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- PDB-7ant: Structure of CYP153A from Polaromonas sp. -

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Basic information

Entry
Database: PDB / ID: 7ant
TitleStructure of CYP153A from Polaromonas sp.
ComponentsCytochrome P450
KeywordsOXIDOREDUCTASE / P450 / alkane / cytochrome / CYP
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
HEME C / Cytochrome P450
Similarity search - Component
Biological speciesPolaromonas sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.52 Å
AuthorsZukic, E. / Rowlinson, B. / Sharma, M. / Hoffman, S. / Hauer, B. / Grogan, G.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/M006832/1 United Kingdom
CitationJournal: Acs Catalysis / Year: 2021
Title: Substrate Anchoring and Flexibility Reduction in CYP153AM.aq Leads to Highly Improved Efficiency toward Octanoic Acid
Authors: Rapp, L.R. / Marques, S.M. / Zukic, E. / Rowlinson, B. / Sharma, M. / Grogan, G. / Damborsky, J. / Hauer, B.
History
DepositionOct 12, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 7, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)97,00015
Polymers95,0812
Non-polymers1,92013
Water7,296405
1
A: Cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5318
Polymers47,5401
Non-polymers9917
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4697
Polymers47,5401
Non-polymers9296
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.852, 98.501, 112.627
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ILE / Beg label comp-ID: ILE / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: _ / Auth seq-ID: 19 - 418 / Label seq-ID: 19 - 418

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Cytochrome P450


Mass: 47540.301 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Polaromonas sp. (strain JS666 / ATCC BAA-500) (bacteria)
Strain: JS666 / ATCC BAA-500 / Gene: Bpro_5301 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q11ZY2
#2: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 405 / Source method: isolated from a natural source / Formula: H2O
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: 2.24 Å3/Da / Density % sol: 45 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.2 M ammonium chloride, 0.1 M MES, pH 6.0 and 20 % (w/v) PEG 6K.

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Data collection

DiffractionMean temperature: 120 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92819 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 8, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92819 Å / Relative weight: 1
ReflectionResolution: 1.52→72.84 Å / Num. obs: 125021 / % possible obs: 100 % / Redundancy: 6.2 % / Biso Wilson estimate: 12 Å2 / CC1/2: 0.98 / Rmerge(I) obs: 0.12 / Rpim(I) all: 0.08 / Net I/σ(I): 6
Reflection shellResolution: 1.52→1.56 Å / Rmerge(I) obs: 1.03 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 9158 / CC1/2: 0.57 / Rpim(I) all: 0.74

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3RWL

3rwl


Resolution: 1.52→58.64 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.943 / SU B: 2.245 / SU ML: 0.076 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.089 / ESU R Free: 0.087 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2309 6247 5.1 %RANDOM
Rwork0.2066 ---
obs0.2078 117070 98.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 71.57 Å2 / Biso mean: 16.772 Å2 / Biso min: 1.81 Å2
Baniso -1Baniso -2Baniso -3
1--0.44 Å20 Å20 Å2
2--0 Å20 Å2
3---0.44 Å2
Refinement stepCycle: final / Resolution: 1.52→58.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6325 0 130 405 6860
Biso mean--16.35 24.55 -
Num. residues----796
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0136621
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176177
X-RAY DIFFRACTIONr_angle_refined_deg1.771.6739001
X-RAY DIFFRACTIONr_angle_other_deg1.4251.58314284
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6685793
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.64221.448359
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.886151112
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2151557
X-RAY DIFFRACTIONr_chiral_restr0.0890.2843
X-RAY DIFFRACTIONr_gen_planes_refined0.010.027351
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021416
Refine LS restraints NCS

Ens-ID: 1 / Number: 11842 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.13 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.52→1.56 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.355 447 -
Rwork0.37 8429 -
all-8876 -
obs--97.01 %

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