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- PDB-1ued: Crystal Structure of OxyC a Cytochrome P450 Implicated in an Oxid... -

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Basic information

Entry
Database: PDB / ID: 1ued
TitleCrystal Structure of OxyC a Cytochrome P450 Implicated in an Oxidative C-C Coupling Reaction During Vancomycin Biosynthesis.
ComponentsP450 monooxygenaseCytochrome P450
KeywordsOXIDOREDUCTASE / Cytochrome P450 vancomycin biosynthesis
Function / homology
Function and homology information


vancomycin biosynthetic process / Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen / 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 / DI(HYDROXYETHYL)ETHER / Cytochrome P450 165C4
Similarity search - Component
Biological speciesAmycolatopsis orientalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsPylypenko, O. / Vitali, F. / Zerbe, K. / Robinson, J.A. / Schlichting, I.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: Crystal structure of OxyC, a cytochrome P450 implicated in an oxidative C-C coupling reaction during vancomycin biosynthesis
Authors: Pylypenko, O. / Vitali, F. / Zerbe, K. / Robinson, J.A. / Schlichting, I.
History
DepositionMay 11, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 9, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 2023Group: 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 / pdbx_initial_refinement_model / struct_conn / struct_site
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_conn.ptnr2_label_seq_id / _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: P450 monooxygenase
B: P450 monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,3248
Polymers90,4912
Non-polymers1,8346
Water10,881604
1
A: P450 monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,1624
Polymers45,2451
Non-polymers9173
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: P450 monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,1624
Polymers45,2451
Non-polymers9173
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.063, 99.270, 105.081
Angle α, β, γ (deg.)90.00, 96.11, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein P450 monooxygenase / Cytochrome P450 / P450 OxyC


Mass: 45245.379 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Amycolatopsis orientalis (bacteria) / Plasmid: pET14b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS
References: UniProt: Q8RN03, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 604 / 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: 44.04 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 500MME, di-ammonium tartrate, DTE, K-Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
115 mg/mlprotein1drop
220 mM1dropKCl
35 mMdithioerythritol1drop
420 mMpotassium HEPES1droppH7.0
50.1 Mdi-ammonium tartrate1reservoir
65 mMdithioerythritol1reservoir
7100 mMpotassium HEPES1reservoirpH7.5
812 %PEG550 MME1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.93 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationMonochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 1.9→28.8 Å / Num. obs: 65815 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.56 % / Biso Wilson estimate: 29.2 Å2 / Rsym value: 0.09
Reflection shellResolution: 1.9→2.02 Å / Rsym value: 0.318 / % possible all: 99.9
Reflection
*PLUS
Num. measured all: 234465 / Rmerge(I) obs: 0.09
Reflection shell
*PLUS
% possible obs: 99.9 % / Rmerge(I) obs: 0.318 / Mean I/σ(I) obs: 3.6

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Processing

Software
NameVersionClassification
CNS1refinement
XDSdata reduction
XDSdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1lfk

1lfk


Resolution: 1.9→20 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1770996.35 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.235 3311 5 %RANDOM
Rwork0.196 ---
obs0.196 65757 99.6 %-
all-65757 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 52.1383 Å2 / ksol: 0.364879 e/Å3
Displacement parametersBiso mean: 27.4 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6137 0 112 618 6867
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.014
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d21.4
X-RAY DIFFRACTIONc_improper_angle_d1.33
X-RAY DIFFRACTIONc_mcbond_it1.471.5
X-RAY DIFFRACTIONc_mcangle_it2.122
X-RAY DIFFRACTIONc_scbond_it2.342
X-RAY DIFFRACTIONc_scangle_it3.472.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.272 587 5.4 %
Rwork0.231 10370 -
obs--99.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2PG4_XPLOR_PARAM
X-RAY DIFFRACTION3HEME-PEG.PARAM
X-RAY DIFFRACTION4WATER.PARAM
Refinement
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 28.8 Å / % reflection Rfree: 5 % / Rfactor Rwork: 0.195
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.33

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