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- PDB-4tvf: OxyB from Actinoplanes teichomyceticus -

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Basic information

Entry
Database: PDB / ID: 4tvf
TitleOxyB from Actinoplanes teichomyceticus
ComponentsOxyB
KeywordsOXIDOREDUCTASE / Cytochrome P450 phenolic coupling enzyme teicoplanin biosynthesis
Function / homology
Function and homology information


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 CepF/oxidation protein CepG
Similarity search - Component
Biological speciesActinoplanes teichomyceticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsHaslinger, K. / Cryle, M.J.
CitationJournal: Chembiochem / Year: 2014
Title: Cytochrome P450 OxyBtei Catalyzes the First Phenolic Coupling Step in Teicoplanin Biosynthesis.
Authors: Haslinger, K. / Maximowitsch, E. / Brieke, C. / Koch, A. / Cryle, M.J.
History
DepositionJun 26, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Nov 12, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 17, 2014Group: Database references
Revision 1.2Dec 24, 2014Group: Database references
Revision 1.3Dec 20, 2023Group: 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

Downloads & links

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Assembly

Deposited unit
A: OxyB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,2712
Polymers47,6541
Non-polymers6161
Water3,135174
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1270 Å2
ΔGint-26 kcal/mol
Surface area16170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)153.830, 45.300, 60.430
Angle α, β, γ (deg.)90.00, 102.46, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein OxyB


Mass: 47654.285 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Actinoplanes teichomyceticus (bacteria)
Gene: tcp20 / Plasmid: pET28a(+) / Production host: Escherichia coli KRX (bacteria) / References: UniProt: Q70AY8, unspecific monooxygenase
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C34H32FeN4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 174 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.16 Å3/Da / Density % sol: 42.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 90 mM Mes pH 6.0, 13.5% PEG 3,350 18% glycerol / PH range: 6.0-6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9718 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 30, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9718 Å / Relative weight: 1
ReflectionResolution: 1.9→43.36 Å / Num. obs: 32255 / % possible obs: 99.6 % / Redundancy: 3.7 % / Net I/σ(I): 13.24
Reflection shellResolution: 1.9→2 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 3.27 / % possible all: 98.8

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LFK

1lfk


Resolution: 1.9→43.36 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.923 / SU B: 3.619 / SU ML: 0.109 / Cross valid method: THROUGHOUT / ESU R: 0.179 / ESU R Free: 0.153 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25071 1613 5 %RANDOM
Rwork0.22859 ---
obs0.22972 30640 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.488 Å2
Baniso -1Baniso -2Baniso -3
1-0.87 Å20 Å20.09 Å2
2---1.12 Å20 Å2
3---0.29 Å2
Refinement stepCycle: 1 / Resolution: 1.9→43.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2742 0 43 174 2959
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0222941
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.8742.0214025
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.85372
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.93822.059136
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.51315486
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5851538
X-RAY DIFFRACTIONr_chiral_restr0.0560.2449
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0212280
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_it0.2281.51807
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.42122924
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.39731134
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it0.7094.51094
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 117 -
Rwork0.284 2233 -
obs--100 %

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