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- PDB-1s1f: Crystal Structure of Streptomyces Coelicolor A3(2) CYP158A2 from ... -

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Basic information

Entry
Database: PDB / ID: 1s1f
TitleCrystal Structure of Streptomyces Coelicolor A3(2) CYP158A2 from antibiotic biosynthetic pathways
Componentsputative cytochrome P450
KeywordsOXIDOREDUCTASE / streptomyces / Cytochrome P450 oxidoreductase / CYP158A2 / antibiotic biosynthesis
Function / homology
Function and homology information


biflaviolin synthase / pigment metabolic process / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / cholest-4-en-3-one 26-monooxygenase activity / steroid hydroxylase activity / cholesterol catabolic process / 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 / : / MALONIC ACID / 4-PHENYL-1H-IMIDAZOLE / : / Biflaviolin synthase CYP158A2
Similarity search - Component
Biological speciesStreptomyces coelicolor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / combination with MAD phase, SIR phase / Resolution: 1.5 Å
AuthorsZhao, B. / Lamb, D.C. / Lei, L. / Sundaramoorthy, M. / Podust, L.M. / Waterman, M.R.
CitationJournal: 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
DepositionJan 6, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 11, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Apr 29, 2015Group: Non-polymer description
Revision 1.4Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.5Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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

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Assembly

Deposited unit
A: putative cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0808
Polymers44,6181
Non-polymers1,4627
Water5,873326
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.250, 65.553, 104.245
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein putative cytochrome P450 / Cytochrome P450 CYP158A2


Mass: 44617.715 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: GenBank: 21219717, UniProt: Q9FCA6*PLUS

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Non-polymers , 6 types, 333 molecules

#2: Chemical ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Hg
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical ChemComp-PIM / 4-PHENYL-1H-IMIDAZOLE


Mass: 144.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H8N2
#5: Chemical ChemComp-MLA / MALONIC ACID / DICARBOXYLIC ACID C3 / PROPANEDIOLIC ACID / METHANEDICARBOXYLIC ACID


Mass: 104.061 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H4O4
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 326 / 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: 3

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Sample preparation

CrystalDensity Matthews: 2.08 Å3/Da / Density % sol: 40.79 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6
Details: sodium, malonic acid, glycerol, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12001
22001
32001
1,2,31
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
SYNCHROTRONAPS 22-ID10.9975,1.0055,1.0090
ROTATING ANODERIGAKU RU20021.5418
SYNCHROTRONAPS 22-ID31.6513,1.72,1.741
Detector
TypeIDDetectorDate
BRUKER PROTEUM 3001CCDOct 26, 2002
RIGAKU RAXIS2IMAGE PLATESep 28, 2002
BRUKER PROTEUM 3003CCDMar 18, 2003
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si 220 CHANNELMADMx-ray1
2GRAPHITESINGLE WAVELENGTHMx-ray1
3Si 220 CHANNELMADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.99751
21.00551
31.0091
41.54181
51.65131
61.721
71.7411
ReflectionResolution: 1.5→29.26 Å / Num. all: 60354 / Num. obs: 55989 / % possible obs: 92.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 25.8 % / Biso Wilson estimate: 21 Å2 / Rmerge(I) obs: 0.067 / Rsym value: 0.059 / Net I/σ(I): 27.6
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 1.5 / Num. unique all: 5098 / Rsym value: 0.76 / % possible all: 85.5

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Processing

Software
NameVersionClassification
CNS1.1refinement
MAR345data collection
SCALEPACKdata scaling
SOLVEV. 2.03phasing
RefinementMethod to determine structure: combination with MAD phase, SIR phase
Resolution: 1.5→29.26 Å / Rfactor Rfree error: 0.003 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.216 5513 10.2 %RANDOM
Rwork0.202 ---
all0.203 60283 --
obs0.203 54123 89.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 47.8372 Å2 / ksol: 0.379164 e/Å3
Displacement parametersBiso mean: 22.9 Å2
Baniso -1Baniso -2Baniso -3
1-1.07 Å20 Å20 Å2
2---1.27 Å20 Å2
3---0.2 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.16 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 1.5→29.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3053 0 76 326 3455
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d21.2
X-RAY DIFFRACTIONc_improper_angle_d0.92
X-RAY DIFFRACTIONc_mcbond_it1.171.5
X-RAY DIFFRACTIONc_mcangle_it1.842
X-RAY DIFFRACTIONc_scbond_it1.922
X-RAY DIFFRACTIONc_scangle_it2.772.5
LS refinement shellResolution: 1.5→1.59 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.289 797 10.2 %
Rwork0.253 7012 -
obs--78.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2HEM.PARAMHEM.TOP
X-RAY DIFFRACTION3PIMGOLMLA.PARAMPIMGOLMLA.TOP
X-RAY DIFFRACTION4WATER_REP.PARAMWATER_REP.TOP
X-RAY DIFFRACTION5ION.PARAMION.TOP

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