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- PDB-5iuz: STRUCTURE OF P450 2B4 F202W MUTANT (CYMAL-5) -

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Basic information

Entry
Database: PDB / ID: 5iuz
TitleSTRUCTURE OF P450 2B4 F202W MUTANT (CYMAL-5)
ComponentsCytochrome P450 2B4
KeywordsOXIDOREDUCTASE / MONOOXYGENASE / MEMBRANE PROTEIN
Function / homology
Function and homology information


arachidonate epoxygenase activity / epoxygenase P450 pathway / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen / unspecific monooxygenase / xenobiotic metabolic process / iron ion binding / heme binding / endoplasmic reticulum membrane
Similarity search - Function
Cytochrome P450, E-class, group I, CYP2B-like / : / Cytochrome P450, E-class, group I / Cytochrome p450 / Cytochrome P450 / Cytochrome P450, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450 ...Cytochrome P450, E-class, group I, CYP2B-like / : / Cytochrome P450, E-class, group I / 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 / Cytochrome P450 2B4
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.73 Å
AuthorsJang, H.-H. / Halpert, J.R. / Shah, M.B.
CitationJournal: Biophys.Chem. / Year: 2016
Title: Effect of detergent binding on cytochrome P450 2B4 structure as analyzed by X-ray crystallography and deuterium-exchange mass spectrometry.
Authors: Shah, M.B. / Jang, H.H. / Wilderman, P.R. / Lee, D. / Li, S. / Zhang, Q. / Stout, C.D. / Halpert, J.R.
History
DepositionMar 18, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 8, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 22, 2016Group: Database references
Revision 1.2Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytochrome P450 2B4
B: Cytochrome P450 2B4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,1808
Polymers108,9692
Non-polymers3,2116
Water5,044280
1
A: Cytochrome P450 2B4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,0904
Polymers54,4841
Non-polymers1,6063
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cytochrome P450 2B4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,0904
Polymers54,4841
Non-polymers1,6063
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)91.610, 91.610, 150.931
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1112A28 - 134
2112B28 - 134
1212A140 - 492
2212B140 - 492

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Components

#1: Protein Cytochrome P450 2B4 / CYPIIB4 / Cytochrome P450 isozyme 2 / Cytochrome P450 LM2 / Cytochrome P450 type B0 / Cytochrome P450 type B1


Mass: 54484.406 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 30-491 / Mutation: F202W, P221S, H226Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Gene: CYP2B4 / Plasmid: PKK / Production host: Escherichia coli (E. coli) / Strain (production host): TOPP3 / References: UniProt: P00178, unspecific monooxygenase
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical
ChemComp-CM5 / 5-CYCLOHEXYL-1-PENTYL-BETA-D-MALTOSIDE / 5-CYCLOHEXYLPENTYL 4-O-ALPHA-D-GLUCOPYRANOSYL-BETA-D-GLUCOPYRANOSIDE / CYMAL-5


Mass: 494.573 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C23H42O11 / Comment: detergent*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 280 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAUTHORS INDICATE THAT THERE IS AN ERROR IN THE SEQUENCE DATABASE REFERENCE AT RESIDUE 221

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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: 3.37 Å3/Da / Density % sol: 63.53 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 5% V/V TACSIMATE, PH 7.0, 0.1 M HEPES, PH 7.0, 10% V/V PEG5000 MME, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291K
PH range: 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 27, 2013
RadiationMonochromator: SI(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.72→54.6 Å / Num. obs: 37793 / % possible obs: 90.5 % / Observed criterion σ(I): 0 / Redundancy: 5.95 % / Rmerge(I) obs: 0.105 / Net I/σ(I): 16.1
Reflection shellResolution: 2.72→2.79 Å / Rmerge(I) obs: 0.438 / Mean I/σ(I) obs: 2.1 / % possible all: 25

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
REFMAC5.5.0072refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3MVR

3mvr


Resolution: 2.73→20 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.89 / SU B: 11.671 / SU ML: 0.242 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 2.534 / ESU R Free: 0.354 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.248 1706 5 %RANDOM
Rwork0.18 ---
obs0.183 32396 90.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso mean: 39.37 Å2
Baniso -1Baniso -2Baniso -3
1-1.18 Å20.59 Å20 Å2
2--1.18 Å20 Å2
3----1.77 Å2
Refinement stepCycle: LAST / Resolution: 2.73→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7395 0 222 280 7897
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0227811
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7472.03110609
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4265917
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.40722.64356
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.656151273
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1741569
X-RAY DIFFRACTIONr_chiral_restr0.1180.21175
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215929
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.711.54605
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.37327476
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.06433206
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.6184.53133
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
1834tight positional0.030.05
1846medium positional0.060.5
1834tight thermal0.080.5
1846medium thermal0.112
LS refinement shellResolution: 2.73→2.8 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.41 43 -
Rwork0.288 662 -
obs--25.72 %

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