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- PDB-8hgb: Crystal structure of the CYP199A4 mutant F182G in complex with 3-... -

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Basic information

Entry
Database: PDB / ID: 8hgb
TitleCrystal structure of the CYP199A4 mutant F182G in complex with 3-hydroxy-4-methoxybenzoic acid
ComponentsCytochrome P450
KeywordsOXIDOREDUCTASE / CYP199A4 / Complex
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
PROTOPORPHYRIN IX CONTAINING FE / 4-methoxy-3-oxidanyl-benzoic acid / Cytochrome P450
Similarity search - Component
Biological speciesRhodopseudomonas palustris HaA2 (phototrophic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.54 Å
AuthorsJiang, Y. / Cong, Z.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)21977104 China
CitationJournal: To Be Published
Title: Crystal structure of the CYP199A4 mutant F182G in complex with 3-hydroxy-4-methoxybenzoic acid
Authors: Jiang, Y. / Cong, Z.
History
DepositionNov 14, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 22, 2023Provider: repository / Type: Initial release

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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)46,6334
Polymers45,7571
Non-polymers8773
Water9,512528
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1230 Å2
ΔGint-24 kcal/mol
Surface area14940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.551, 51.708, 78.797
Angle α, β, γ (deg.)90.00, 93.14, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Cytochrome P450 /


Mass: 45756.695 Da / Num. of mol.: 1 / Mutation: F182G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodopseudomonas palustris HaA2 (phototrophic)
Strain: HaA2 / Gene: RPB_3613 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q2IU02
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-L6X / 4-methoxy-3-oxidanyl-benzoic acid


Mass: 168.147 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H8O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 528 / 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: 1.98 Å3/Da / Density % sol: 37.9 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.2 M MgAc, 0.1 M Bis-tris 5.5, 27% PEG3350 / PH range: 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 21, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.5→78.68 Å / Num. obs: 51643 / % possible obs: 89.3 % / Redundancy: 2.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.035 / Rrim(I) all: 0.06 / Χ2: 0.46 / Net I/σ(I): 8.9 / Num. measured all: 142907
Reflection shellResolution: 1.5→1.58 Å / % possible obs: 49.7 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.474 / Num. measured all: 11517 / Num. unique obs: 4173 / CC1/2: 0.815 / Rpim(I) all: 0.339 / Rrim(I) all: 0.585 / Χ2: 0.48 / Net I/σ(I) obs: 2.6

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Processing

Software
NameVersionClassification
PHENIX1.18.2refinement
Aimlessdata scaling
XDSdata reduction
PHENIX1.18.2phasing
PDB_EXTRACT4data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6PQD

6pqd


Resolution: 1.54→39.34 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 17.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1774 5138 10.06 %
Rwork0.1533 --
obs0.1558 51073 96.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.54→39.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3000 0 61 528 3589
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053151
X-RAY DIFFRACTIONf_angle_d0.8484307
X-RAY DIFFRACTIONf_dihedral_angle_d22.2831152
X-RAY DIFFRACTIONf_chiral_restr0.052469
X-RAY DIFFRACTIONf_plane_restr0.006571
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.54-1.560.28981840.24441524X-RAY DIFFRACTION100
1.56-1.580.24161760.2371582X-RAY DIFFRACTION100
1.58-1.60.2731840.22661574X-RAY DIFFRACTION99
1.6-1.620.26771610.20381579X-RAY DIFFRACTION100
1.62-1.640.24221850.21451571X-RAY DIFFRACTION100
1.64-1.660.23661760.20141602X-RAY DIFFRACTION99
1.66-1.680.21081800.19621566X-RAY DIFFRACTION100
1.68-1.710.20931670.18961593X-RAY DIFFRACTION100
1.71-1.730.22411650.18011580X-RAY DIFFRACTION100
1.73-1.760.22051910.17221557X-RAY DIFFRACTION100
1.76-1.790.20061770.17511595X-RAY DIFFRACTION100
1.79-1.830.18481610.17081562X-RAY DIFFRACTION100
1.83-1.860.19661830.16961613X-RAY DIFFRACTION100
1.86-1.90.20441690.17841533X-RAY DIFFRACTION97
1.9-1.940.19811770.17381557X-RAY DIFFRACTION98
1.94-1.990.21811730.16041534X-RAY DIFFRACTION99
1.99-2.030.20011760.14971596X-RAY DIFFRACTION100
2.04-2.090.15461740.14251572X-RAY DIFFRACTION99
2.09-2.150.17791900.14551576X-RAY DIFFRACTION99
2.15-2.220.18261690.14071581X-RAY DIFFRACTION99
2.22-2.30.16351050.1327950X-RAY DIFFRACTION60
2.3-2.390.16591800.14251563X-RAY DIFFRACTION98
2.39-2.50.16351670.15331571X-RAY DIFFRACTION98
2.5-2.630.17261780.14511582X-RAY DIFFRACTION98
2.63-2.80.15531380.15221221X-RAY DIFFRACTION77
2.8-3.010.16991810.14541558X-RAY DIFFRACTION97
3.01-3.320.16221670.14331541X-RAY DIFFRACTION96
3.32-3.80.14611600.1291394X-RAY DIFFRACTION86
3.8-4.780.13931650.11861542X-RAY DIFFRACTION96
4.78-39.340.16031790.15131566X-RAY DIFFRACTION94
Refinement TLS params.Method: refined / Origin x: 5.3029 Å / Origin y: -6.3995 Å / Origin z: 19.2623 Å
111213212223313233
T0.1351 Å2-0.0008 Å20.0104 Å2-0.0965 Å2-0.0019 Å2--0.0923 Å2
L0.2672 °2-0.05 °2-0.0538 °2-0.9827 °20.1948 °2--0.4833 °2
S-0.0106 Å °-0.0061 Å °0.0055 Å °-0.1454 Å °0.0233 Å °-0.0359 Å °0.0053 Å °0.0071 Å °-0.0083 Å °
Refinement TLS groupSelection details: all

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