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- PDB-4yt3: CYP106A2 -

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Basic information

Entry
Database: PDB / ID: 4yt3
TitleCYP106A2
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
ACETATE ION / PROTOPORPHYRIN IX CONTAINING FE / Cytochrome P450(MEG)
Similarity search - Component
Biological speciesBacillus megaterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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 REGIO-SELECTIVE 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 17, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Feb 24, 2016Provider: repository / Type: Initial release
Revision 1.1May 11, 2016Group: Database references
Revision 1.2Jun 12, 2019Group: Data collection / Database references / Category: citation_author / Item: _citation_author.name
Revision 1.3Jan 10, 2024Group: 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 / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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)95,3826
Polymers94,0312
Non-polymers1,3514
Water9,602533
1
A: Cytochrome P450(MEG)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6913
Polymers47,0151
Non-polymers6762
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cytochrome P450(MEG)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6913
Polymers47,0151
Non-polymers6762
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.060, 114.060, 83.450
Angle α, β, γ (deg.)90.00, 103.14, 90.00
Int Tables number4
Space group name H-MP1211
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: MET / End label comp-ID: MET / Refine code: _ / Auth seq-ID: 4 - 410 / Label seq-ID: 4 - 410

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

NCS oper: (Code: given
Matrix: (0.9999, -0.01012, -0.004943), (-0.01032, -0.999, -0.04294), (-0.004504, 0.04299, -0.9991)
Vector: 23.5, -24.93, 40.37)

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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-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 533 / 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: 2.22 Å3/Da / Density % sol: 44.16 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 4.2
Details: PEG 4000, ammonium acetate, sodium acetate trihydrate
PH range: 4.2

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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: 1.8→66.18 Å / Num. obs: 79257 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 5.6 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 7.5
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 4 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 3 / % possible all: 100

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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: 1.8→66.18 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.947 / SU B: 2.548 / SU ML: 0.08 / Cross valid method: THROUGHOUT / ESU R: 0.114 / ESU R Free: 0.111 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19876 3978 5 %RANDOM
Rwork0.16282 ---
obs0.16462 75208 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.394 Å2
Baniso -1Baniso -2Baniso -3
1-0.52 Å2-0 Å20.14 Å2
2---0.54 Å2-0 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.8→66.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6221 0 94 533 6848
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0196563
X-RAY DIFFRACTIONr_bond_other_d0.0060.026309
X-RAY DIFFRACTIONr_angle_refined_deg1.8661.9928934
X-RAY DIFFRACTIONr_angle_other_deg1.235314556
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0855799
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.40124.463307
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.844151174
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8181542
X-RAY DIFFRACTIONr_chiral_restr0.1150.2995
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0217328
X-RAY DIFFRACTIONr_gen_planes_other0.0060.021458
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_it2.3672.2223129
X-RAY DIFFRACTIONr_mcbond_other2.3552.223126
X-RAY DIFFRACTIONr_mcangle_it3.3113.313904
X-RAY DIFFRACTIONr_mcangle_other3.313.3113905
X-RAY DIFFRACTIONr_scbond_it3.5772.6033434
X-RAY DIFFRACTIONr_scbond_other3.5772.6033435
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.6263.7225016
X-RAY DIFFRACTIONr_long_range_B_refined7.26218.3547929
X-RAY DIFFRACTIONr_long_range_B_other7.26318.3577930
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 23597 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.12 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.222 283 -
Rwork0.198 5571 -
obs--100 %

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