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- PDB-6gmf: Structure of Cytochrome P450 CYP109Q5 from Chondromyces apiculatus -

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Basic information

Entry
Database: PDB / ID: 6gmf
TitleStructure of Cytochrome P450 CYP109Q5 from Chondromyces apiculatus
ComponentsPutative cytochrome P450 hydroxylase
KeywordsOXIDOREDUCTASE / P450 / terpene / biocatalysis
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 / Putative cytochrome P450 hydroxylase
Similarity search - Component
Biological speciesChondromyces apiculatus DSM 436 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsGrogan, G. / Dubiel, P. / Sharma, M. / Klenk, J. / Hauer, B.
CitationJournal: Microb Biotechnol / Year: 2019
Title: Characterization and structure-guided engineering of the novel versatile terpene monooxygenase CYP109Q5 from Chondromyces apiculatus DSM436.
Authors: Klenk, J.M. / Dubiel, P. / Sharma, M. / Grogan, G. / Hauer, B.
History
DepositionMay 25, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 27, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 17, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative cytochrome P450 hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,5362
Polymers43,9191
Non-polymers6161
Water4,558253
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1210 Å2
ΔGint-24 kcal/mol
Surface area16370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.690, 55.020, 74.800
Angle α, β, γ (deg.)90.00, 91.67, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Putative cytochrome P450 hydroxylase


Mass: 43919.141 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chondromyces apiculatus DSM 436 (bacteria)
Gene: CAP_4855 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A017T5A5
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 253 / 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: 2.13 Å3/Da / Density % sol: 42 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M Tris-HCl pH 8.5, 28% (w/v) PEG 3350, 0.1 M NaCl

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.55→55.02 Å / Num. obs: 52220 / % possible obs: 99.8 % / Redundancy: 3.9 % / CC1/2: 1 / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.04 / Net I/σ(I): 11.6
Reflection shellResolution: 1.55→1.58 Å / Redundancy: 4 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 2 / Num. unique obs: 2586 / CC1/2: 0.82 / Rpim(I) all: 0.45 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5OFQ

5ofq


Resolution: 1.55→44.71 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.956 / SU B: 2.217 / SU ML: 0.078 / Cross valid method: THROUGHOUT / ESU R: 0.087 / ESU R Free: 0.089 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2195 2529 4.8 %RANDOM
Rwork0.18494 ---
obs0.18669 49666 98.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 24.768 Å2
Baniso -1Baniso -2Baniso -3
1--1.76 Å20 Å2-0.36 Å2
2---1.13 Å2-0 Å2
3---2.9 Å2
Refinement stepCycle: 1 / Resolution: 1.55→44.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2932 0 43 255 3230
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0143063
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172757
X-RAY DIFFRACTIONr_angle_refined_deg1.5891.6814194
X-RAY DIFFRACTIONr_angle_other_deg1.0761.6366436
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9535394
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.07320.13154
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.45215481
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5311530
X-RAY DIFFRACTIONr_chiral_restr0.0860.2413
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023500
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02552
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_it1.982.471552
X-RAY DIFFRACTIONr_mcbond_other1.9712.4671551
X-RAY DIFFRACTIONr_mcangle_it2.7353.71939
X-RAY DIFFRACTIONr_mcangle_other2.7353.7041940
X-RAY DIFFRACTIONr_scbond_it2.6592.6221511
X-RAY DIFFRACTIONr_scbond_other2.6612.6231509
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.8043.8462250
X-RAY DIFFRACTIONr_long_range_B_refined4.94229.9923592
X-RAY DIFFRACTIONr_long_range_B_other4.89929.7353545
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 180 -
Rwork0.275 3677 -
obs--99.74 %

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