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- PDB-7f3w: Crystal structure of cytochrome P450DA mutant (N190F/V356L/A486E)... -

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Basic information

Entry
Database: PDB / ID: 7f3w
TitleCrystal structure of cytochrome P450DA mutant (N190F/V356L/A486E) heme domain
Componentscytochrome P450
KeywordsOXIDOREDUCTASE / cytochrome P450
Function / homologyPROTOPORPHYRIN IX CONTAINING FE
Function and homology information
Biological speciesDeinococcus apachensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.86 Å
AuthorsWan, N.W.
CitationJournal: To Be Published
Title: Crystal structure of cytochrome P450DA mutant (N190F/V356L/A486E) heme domain
Authors: Wan, N.W.
History
DepositionJun 17, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 28, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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

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Assembly

Deposited unit
A: cytochrome P450
B: cytochrome P450
C: cytochrome P450
D: cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)227,30518
Polymers223,8794
Non-polymers3,42714
Water00
1
A: cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,7784
Polymers55,9701
Non-polymers8093
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1310 Å2
ΔGint-24 kcal/mol
Surface area21100 Å2
MethodPISA
2
B: cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,8745
Polymers55,9701
Non-polymers9054
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1300 Å2
ΔGint-24 kcal/mol
Surface area20340 Å2
MethodPISA
3
C: cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,8745
Polymers55,9701
Non-polymers9054
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1290 Å2
ΔGint-24 kcal/mol
Surface area20400 Å2
MethodPISA
4
D: cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,7784
Polymers55,9701
Non-polymers8093
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1470 Å2
ΔGint-37 kcal/mol
Surface area19450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)426.822, 63.896, 95.958
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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Components

#1: Protein
cytochrome P450


Mass: 55969.648 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus apachensis (bacteria) / Production host: Escherichia coli (E. coli)
#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
Has ligand of interestN

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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: 2.92 Å3/Da / Density % sol: 57.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1 M MES 6.0, 10 % w/v Polyethylene glycol 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 27, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.86→50 Å / Num. obs: 80451 / % possible obs: 91.9 % / Redundancy: 9.6 % / Biso Wilson estimate: 45.62 Å2 / Rmerge(I) obs: 0.161 / Rpim(I) all: 0.068 / Net I/σ(I): 11
Reflection shellResolution: 2.86→2.92 Å / Rmerge(I) obs: 0.751 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2460 / Rpim(I) all: 0.342

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Processing

Software
NameVersionClassification
PHENIX1.18.1_3865refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1zoa

1zoa


Resolution: 2.86→29.14 Å / SU ML: 0.3348 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.5234
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.243 3087 3.84 %
Rwork0.193 77364 -
obs0.1949 80451 68.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.1 Å2
Refinement stepCycle: LAST / Resolution: 2.86→29.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14662 0 222 0 14884
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.010215292
X-RAY DIFFRACTIONf_angle_d1.318920825
X-RAY DIFFRACTIONf_chiral_restr0.07142209
X-RAY DIFFRACTIONf_plane_restr0.00882709
X-RAY DIFFRACTIONf_dihedral_angle_d20.56935651
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.86-2.90.4572450.2911171X-RAY DIFFRACTION22.47
2.9-2.950.3263670.29091693X-RAY DIFFRACTION33.44
2.95-30.3725720.26981907X-RAY DIFFRACTION37.33
3-3.060.3043810.28712000X-RAY DIFFRACTION38.85
3.06-3.120.291910.26892265X-RAY DIFFRACTION44.28
3.12-3.180.3829920.24262418X-RAY DIFFRACTION47.12
3.18-3.250.30731080.2442622X-RAY DIFFRACTION51.68
3.25-3.320.29031170.24432786X-RAY DIFFRACTION54.2
3.32-3.410.29821270.23482986X-RAY DIFFRACTION58.71
3.41-3.50.23161330.22133241X-RAY DIFFRACTION63.39
3.5-3.60.27041410.2223522X-RAY DIFFRACTION68.91
3.6-3.720.2881470.21133817X-RAY DIFFRACTION73.98
3.72-3.850.24921630.20964016X-RAY DIFFRACTION78.95
3.85-40.21891660.1964231X-RAY DIFFRACTION81.79
4-4.190.27231710.19274500X-RAY DIFFRACTION88.47
4.19-4.410.2441810.17654586X-RAY DIFFRACTION89.88
4.41-4.680.23911920.15774759X-RAY DIFFRACTION92.96
4.68-5.040.19491950.16894911X-RAY DIFFRACTION95.67
5.04-5.540.25521930.18465015X-RAY DIFFRACTION98.25
5.54-6.340.23412080.20255097X-RAY DIFFRACTION98.79
6.34-7.960.22652040.17635053X-RAY DIFFRACTION98.52
7.96-29.140.16171930.14044768X-RAY DIFFRACTION93.76

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