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- PDB-7ao7: Structure of CYP153A from Polaromonas sp. in complex with octan-1-ol -

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Basic information

Entry
Database: PDB / ID: 7ao7
TitleStructure of CYP153A from Polaromonas sp. in complex with octan-1-ol
ComponentsCytochrome P450
KeywordsOXIDOREDUCTASE / P450 / heme / CYP / cytochrome
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 / OCTAN-1-OL / Cytochrome P450
Similarity search - Component
Biological speciesPolaromonas sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsZukic, E. / Rowlinson, B. / Sharma, M. / Hoffmann, 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 13, 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

Downloads & links

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Assembly

Deposited unit
A: Cytochrome P450
B: Cytochrome P450
C: Cytochrome P450
D: Cytochrome P450
E: Cytochrome P450
F: Cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)289,59217
Polymers285,2426
Non-polymers4,35011
Water6,521362
1
A: Cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,2873
Polymers47,5401
Non-polymers7472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,2873
Polymers47,5401
Non-polymers7472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,2873
Polymers47,5401
Non-polymers7472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,2873
Polymers47,5401
Non-polymers7472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,2873
Polymers47,5401
Non-polymers7472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1572
Polymers47,5401
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.503, 116.194, 288.309
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
12A
22C
13A
23D
14A
24E
15A
25F
16B
26C
17B
27D
18B
28E
19B
29F
110C
210D
111C
211E
112C
212F
113D
213E
114D
214F
115E
215F

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALAALAALAAA18 - 41818 - 418
21ALAALAALAALABB18 - 41818 - 418
12ALAALAALAALAAA18 - 41818 - 418
22ALAALAALAALACC18 - 41818 - 418
13ALAALAALAALAAA18 - 41818 - 418
23ALAALAALAALADD18 - 41818 - 418
14ALAALAALAALAAA18 - 41818 - 418
24ALAALAALAALAEE18 - 41818 - 418
15PROPROASNASNAA20 - 41720 - 417
25PROPROASNASNFF20 - 41720 - 417
16ALAALAALAALABB18 - 41818 - 418
26ALAALAALAALACC18 - 41818 - 418
17ALAALAALAALABB16 - 41816 - 418
27ALAALAALAALADD16 - 41816 - 418
18TYRTYRALAALABB17 - 41817 - 418
28TYRTYRALAALAEE17 - 41817 - 418
19PROPROILEILEBB20 - 41620 - 416
29PROPROILEILEFF20 - 41620 - 416
110ALAALAALAALACC18 - 41818 - 418
210ALAALAALAALADD18 - 41818 - 418
111ALAALAALAALACC18 - 41818 - 418
211ALAALAALAALAEE18 - 41818 - 418
112PROPROASNASNCC20 - 41720 - 417
212PROPROASNASNFF20 - 41720 - 417
113TYRTYRALAALADD17 - 41817 - 418
213TYRTYRALAALAEE17 - 41817 - 418
114PROPROASNASNDD20 - 41720 - 417
214PROPROASNASNFF20 - 41720 - 417
115PROPROASNASNEE20 - 41720 - 417
215PROPROASNASNFF20 - 41720 - 417

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

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Components

#1: Protein
Cytochrome P450


Mass: 47540.301 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Polaromonas sp. (bacteria) / Gene: Bpro_5301 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q11ZY2
#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical
ChemComp-OC9 / OCTAN-1-OL


Mass: 130.228 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C8H18O / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 362 / 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: 2.13 Å3/Da / Density % sol: 42.22 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M Bis-Tris pH 6.5, 25% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 120 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97949 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.55→45.17 Å / Num. obs: 80491 / % possible obs: 100 % / Redundancy: 6.7 % / Biso Wilson estimate: 38 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.14 / Rpim(I) all: 0.08 / Net I/σ(I): 10.4
Reflection shellResolution: 2.55→2.6 Å / Rmerge(I) obs: 0.96 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 4553 / CC1/2: 0.65 / Rpim(I) all: 0.62 / % possible all: 100

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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: 7ANT

7ant


Resolution: 2.55→45.17 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.91 / SU B: 12.932 / SU ML: 0.271 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 5.466 / ESU R Free: 0.329 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2536 4029 5 %RANDOM
Rwork0.2048 ---
obs0.2072 76372 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 131 Å2 / Biso mean: 44.634 Å2 / Biso min: 6.69 Å2
Baniso -1Baniso -2Baniso -3
1--2.27 Å20 Å20 Å2
2--2.64 Å20 Å2
3----0.37 Å2
Refinement stepCycle: final / Resolution: 2.55→45.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18383 0 303 362 19048
Biso mean--31.53 36.51 -
Num. residues----2388
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01319168
X-RAY DIFFRACTIONr_bond_other_d0.0010.01717497
X-RAY DIFFRACTIONr_angle_refined_deg1.5891.6726208
X-RAY DIFFRACTIONr_angle_other_deg1.2911.58840310
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.50652375
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.21921.376952
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.673152956
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.17515146
X-RAY DIFFRACTIONr_chiral_restr0.0810.22523
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0221570
X-RAY DIFFRACTIONr_gen_planes_other0.0030.024121
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A117810.11
12B117810.11
21A121540.1
22C121540.1
31A118170.11
32D118170.11
41A125610.08
42E125610.08
51A113980.11
52F113980.11
61B116050.12
62C116050.12
71B123010.1
72D123010.1
81B119850.1
82E119850.1
91B116480.09
92F116480.09
101C117720.12
102D117720.12
111C123480.1
112E123480.1
121C112600.12
122F112600.12
131D122340.1
132E122340.1
141D117370.1
142F117370.1
151E115080.11
152F115080.11
LS refinement shellResolution: 2.55→2.616 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.366 304 -
Rwork0.3 5592 -
all-5896 -
obs--99.97 %

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