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- PDB-5iki: CYP106A2 WITH SUBSTRATE ABIETIC ACID -

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Basic information

Entry
Database: PDB / ID: 5iki
TitleCYP106A2 WITH SUBSTRATE ABIETIC ACID
ComponentsCytochrome P450(MEG)
KeywordsOXIDOREDUCTASE / MONO-OXYGENASE / CYTOCHROME P450 / 15-BETA-HYDROXYLASE
Function / homology
Function and homology information


steroid 15beta-monooxygenase / Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; Miscellaneous / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / monooxygenase activity / iron ion binding / heme binding / cytoplasm
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
Abietic acid / PROTOPORPHYRIN IX CONTAINING FE / Cytochrome P450(MEG)
Similarity search - Component
Biological speciesBacillus megaterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsJanocha, S. / Carius, Y. / Bernhardt, R. / Lancaster, C.R.D.
Citation
Journal: Chembiochem / Year: 2016
Title: Crystal Structure of CYP106A2 in Substrate-Free and Substrate-Bound Form.
Authors: Janocha, S. / Carius, Y. / Hutter, M. / Lancaster, C.R. / Bernhardt, R.
#1: Journal: Chembiochem / Year: 2011
Title: Identification of CYP106A2 as a regioselective allylic bacterial diterpene hydroxylase.
Authors: Bleif, S. / Hannemann, F. / Lisurek, M. / Von Kries, J.P. / Zapp, J. / Dietzen, M. / Antes, I. / Bernhardt, R.
History
DepositionMar 3, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 25, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2019Group: Data collection / Structure summary
Category: audit_author / database_PDB_rev / database_PDB_rev_record
Item: _audit_author.name
Revision 1.2Jan 10, 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(MEG)
B: Cytochrome P450(MEG)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,5665
Polymers94,0312
Non-polymers1,5353
Water97354
1
A: Cytochrome P450(MEG)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6322
Polymers47,0151
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cytochrome P450(MEG)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,9343
Polymers47,0151
Non-polymers9192
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.910, 57.390, 84.240
Angle α, β, γ (deg.)72.37, 75.19, 75.70
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: _ / Auth seq-ID: 4 - 409 / Label seq-ID: 4 - 409

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

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Components

#1: Protein Cytochrome P450(MEG) / Steroid 15-beta-hydroxylase / Steroid 15-beta-monooxygenase


Mass: 47015.477 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus megaterium (bacteria) / Gene: cyp106A2 / Plasmid: PKKHC / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): JM109
References: UniProt: Q06069, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; Miscellaneous, steroid 15beta-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-A9H / Abietic acid


Mass: 302.451 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H30O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / 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: 2.28 Å3/Da / Density % sol: 45.99 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: PEG 4000 AMMONIUM ACETATE SODIUM ACETATE TRIHYDRATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9393 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 17, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9393 Å / Relative weight: 1
ReflectionResolution: 2.4→78.98 Å / Num. obs: 32407 / % possible obs: 94.93 % / Redundancy: 3.82 % / Biso Wilson estimate: 46.2 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 6.39
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 4.11 % / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 2.94 / % possible all: 95.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
iMOSFLM7.1.1data reduction
SCALACCP4_3.3.21data scaling
MOLREP12.02.08phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1F4T

1f4t


Resolution: 2.4→78.73 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.932 / SU B: 14.552 / SU ML: 0.309 / Cross valid method: THROUGHOUT / ESU R: 0.67 / ESU R Free: 0.304 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26091 1556 5.1 %RANDOM
Rwork0.2012 ---
obs0.2044 29207 94.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 63.362 Å2
Baniso -1Baniso -2Baniso -3
1-9.05 Å2-1.71 Å24.86 Å2
2---4.53 Å2-0.51 Å2
3----2.4 Å2
Refinement stepCycle: 1 / Resolution: 2.4→78.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6248 0 108 54 6410
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0196503
X-RAY DIFFRACTIONr_bond_other_d0.0060.026224
X-RAY DIFFRACTIONr_angle_refined_deg1.5181.9938847
X-RAY DIFFRACTIONr_angle_other_deg1.0683.00114351
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4445777
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.57824.527296
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.509151136
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8771538
X-RAY DIFFRACTIONr_chiral_restr0.0880.2991
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0217223
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021429
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_it4.2986.1473123
X-RAY DIFFRACTIONr_mcbond_other4.296.1463122
X-RAY DIFFRACTIONr_mcangle_it6.519.213895
X-RAY DIFFRACTIONr_mcangle_other6.5119.2113896
X-RAY DIFFRACTIONr_scbond_it4.3156.4673380
X-RAY DIFFRACTIONr_scbond_other4.3156.4683381
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.8929.5194953
X-RAY DIFFRACTIONr_long_range_B_refined9.62248.7757687
X-RAY DIFFRACTIONr_long_range_B_other9.62148.7797688
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 21173 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.18 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.386 105 -
Rwork0.357 2160 -
obs--95.45 %

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