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- PDB-2d09: A Role for Active Site Water Molecules and Hydroxyl Groups of Sub... -

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Basic information

Entry
Database: PDB / ID: 2d09
TitleA Role for Active Site Water Molecules and Hydroxyl Groups of Substrate for Oxygen Activation in Cytochrome P450 158A2
Componentsputative cytochrome P450
KeywordsOXIDOREDUCTASE / streptomyces / Cytochrome P450 oxidoreductase / CYP158A2 / proton transfer / dioxygen activation
Function / homology
Function and homology information


biflaviolin synthase / pigment metabolic process / 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
FLAVIOLIN / PROTOPORPHYRIN IX CONTAINING FE / OXYGEN MOLECULE / Biflaviolin synthase CYP158A2
Similarity search - Component
Biological speciesStreptomyces coelicolor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / structure refinement with starting model / Resolution: 1.8 Å
AuthorsZhao, B. / Waterman, M.R.
Citation
Journal: J.Biol.Chem. / Year: 2005
Title: Role of active site water molecules and substrate hydroxyl groups in oxygen activation by cytochrome P450 158A2: a new mechanism of proton transfer
Authors: Zhao, B. / Guengerich, F.P. / Voehler, M. / Waterman, M.R.
#1: Journal: J.Biol.Chem. / Year: 2005
Title: Binding of two flaviolin substrate molecules, oxidative coupling, and crystal structure of Streptomyces coelicolor A3(2) cytochrome P450 158A2
Authors: Zhao, B. / Guengerich, F.P. / Bellamine, A. / Lamb, D.C. / Izumikawa, M. / Lei, L. / Podust, L.M. / Sundaramoorthy, M. / Kalaitzis, J.A. / Reddy, L.M. / Kelly, S.L. / Moore, B.S. / Stec, D. ...Authors: Zhao, B. / Guengerich, F.P. / Bellamine, A. / Lamb, D.C. / Izumikawa, M. / Lei, L. / Podust, L.M. / Sundaramoorthy, M. / Kalaitzis, J.A. / Reddy, L.M. / Kelly, S.L. / Moore, B.S. / Stec, D. / Voehler, M. / Falck, J.R. / Shimada, T. / Waterman, M.R.
History
DepositionJul 30, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 25, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Oct 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_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_ref_seq_dif.details / _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

Downloads & links

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Assembly

Deposited unit
A: putative cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,6835
Polymers44,6221
Non-polymers1,0614
Water4,648258
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.000, 70.935, 102.950
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein putative cytochrome P450


Mass: 44621.727 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces coelicolor (bacteria) / Strain: A3(2) / Plasmid: pET17b / Production host: Escherichia coli (E. coli) / Strain (production host): HMS174(DE3)
References: UniProt: Q9FCA6, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-FLV / FLAVIOLIN / 2,5,7-TRIHYDROXYNAPHTHOQUINONE


Mass: 206.152 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H6O5
#4: Chemical ChemComp-OXY / OXYGEN MOLECULE


Mass: 31.999 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 258 / 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: 2.449 Å3/Da / Density % sol: 47.84 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 3350, flaviolin, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 0.95 Å
DetectorType: BRUKER PROTEUM 225 / Detector: CCD / Date: Jun 23, 2005
RadiationMonochromator: Si 220 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 1.8→37.4 Å / Num. all: 37024 / Num. obs: 35918 / % possible obs: 97 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.085 / Rsym value: 0.104
Reflection shellResolution: 1.8→1.86 Å / Rmerge(I) obs: 0.352 / Mean I/σ(I) obs: 2.6 / Rsym value: 0.336 / % possible all: 89.6

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT1.7data extraction
MAR345data collection
CNSphasing
RefinementMethod to determine structure: structure refinement with starting model
Starting model: PDB ENTRY 1T93

1t93


Resolution: 1.8→15 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.239 3174 8.4 %RANDOM
Rwork0.232 ---
all0.245 35925 --
obs0.245 31890 83.9 %-
Solvent computationBsol: 49.895 Å2
Displacement parametersBiso mean: 26.811 Å2
Baniso -1Baniso -2Baniso -3
1-1.273 Å20 Å20 Å2
2---0.082 Å20 Å2
3----1.192 Å2
Refinement stepCycle: LAST / Resolution: 1.8→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3102 0 75 258 3435
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
LS refinement shellResolution: 1.8→1.88 Å / Rfactor Rfree error: 0.012
RfactorNum. reflection% reflection
Rfree0.217 265 -
Rwork0.231 --
obs-2407 90 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2hemoxy.param
X-RAY DIFFRACTION3flav.param
X-RAY DIFFRACTION4water_rep.param

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