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- PDB-6m4s: Crystal Structure Analysis of the cytochrome P450 CYP-Sb21 -

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Basic information

Entry
Database: PDB / ID: 6m4s
TitleCrystal Structure Analysis of the cytochrome P450 CYP-Sb21
ComponentsCytochrome P450 hydroxylase sb21
KeywordsOXIDOREDUCTASE / Cytochrome P450 / CYP-Sb21
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 / Cytochrome P450 hydroxylase sb21
Similarity search - Component
Biological speciesNonomuraea dietziae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsLi, F.W. / Li, S.Y.
CitationJournal: Synth Syst Biotechnol / Year: 2020
Title: Structure-guided manipulation of the regioselectivity of the cyclosporine A hydroxylase CYP-sb21 from Sebekia benihana .
Authors: Li, F. / Ma, L. / Zhang, X. / Chen, J. / Qi, F. / Huang, Y. / Qu, Z. / Yao, L. / Zhang, W. / Kim, E.S. / Li, S.
History
DepositionMar 9, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 3, 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 hydroxylase sb21
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,28010
Polymers45,9271
Non-polymers1,3539
Water4,810267
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1220 Å2
ΔGint-26 kcal/mol
Surface area17540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.636, 91.092, 52.975
Angle α, β, γ (deg.)90.000, 94.650, 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 hydroxylase sb21


Mass: 45926.938 Da / Num. of mol.: 1 / Fragment: CYP-Sb21
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nonomuraea dietziae (bacteria) / Plasmid: pET28b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: M1GMS4

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Non-polymers , 5 types, 276 molecules

#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 267 / 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: 2.18 Å3/Da / Density % sol: 43.58 % / Mosaicity: 0.95 °
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 6.5 / Details: BIS-TRIS, PEG 8000, Ca-acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.976 Å
DetectorType: SIEMENS-NICOLET / Detector: PIXEL / Date: May 9, 2018 / Details: mirrors
RadiationMonochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.85→52.8 Å / Num. obs: 33433 / % possible obs: 99.4 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.027 / Rrim(I) all: 0.072 / Χ2: 0.811 / Net I/σ(I): 7.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.85-1.886.40.53216790.9020.2240.5780.87399.2
1.88-1.926.50.48216320.9140.2020.5240.88799.1
1.92-1.956.70.39216690.940.1610.4240.83499.2
1.95-1.996.70.35616730.9480.1470.3850.87799.3
1.99-2.046.60.31416370.9510.130.340.89799.3
2.04-2.086.60.24817090.9660.1040.2690.87499.4
2.08-2.146.50.21816290.9680.0920.2370.89399.3
2.14-2.1960.18416720.9690.080.2020.89498.2
2.19-2.266.90.17316390.980.070.1870.88599.8
2.26-2.3370.13917000.9860.0560.150.87299.8
2.33-2.4170.12616550.9880.0510.1360.87599.3
2.41-2.516.90.10816880.9880.0440.1170.83199.8
2.51-2.636.80.09116620.9920.0370.0980.82499.8
2.63-2.766.40.08116800.990.0350.0890.81399.8
2.76-2.946.70.06716840.9940.0270.0720.7498.9
2.94-3.167.20.05616550.9960.0220.060.73899.7
3.16-3.4870.04517000.9970.0180.0480.75499.9
3.48-3.996.60.03816820.9960.0160.0410.67699.9
3.99-5.026.80.03416790.9930.0140.0360.60698.4
5.02-506.80.03917090.990.0160.0420.60499.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data scaling
PDB_EXTRACT3.24data extraction
HKL-3000data reduction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5NWS

5nws


Resolution: 1.85→50 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.942 / SU B: 2.773 / SU ML: 0.084 / SU R Cruickshank DPI: 0.1307 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.131 / ESU R Free: 0.127
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1974 1658 5.2 %RANDOM
Rwork0.1509 ---
obs0.1534 30220 94.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 96.01 Å2 / Biso mean: 23.702 Å2 / Biso min: 10.13 Å2
Baniso -1Baniso -2Baniso -3
1--0.15 Å20 Å20.07 Å2
2---0.34 Å2-0 Å2
3---0.48 Å2
Refinement stepCycle: final / Resolution: 1.85→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3038 0 90 267 3395
Biso mean--25.25 34.33 -
Num. residues----389
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0193192
X-RAY DIFFRACTIONr_bond_other_d0.0030.023060
X-RAY DIFFRACTIONr_angle_refined_deg1.9582.0124346
X-RAY DIFFRACTIONr_angle_other_deg1.14637012
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0295387
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.44521.702141
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.63715510
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5071541
X-RAY DIFFRACTIONr_chiral_restr0.1250.2488
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0213523
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02682
LS refinement shellResolution: 1.85→1.897 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.23 80 -
Rwork0.179 1706 -
obs--70.93 %

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