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- PDB-4fb2: Crystal Structure of Substrate-Free P450cin -

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Basic information

Entry
Database: PDB / ID: 4fb2
TitleCrystal Structure of Substrate-Free P450cin
ComponentsP450cin1,8-Cineole 2-endo-monooxygenase
KeywordsOXIDOREDUCTASE / HEME / MONOOXYGENASE / CINDOXIN
Function / homology
Function and homology information


1,8-cineole 2-endo-monooxygenase / carbazole catabolic process / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen / iron ion binding / heme binding
Similarity search - Function
Cytochrome P450, B-class / Cytochrome p450 / Cytochrome P450 / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / 1,8-cineole 2-endo-monooxygenase
Similarity search - Component
Biological speciesCitrobacter braakii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.37 Å
AuthorsMadrona, Y. / Tripathi, S.M. / Li, H. / Poulos, T.L.
CitationJournal: Biochemistry / Year: 2012
Title: Crystal structures of substrate-free and nitrosyl cytochrome p450cin: implications for o(2) activation.
Authors: Madrona, Y. / Tripathi, S. / Li, H. / Poulos, T.L.
History
DepositionMay 22, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 18, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 22, 2012Group: Database references
Revision 1.2Sep 5, 2012Group: Database references
Revision 1.3May 28, 2014Group: Data collection
Revision 1.4Sep 13, 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 / 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_asym_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _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

Downloads & links

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Assembly

Deposited unit
A: P450cin
B: P450cin
C: P450cin
D: P450cin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)182,07017
Polymers179,1524
Non-polymers2,91813
Water33,1121838
1
A: P450cin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,5024
Polymers44,7881
Non-polymers7143
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: P450cin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,5024
Polymers44,7881
Non-polymers7143
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: P450cin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,6266
Polymers44,7881
Non-polymers8385
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: P450cin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4403
Polymers44,7881
Non-polymers6522
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.383, 83.912, 88.192
Angle α, β, γ (deg.)96.81, 96.39, 89.94
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
P450cin / 1,8-Cineole 2-endo-monooxygenase


Mass: 44787.879 Da / Num. of mol.: 4 / Fragment: UNP residues 8-404
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Citrobacter braakii (bacteria) / Gene: cinA / Plasmid: pCWori-P450cin / Production host: Escherichia coli (E. coli) / Strain (production host): DH5-alpha / References: UniProt: Q8VQF6
#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1838 / 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: 2.46 Å3/Da / Density % sol: 50.02 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 13% PEG 4000, 0.1M hepes pH 7, 0.1M magnesium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 70 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 28, 2010 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.37→50 Å / Num. all: 343124 / Num. obs: 343124 / % possible obs: 95.7 % / Observed criterion σ(F): 0.02 / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Rmerge(I) obs: 0.073 / Rsym value: 0.081 / Net I/σ(I): 32.4
Reflection shell
Resolution (Å)Redundancy (%)Mean I/σ(I) obsRsym valueDiffraction-ID% possible all
1.37-1.393.22.30.571193.1
1.39-1.423.32.90.491193.3
1.42-1.453.33.50.424193.5
1.45-1.483.44.60.339194
1.48-1.513.45.70.281194.1
1.51-1.543.46.90.241194.4
1.54-1.583.47.80.212194.5
1.58-1.623.49.70.176195
1.62-1.673.411.30.155195.1
1.67-1.733.4130.137195.4
1.73-1.793.415.50.119195.6
1.79-1.863.4190.101195.9
1.86-1.943.422.20.09196.1
1.94-2.053.326.80.076196.3
2.05-2.173.331.80.064196.4
2.17-2.343.8360.085196.8
2.34-2.58741.60.13197.8
2.58-2.956.846.40.101198.3
2.95-3.725.844.60.072198.7
3.72-503.842.40.048198.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1T2B

1t2b


Resolution: 1.37→41.657 Å / SU ML: 0.12 / σ(F): 0.02 / Phase error: 15.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1669 16574 5.03 %
Rwork0.1364 --
obs0.1379 329527 91.79 %
all-329527 -
Solvent computationShrinkage radii: 0.89 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.471 Å2 / ksol: 0.394 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.5416 Å2-1.7103 Å21.3193 Å2
2---5.6221 Å21.5606 Å2
3---2.0804 Å2
Refinement stepCycle: LAST / Resolution: 1.37→41.657 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12420 0 196 1838 14454
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01213132
X-RAY DIFFRACTIONf_angle_d1.41617935
X-RAY DIFFRACTIONf_dihedral_angle_d13.5564824
X-RAY DIFFRACTIONf_chiral_restr0.0871943
X-RAY DIFFRACTIONf_plane_restr0.0092319
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.37-1.38570.22394520.15698664X-RAY DIFFRACTION76
1.3857-1.4020.18915030.14399042X-RAY DIFFRACTION79
1.402-1.41910.20255200.13469194X-RAY DIFFRACTION81
1.4191-1.43710.18424870.12869505X-RAY DIFFRACTION83
1.4371-1.4560.18354790.12529524X-RAY DIFFRACTION84
1.456-1.47590.17074950.11569788X-RAY DIFFRACTION86
1.4759-1.4970.17025200.10799808X-RAY DIFFRACTION86
1.497-1.51940.15815140.108810068X-RAY DIFFRACTION88
1.5194-1.54310.1634950.102410175X-RAY DIFFRACTION89
1.5431-1.56840.15725320.101710181X-RAY DIFFRACTION90
1.5684-1.59550.14885610.09710289X-RAY DIFFRACTION91
1.5955-1.62450.14775710.098410397X-RAY DIFFRACTION92
1.6245-1.65570.14655340.10210489X-RAY DIFFRACTION92
1.6557-1.68950.15655400.105210592X-RAY DIFFRACTION93
1.6895-1.72630.15866180.106710646X-RAY DIFFRACTION94
1.7263-1.76640.14925640.108210677X-RAY DIFFRACTION94
1.7664-1.81060.15725840.111610701X-RAY DIFFRACTION95
1.8106-1.85950.1645910.116210742X-RAY DIFFRACTION95
1.8595-1.91430.16285510.120210857X-RAY DIFFRACTION95
1.9143-1.9760.1535780.121810827X-RAY DIFFRACTION96
1.976-2.04670.1565660.124210979X-RAY DIFFRACTION96
2.0467-2.12860.14996190.119910851X-RAY DIFFRACTION96
2.1286-2.22550.14355960.115910995X-RAY DIFFRACTION97
2.2255-2.34280.1575740.122211002X-RAY DIFFRACTION97
2.3428-2.48960.15855440.130511061X-RAY DIFFRACTION97
2.4896-2.68180.17956040.146511068X-RAY DIFFRACTION98
2.6818-2.95160.1766030.155411173X-RAY DIFFRACTION98
2.9516-3.37850.17535780.160411230X-RAY DIFFRACTION99
3.3785-4.25590.17176280.152811187X-RAY DIFFRACTION99
4.2559-41.67590.1815730.167411241X-RAY DIFFRACTION99

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