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- PDB-1se6: Crystal Structure of Streptomyces Coelicolor A3(2) CYP158A2 from ... -

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Basic information

Entry
Database: PDB / ID: 1se6
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 / cholest-4-en-3-one 26-monooxygenase activity / steroid hydroxylase activity / cholesterol catabolic 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
PROTOPORPHYRIN IX CONTAINING FE / SPERMINE (FULLY PROTONATED FORM) / Biflaviolin synthase CYP158A2
Similarity search - Component
Biological speciesStreptomyces coelicolor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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
DepositionFeb 16, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 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 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Aug 23, 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.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_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
B: putative cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,0046
Polymers89,3702
Non-polymers1,6354
Water9,710539
1
A: putative cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,7034
Polymers44,6851
Non-polymers1,0183
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: putative cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3012
Polymers44,6851
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.554, 79.206, 87.430
Angle α, β, γ (deg.)90.00, 92.26, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein putative cytochrome P450 /


Mass: 44684.781 Da / Num. of mol.: 2
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
#2: Chemical ChemComp-SPK / SPERMINE (FULLY PROTONATED FORM) / Spermine


Mass: 206.372 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H30N4
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 539 / 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: 2.38 Å3/Da / Density % sol: 47.82 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 2000 monomethylether, tetrahydrocloride spermine, 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-ID / Wavelength: 1 Å
DetectorType: BRUKER PROTEUM 300 / Detector: CCD / Date: Mar 18, 2003
RadiationMonochromator: Si 220 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→35.9 Å / Num. all: 81963 / Num. obs: 73147 / % possible obs: 89.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 18.6 % / Biso Wilson estimate: 11 Å2 / Rmerge(I) obs: 0.058 / Rsym value: 0.052 / Net I/σ(I): 21.8
Reflection shellResolution: 1.75→1.8 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.18 / Mean I/σ(I) obs: 6.5 / Num. unique all: 5988 / Rsym value: 0.25 / % possible all: 92.4

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Processing

Software
NameVersionClassification
CNS1.1refinement
MAR345data collection
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1S1F

1s1f


Resolution: 1.75→35.9 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 861760.16 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.268 7156 10 %RANDOM
Rwork0.234 ---
all0.234 81839 --
obs0.234 71548 87.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 45.8769 Å2 / ksol: 0.377658 e/Å3
Displacement parametersBiso mean: 17.6 Å2
Baniso -1Baniso -2Baniso -3
1--5.36 Å20 Å2-0.61 Å2
2--2.74 Å20 Å2
3---2.62 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 1.75→35.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6045 0 112 539 6696
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.92
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.261.5
X-RAY DIFFRACTIONc_mcangle_it1.962
X-RAY DIFFRACTIONc_scbond_it2.022
X-RAY DIFFRACTIONc_scangle_it2.792.5
LS refinement shellResolution: 1.75→1.86 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.275 1159 10.1 %
Rwork0.231 10345 -
obs--84.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2HEM.PARHEM.TOP
X-RAY DIFFRACTION3SPK.PARSPK.TOP
X-RAY DIFFRACTION4WATER_REP.PARAMWATER_REP.TOP

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