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- PDB-4fyz: Crystal Structure of Nitrosyl Cytochrome P450cin -

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Basic information

Entry
Database: PDB / ID: 4fyz
TitleCrystal Structure of Nitrosyl Cytochrome P450cin
ComponentsP450cin
KeywordsOXIDOREDUCTASE / P450 / 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
1,3,3-TRIMETHYL-2-OXABICYCLO[2.2.2]OCTANE / PROTOPORPHYRIN IX CONTAINING FE / NITRIC OXIDE / DI(HYDROXYETHYL)ETHER / 1,8-cineole 2-endo-monooxygenase
Similarity search - Component
Biological speciesCitrobacter braakii (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.32 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
DepositionJul 5, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 25, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 1, 2012Group: Data collection
Revision 1.2Sep 5, 2012Group: Database references
Revision 1.3Sep 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_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,77812
Polymers89,5762
Non-polymers2,20210
Water5,873326
1
A: P450cin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,8896
Polymers44,7881
Non-polymers1,1015
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: P450cin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,8896
Polymers44,7881
Non-polymers1,1015
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.176, 68.437, 104.047
Angle α, β, γ (deg.)90.00, 95.79, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein P450cin


Mass: 44787.879 Da / Num. of mol.: 2 / Fragment: UNP residues 8-404
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Citrobacter braakii (bacteria) / Gene: CIN A, cinA / Plasmid: pcWori-P450cin / Production host: Escherichia coli (E. coli) / Strain (production host): DH5-alpha / References: UniProt: Q8VQF6

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Non-polymers , 6 types, 336 molecules

#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-CNL / 1,3,3-TRIMETHYL-2-OXABICYCLO[2.2.2]OCTANE / 1,8-CINEOLE


Mass: 154.249 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H18O
#4: Chemical ChemComp-NO / NITRIC OXIDE / Nitrogen monoxide


Mass: 30.006 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#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: 1

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Sample preparation

CrystalDensity Matthews: 2.54 Å3/Da / Density % sol: 51.53 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: 6-9% PEG 3350, 100mM Bis-Tris pH 6.2, 100mM Lithium Sulfate, 5mM Cineole, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 70 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Jan 1, 2002
RadiationMonochromator: Cu Filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.32→50 Å / Num. all: 37894 / Num. obs: 37894 / % possible obs: 97.1 % / Observed criterion σ(F): 0.02 / Observed criterion σ(I): -3 / Redundancy: 5 % / Biso Wilson estimate: 30.1 Å2 / Rsym value: 0.071 / Net I/σ(I): 19.8
Reflection shell
Resolution (Å)Diffraction-ID% possible all
2.32-2.4193.9
2.4-2.5195.2
2.5-2.61196.4
2.61-2.75197.7
2.75-2.92198.9
2.92-3.15199.7
3.15-3.47199
3.47-3.97197.7
3.97-5195.1
5-50197.2

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: P450cin wild-type (PDB ID:1T2B)

1t2b


Resolution: 2.32→36.013 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2508 1905 5.03 %RANDOM
Rwork0.1932 ---
obs0.1961 37848 96.56 %-
all-37848 --
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.618 Å2 / ksol: 0.363 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-7.529 Å20 Å23.488 Å2
2---5.9758 Å2-0 Å2
3----1.5532 Å2
Refinement stepCycle: LAST / Resolution: 2.32→36.013 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6298 0 152 326 6776
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0126629
X-RAY DIFFRACTIONf_angle_d1.1559023
X-RAY DIFFRACTIONf_dihedral_angle_d14.7992431
X-RAY DIFFRACTIONf_chiral_restr0.074974
X-RAY DIFFRACTIONf_plane_restr0.0051164
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.32-2.37610.28261220.21742334X-RAY DIFFRACTION87
2.3761-2.44030.31311070.20362508X-RAY DIFFRACTION95
2.4403-2.51210.27551290.19832493X-RAY DIFFRACTION95
2.5121-2.59310.25811470.20412573X-RAY DIFFRACTION96
2.5931-2.68580.29411550.19622553X-RAY DIFFRACTION97
2.6858-2.79330.24761370.20492569X-RAY DIFFRACTION98
2.7933-2.92040.25971500.19982622X-RAY DIFFRACTION99
2.9204-3.07430.26821420.19992636X-RAY DIFFRACTION100
3.0743-3.26670.27351430.21432626X-RAY DIFFRACTION100
3.2667-3.51880.26941380.20192613X-RAY DIFFRACTION99
3.5188-3.87250.24761420.19122596X-RAY DIFFRACTION97
3.8725-4.4320.20621300.1622558X-RAY DIFFRACTION96
4.432-5.58050.20731270.1642582X-RAY DIFFRACTION96
5.5805-36.0130.22841360.20382680X-RAY DIFFRACTION97

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