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- PDB-2z3t: Crystal Structure of Substrate Free Cytochrome P450 StaP (CYP245A1) -

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Basic information

Entry
Database: PDB / ID: 2z3t
TitleCrystal Structure of Substrate Free Cytochrome P450 StaP (CYP245A1)
ComponentsCytochrome P450
KeywordsOXIDOREDUCTASE / cytochrome P450 / monoxygenase / oxydoreductase / heme-enzyme
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
PROTOPORPHYRIN IX CONTAINING FE / IMIDAZOLE / Cytochrome P450
Similarity search - Component
Biological speciesStreptomyces sp. TP-A0274 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsMakino, M. / Sugimoto, H. / Shiro, Y. / Asamizu, S. / Onaka, H. / Nagano, S.
CitationJournal: 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.
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 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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
B: Cytochrome P450
C: Cytochrome P450
D: Cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)192,35021
Polymers189,0494
Non-polymers3,30117
Water7,674426
1
A: Cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0725
Polymers47,2621
Non-polymers8104
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1967
Polymers47,2621
Non-polymers9346
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0104
Polymers47,2621
Non-polymers7483
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0725
Polymers47,2621
Non-polymers8104
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.640, 78.718, 145.656
Angle α, β, γ (deg.)90.000, 107.920, 90.000
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is a monomer.

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Components

#1: Protein
Cytochrome P450


Mass: 47262.262 Da / Num. of mol.: 4
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.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical
ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H5N2
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 426 / 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: 2.58 Å3/Da / Density % sol: 52.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8
Details: 22% PEG 3350, 50mM potassium fluoride, 100mM imidazole, pH 8.0, VAPOR DIFFUSION, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
1901
2901
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSPring-8 BL44B211
SYNCHROTRONSPring-8 BL44B221.7330, 1.7382, 1.7403
Detector
TypeIDDetectorDate
ADSC QUANTUM 2101CCDSep 28, 2006
ADSC QUANTUM 2102CCDSep 28, 2006
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SiSINGLE WAVELENGTHMx-ray1
2SiMADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
111
21.7331
31.73821
41.74031
Reflection twinType: hemihedral / Operator: -h,-k,h+l / Fraction: 0.453
ReflectionResolution: 1.9→20 Å / Num. obs: 138934 / % possible obs: 91.4 % / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 31.42 Å2 / Rsym value: 0.032 / Net I/σ(I): 20.66
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 3.34 / Num. unique all: 10180 / Rsym value: 0.416 / % possible all: 67.1

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Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT2data extraction
BSSdata collection
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.9→20 Å / Cross valid method: THROUGHOUT / σ(F): 11960
Details: Used twin_lsq target. Twin fraction 0.453. Twin low -h, -k, h+l
RfactorNum. reflection% reflectionSelection details
Rfree0.273 5865 3.9 %thin shells, no twin-related reflections spread across both sets
Rwork0.228 ---
obs-119987 79 %-
Solvent computationBsol: 59.704 Å2
Displacement parametersBiso mean: 43.856 Å2
Baniso -1Baniso -2Baniso -3
1--6.129 Å20 Å2-0.076 Å2
2--10.064 Å20 Å2
3----3.935 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.33 Å0.32 Å
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11988 0 228 426 12642
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.536
LS refinement shellResolution: 1.9→1.97 Å
RfactorNum. reflection% reflection
Rfree0.359 448 -
Rwork0.332 --
obs-8000 52.7 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3hem.param
X-RAY DIFFRACTION4ion.param

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