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- PDB-7f3h: Crystal structure of cytochrome P450DA heme domain -

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Basic information

Entry
Database: PDB / ID: 7f3h
TitleCrystal structure of cytochrome P450DA heme domain
ComponentsBifunctional cytochrome P450/NADPH--P450 reductase
KeywordsOXIDOREDUCTASE / cytochrome P450
Function / homologyPROTOPORPHYRIN IX CONTAINING FE / SERINE
Function and homology information
Biological speciesDeinococcus aerius (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsWan, N.W.
Citation
Journal: Catalysis Science And Technology / Year: 2022
Title: Directed evolution of cytochrome P450DA hydroxylase activity for stereoselective biohydroxylation
Authors: Wan, N.W. / Cui, H.B. / Zhao, L. / Shan, J. / Chen, K. / Wang, Z.Q. / Zhou, X.J. / Cui, B.D. / Han, W.Y. / Chen, Y.Z.
#1: Journal: To Be Published
Title: Crystal structure of cytochrome P450DA heme domain
Authors: Wan, N.W.
History
DepositionJun 16, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 28, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 5, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 29, 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

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Assembly

Deposited unit
A: Bifunctional cytochrome P450/NADPH--P450 reductase
B: Bifunctional cytochrome P450/NADPH--P450 reductase
C: Bifunctional cytochrome P450/NADPH--P450 reductase
D: Bifunctional cytochrome P450/NADPH--P450 reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)230,60212
Polymers227,7434
Non-polymers2,8598
Water4,828268
1
A: Bifunctional cytochrome P450/NADPH--P450 reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,7444
Polymers56,9361
Non-polymers8093
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Bifunctional cytochrome P450/NADPH--P450 reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,6573
Polymers56,9361
Non-polymers7222
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Bifunctional cytochrome P450/NADPH--P450 reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,5522
Polymers56,9361
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Bifunctional cytochrome P450/NADPH--P450 reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,6483
Polymers56,9361
Non-polymers7132
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)426.301, 62.799, 95.188
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
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 3 through 190 or resid 207...
d_2ens_1(chain "B" and (resid 3 through 190 or resid 207...
d_3ens_1(chain "C" and (resid 3 through 401 or resid 403 through 463 or resid 501))
d_4ens_1(chain "D" and (resid 3 through 190 or resid 207...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1ARGMETA1 - 188
d_12ens_1ALAGLYA205 - 399
d_13ens_1ARGSERA402 - 462
d_14ens_1HEMHEMB
d_21ens_1ARGMETC1 - 188
d_22ens_1ALAGLYC200 - 394
d_23ens_1ARGPHEC396 - 455
d_24ens_1SERSERD1
d_25ens_1HEMHEME
d_31ens_1ARGGLYF1 - 383
d_32ens_1ARGSERF385 - 445
d_33ens_1HEMHEMG
d_41ens_1ARGMETH1 - 188
d_42ens_1ALAGLYH205 - 399
d_43ens_1ARGSERH401 - 461
d_44ens_1HEMHEMI

NCS oper:
IDCodeMatrixVector
1given(-0.999478112637, 0.0321056427637, -0.00356792132937), (0.0076023064744, 0.341128051608, 0.939986094228), (0.0313959757956, 0.939468402933, -0.341194098125)279.801369619, -23.5307734196, 27.3659891856
2given(0.995306978272, -0.0312609670729, 0.0915793150259), (-0.0966294064545, -0.270467535221, 0.95786745962), (-0.00517463150305, -0.962221421674, -0.272218953895)24.6164170639, -20.6473961671, 2.32871691594
3given(-0.994748055585, 0.094968234183, -0.0381751280968), (0.0987397653281, 0.792144295097, -0.602293843973), (-0.026958572885, -0.602900033373, -0.797361138448)306.030651152, -10.3465406113, 17.7118452889

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Components

#1: Protein
Bifunctional cytochrome P450/NADPH--P450 reductase


Mass: 56935.656 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus aerius (bacteria) / Gene: DAERI_140002 / Production host: Escherichia coli (E. coli)
References: unspecific monooxygenase, NADPH-hemoprotein reductase
#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


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


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-SER / SERINE


Type: L-peptide linking / Mass: 105.093 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 268 / 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: 2.8 Å3/Da / Density % sol: 56.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1 M MES 6.5, 8 % w/v Polyethylene glycol 8000

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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 21, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 80038 / % possible obs: 100 % / Redundancy: 11.4 % / Biso Wilson estimate: 33.9 Å2 / Rmerge(I) obs: 0.198 / Rpim(I) all: 0.074 / Net I/σ(I): 10.9
Reflection shellResolution: 2.5→2.56 Å / Rmerge(I) obs: 0.798 / Mean I/σ(I) obs: 3 / Num. unique obs: 3685 / Rpim(I) all: 0.273 / % possible all: 99.8

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Processing

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

1zoa


Resolution: 2.5→29 Å / SU ML: 0.2997 / Cross valid method: FREE R-VALUE / σ(F): 0.63 / Phase error: 24.4895
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2459 1929 2.41 %
Rwork0.1998 78109 -
obs0.2009 80038 89.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.83 Å2
Refinement stepCycle: LAST / Resolution: 2.5→29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14723 0 193 268 15184
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011415325
X-RAY DIFFRACTIONf_angle_d1.587420859
X-RAY DIFFRACTIONf_chiral_restr0.07582212
X-RAY DIFFRACTIONf_plane_restr0.01112724
X-RAY DIFFRACTIONf_dihedral_angle_d16.29872075
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS1.13188570042
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS0.888995363279
ens_1d_4AX-RAY DIFFRACTIONTorsion NCS1.16039787345
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.560.2889890.2263619X-RAY DIFFRACTION59.24
2.56-2.630.30811000.24114105X-RAY DIFFRACTION66.29
2.63-2.710.28221120.23734563X-RAY DIFFRACTION73.66
2.71-2.80.27011220.2324844X-RAY DIFFRACTION79.09
2.8-2.90.31161360.23875365X-RAY DIFFRACTION86.96
2.9-3.010.29051400.24025798X-RAY DIFFRACTION93.29
3.01-3.150.2791500.22486011X-RAY DIFFRACTION96.39
3.15-3.320.25011490.22746031X-RAY DIFFRACTION97.6
3.32-3.520.30441520.21356151X-RAY DIFFRACTION98.55
3.52-3.80.26291530.20466157X-RAY DIFFRACTION98.87
3.8-4.180.26031530.18576251X-RAY DIFFRACTION99.36
4.18-4.780.19421540.16096293X-RAY DIFFRACTION99.48
4.78-6.010.19461570.18096325X-RAY DIFFRACTION99.36
6.01-290.19861620.1726596X-RAY DIFFRACTION98.89

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