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- PDB-3oo3: Crystal Structure of the Orf6* (CYP165D3) Monooxygenase Involved ... -

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Basic information

Entry
Database: PDB / ID: 3oo3
TitleCrystal Structure of the Orf6* (CYP165D3) Monooxygenase Involved in Teicoplanin Biosynthesis
ComponentsOxy protein
KeywordsOXIDOREDUCTASE / cytochrome P450 / monooxygenase / PCD-teicoplanin aglycone
Function / homology
Function and homology information


acyltransferase activity / ligase activity / glycosyltransferase activity / 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 / Oxidation protein CepE
Similarity search - Component
Biological speciesActinoplanes teichomyceticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsLi, Z. / Nair, S.K.
CitationJournal: Proteins / Year: 2011
Title: Crystal structure of a phenol-coupling P450 monooxygenase involved in teicoplanin biosynthesis.
Authors: Li, Z. / Rupasinghe, S.G. / Schuler, M.A. / Nair, S.K.
History
DepositionAug 30, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 5, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Oxy protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,4782
Polymers42,8611
Non-polymers6161
Water3,315184
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)74.266, 74.266, 75.467
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein Oxy protein / P450 monooxygenase


Mass: 42861.055 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Actinoplanes teichomyceticus (bacteria)
Gene: Orf6*, tcp19 / Plasmid: pET-28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Rosetta / References: UniProt: Q6ZZI7
#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.: 184 / 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: 2.8 Å3/Da / Density % sol: 56.12 %
Crystal growTemperature: 273 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 20% PEG 4000 200 mM sodium acetate 100 mM Tris, pH=8.5, VAPOR DIFFUSION, HANGING DROP, temperature 273K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 22760 / Num. obs: 22760 / % possible obs: 96.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Rsym value: 0.066 / Net I/σ(I): 28.8
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 4.8 / Num. unique all: 1746 / Rsym value: 0.297 / % possible all: 74

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHENIXmodel building
REFMAC5.5.0056refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.2→25 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.892 / SU B: 6.034 / SU ML: 0.156 / Cross valid method: THROUGHOUT / ESU R Free: 0.224 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25797 1170 5.2 %RANDOM
Rwork0.20071 ---
obs0.20364 21363 95.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 31.136 Å2
Baniso -1Baniso -2Baniso -3
1--0.59 Å2-0.29 Å20 Å2
2---0.59 Å20 Å2
3---0.88 Å2
Refinement stepCycle: LAST / Resolution: 2.2→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2898 0 43 184 3125
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0223008
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.292.0294095
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7155368
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.52122.158139
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.04715498
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9061539
X-RAY DIFFRACTIONr_chiral_restr0.0830.2449
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0222321
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.5321.51860
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.03322995
X-RAY DIFFRACTIONr_scbond_it1.76131148
X-RAY DIFFRACTIONr_scangle_it2.9834.51100
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 70 -
Rwork0.265 1121 -
obs--67.79 %

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