.14592830100
2.3544-2.53610.20371400.14972813100
2.5361-2.79130.20711540.15772848100
2.7913-3.19510.18351410.14722853100
3.1951-4.02510.14551490.12452862100
4.0251-44.3230.14371490.12922916100

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