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- PDB-2z3u: Crystal Structure of Chromopyrrolic Acid Bound Cytochrome P450 St... -

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Basic information

Entry
Database: PDB / ID: 2z3u
TitleCrystal Structure of Chromopyrrolic Acid Bound Cytochrome P450 StaP (CYP245A1)
ComponentsCytochrome P450
KeywordsOXIDOREDUCTASE / cytochrome P450 / monoxygenase / oxydoreductase / heme-enzyme / chromopyrrolic acid
Function / homology
Function and homology information


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
Chem-CRR / PROTOPORPHYRIN IX CONTAINING FE / Cytochrome P450
Similarity search - Component
Biological speciesStreptomyces sp. TP-A0274 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsMakino, M. / Sugimoto, H. / Shiro, Y. / Asamizu, S. / Onaka, H. / Nagano, S.
Citation
Journal: Proc.Natl.Acad.Sci.Usa / Year: 2007
Title: Crystal structures and catalytic mechanism of cytochrome P450 StaP that produces the indolocarbazole skeleton
Authors: Makino, M. / Sugimoto, H. / Shiro, Y. / Asamizu, S. / Onaka, H. / Nagano, S.
#1: Journal: J.Am.Chem.Soc. / Year: 2009
Title: Theoretical and experimental studies of the conversion of chromopyrrolic acid to an antitumor derivative by cytochrome P450 StaP: the catalytic role of water molecules
Authors: Wang, Y. / Chen, H. / Makino, M. / Shiro, Y. / Nagano, S. / Asamizu, S. / Onaka, H. / Shaik, S.
History
DepositionJun 6, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 3, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 1, 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_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_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: Cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,2839
Polymers47,2621
Non-polymers2,0218
Water3,387188
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.627, 66.610, 136.813
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Cytochrome P450


Mass: 47262.262 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sp. TP-A0274 (bacteria) / Gene: staP / Plasmid: pET26b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q83WG3, Oxidoreductases
#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-CRR / 3,4-DI-1H-INDOL-3-YL-1H-PYRROLE-2,5-DICARBOXYLIC ACID / CHROMOPYRROLIC ACID


Mass: 385.372 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C22H15N3O4
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 188 / 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: 2.15 Å3/Da / Density % sol: 42.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.8
Details: 2% PEG 4000, 50mM Bis-Tris pH 6.8, 100mM magnesium chloride, 10mM manganese chloride, 5mM chromopyrrolic acid, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 15, 2006
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 16573 / % possible obs: 99.2 % / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Biso Wilson estimate: 20.2 Å2 / Rsym value: 0.074 / Net I/σ(I): 22.46
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 5.6 % / Mean I/σ(I) obs: 6.06 / Num. unique all: 1626 / Rsym value: 0.324 / % possible all: 97.7

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Phasing

Phasing MR
Highest resolutionLowest resolution
Rotation2.5 Å19.96 Å
Translation2.5 Å19.96 Å

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Processing

Software
NameVersionClassificationNB
MOLREPphasing
CNS1.1refinement
PDB_EXTRACT2data extraction
BSSdata collection
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2Z3T

2z3t


Resolution: 2.4→19.96 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1570890.875 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.238 824 5 %RANDOM
Rwork0.191 ---
obs-16451 99 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 41.309 Å2 / ksol: 0.356 e/Å3
Displacement parametersBiso mean: 28.6 Å2
Baniso -1Baniso -2Baniso -3
1--5.72 Å20 Å20 Å2
2--5.81 Å20 Å2
3----0.09 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.3 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 2.4→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3218 0 146 188 3552
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_dihedral_angle_d24.2
X-RAY DIFFRACTIONc_improper_angle_d1.13
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.302 136 5.1 %
Rwork0.216 2513 -
obs-2649 98 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3hem.paramhem.top
X-RAY DIFFRACTION4ion.paramion.top

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