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- PDB-5fyf: Structure of CYP153A from Marinobacter aquaeolei -

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Basic information

Entry
Database: PDB / ID: 5fyf
TitleStructure of CYP153A from Marinobacter aquaeolei
ComponentsCYTOCHROME P450
KeywordsOXIDOREDUCTASE / P450 / HYDROXYLATION / BIOCATALYST / HEME
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 / 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
Similarity search - Component
Biological speciesMARINOBACTER HYDROCARBONOCLASTICUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.04 Å
AuthorsDanesh Azari, H.R. / Spandolf, C. / Hoffman, S.M. / Weissenborn, M. / Hauer, B. / Grogan, G.
CitationJournal: Chemcatchem / Year: 2016
Title: Structure-Guided Redesign of CYP153AM.aqfor the Improved Terminal Hydroxylation of Fatty Acids
Authors: Hoffman, S.M. / Danesh Azari, H.-R. / Spandolf, C. / Weissenborn, M. / Grogan, G. / Hauer, B.
History
DepositionMar 7, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 18, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CYTOCHROME P450
B: CYTOCHROME P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,4587
Polymers108,0392
Non-polymers1,4195
Water5,152286
1
A: CYTOCHROME P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,7604
Polymers54,0201
Non-polymers7413
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: CYTOCHROME P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,6983
Polymers54,0201
Non-polymers6792
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.590, 71.110, 215.180
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: generate
Matrix: (-0.9521, 0.2164, -0.216), (0.2225, 0.005642, -0.9749), (-0.2098, -0.9763, -0.0532)
Vector: 43.52, 100, 112.6)

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Components

#1: Protein CYTOCHROME P450


Mass: 54019.652 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MARINOBACTER HYDROCARBONOCLASTICUS (bacteria)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA PLYSS / References: UniProt: A1TY82
#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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 286 / Source method: isolated from a natural source / Formula: H2O

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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: 2.1 Å3/Da / Density % sol: 41.3 % / Description: NONE
Crystal growpH: 5.5
Details: PH 5.5 0.1 M BIS-TRIS PROPANE; 25% (W/V) PEG 3350; 30 MG PER ML PROTEIN

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97623
DetectorType: DECTRIS PIXEL / Detector: PIXEL / Date: Dec 7, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97623 Å / Relative weight: 1
ReflectionResolution: 2.04→107.59 Å / Num. obs: 59290 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 6.5 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 15.6
Reflection shellResolution: 2.04→2.09 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 2.8 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3RWL

3rwl


Resolution: 2.04→107.59 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.941 / SU B: 4.784 / SU ML: 0.13 / Cross valid method: THROUGHOUT / ESU R: 0.202 / ESU R Free: 0.172 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.23694 2918 4.9 %RANDOM
Rwork0.19845 ---
obs0.20035 56289 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 45.932 Å2
Baniso -1Baniso -2Baniso -3
1--1.29 Å20 Å20 Å2
2--0.23 Å20 Å2
3---1.06 Å2
Refinement stepCycle: LAST / Resolution: 2.04→107.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6485 0 98 286 6869
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0196758
X-RAY DIFFRACTIONr_bond_other_d0.0070.026254
X-RAY DIFFRACTIONr_angle_refined_deg1.9151.9729184
X-RAY DIFFRACTIONr_angle_other_deg1.507314294
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3595825
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.19523.364321
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.213151076
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6751562
X-RAY DIFFRACTIONr_chiral_restr0.1220.2978
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0217729
X-RAY DIFFRACTIONr_gen_planes_other0.0060.021621
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_it4.4144.5693318
X-RAY DIFFRACTIONr_mcbond_other4.4124.5683317
X-RAY DIFFRACTIONr_mcangle_it5.7126.8274137
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.84.7813440
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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
LS refinement shellResolution: 2.04→2.093 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 209 -
Rwork0.268 4118 -
obs--100 %

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