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- PDB-1o76: CYANIDE COMPLEX OF P450CAM FROM PSEUDOMONAS PUTIDA -

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Basic information

Entry
Database: PDB / ID: 1o76
TitleCYANIDE COMPLEX OF P450CAM FROM PSEUDOMONAS PUTIDA
ComponentsCYTOCHROME P450-CAM
KeywordsOXIDOREDUCTASE / MONO-OXYGENASE / HEME / ELECTRON TRANSPORT
Function / homology
Function and homology information


camphor 5-monooxygenase / camphor 5-monooxygenase activity / (+)-camphor catabolic process / iron ion binding / heme binding / cytoplasm
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
CAMPHOR / CYANIDE ION / PROTOPORPHYRIN IX CONTAINING FE / : / Camphor 5-monooxygenase
Similarity search - Component
Biological speciesPSEUDOMONAS PUTIDA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.8 Å
AuthorsFedorov, R. / Ghosh, D. / Schlichting, I.
Citation
Journal: Arch.Biochem.Biophys. / Year: 2003
Title: Crystal Structures of Cyanide Complexes of P450Cam and the Oxygenase Domain of Inducible Nitric Oxide Synthase-Structural Models of the Short-Lived Oxygen Complexes
Authors: Fedorov, R. / Ghosh, D. / Schlichting, I.
#1: Journal: Science / Year: 2000
Title: The Catalytic Pathway of Cytochrome P450Cam at Atomic Resolution
Authors: Schlichting, I. / Berendzen, J. / Chu, K. / Stock, A.M. / Maves, S.A. / Benson, D.E. / Sweet, R.M. / Ringe, D. / Petsko, G.A. / Sligar, S.G.
#2: Journal: J.Mol.Biol. / Year: 1987
Title: High-Resolution Crystal Structure of Cytochrome P450Cam
Authors: Poulos, T.L. / Finzel, B.C. / Howard, A.J.
History
DepositionOct 23, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 19, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 3, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_biol
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.4May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_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_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CYTOCHROME P450-CAM
B: CYTOCHROME P450-CAM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,00512
Polymers93,1762
Non-polymers1,82910
Water17,132951
1
A: CYTOCHROME P450-CAM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,5055
Polymers46,5881
Non-polymers9174
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: CYTOCHROME P450-CAM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,5007
Polymers46,5881
Non-polymers9126
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)67.000, 61.800, 94.600
Angle α, β, γ (deg.)90.00, 90.40, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.9748, 0.0137, 0.2227), (0.0195, 0.9995, 0.0239), (-0.2223, 0.0277, -0.9746)
Vector: 32.8412, -29.8396, 46.7099)

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein CYTOCHROME P450-CAM / CAMPHOR 5-MONOOXYGENASE / P450CAM


Mass: 46587.895 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: CYANIDE BOUND TO HEME IRON. HEME ATTACHED VIA CYS357
Source: (gene. exp.) PSEUDOMONAS PUTIDA (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P00183, camphor 5-monooxygenase

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Non-polymers , 6 types, 961 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-CYN / CYANIDE ION


Mass: 26.017 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CN
#4: Chemical ChemComp-CAM / CAMPHOR


Mass: 152.233 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16O
#5: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#6: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 951 / 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: 1.87 Å3/Da / Density % sol: 33.71 %
Crystal growTemperature: 275 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: CRYSTALS WERE GROWN USING THE SITTING DROP GEOMETRY AT 2 DEG. C. 5 UL OF 30 MG/ML P450 IN 50 MM TRIS HCL, 250 MM KCL, 0.5 MM CAMPHOR WERE MIXED WITH AN EQUAL VOLUME OF THE RESERVOIR SOLUTION ...Details: CRYSTALS WERE GROWN USING THE SITTING DROP GEOMETRY AT 2 DEG. C. 5 UL OF 30 MG/ML P450 IN 50 MM TRIS HCL, 250 MM KCL, 0.5 MM CAMPHOR WERE MIXED WITH AN EQUAL VOLUME OF THE RESERVOIR SOLUTION (27-30% PEG 4000, 100 MM DTE, SAME BUFFER AS PROTEIN)., pH 7.40
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
115 mg/mlprotein1drop
240 mMEPPS1droppH7.6
3150 mM1dropNaCl
45 %glycerol1drop
54000 nMH4B1drop
62 mMbeta-mercaptoethanol1drop
750 mMbeta-octylglucoside1drop
8100 mMNa+-L-Arg1reservoirpH7.0
960 mM1reservoirKCN
10100 mMdithiothreitol1reservoir
11100 mMNa+-MES1reservoirpH6.5
120.7 MNa+-malonate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1
DetectorType: BRANDEIS / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. obs: 67892 / % possible obs: 94.5 % / Redundancy: 3.49 % / Biso Wilson estimate: 27 Å2 / Rsym value: 0.082 / Net I/σ(I): 8.2
Reflection shellResolution: 1.8→2 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 4 / Rsym value: 0.242 / % possible all: 88.9
Reflection
*PLUS
Highest resolution: 1.8 Å / Num. measured all: 237007 / Rmerge(I) obs: 0.082
Reflection shell
*PLUS
% possible obs: 88.9 % / Rmerge(I) obs: 0.242

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Processing

Software
NameVersionClassification
CNS1refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.8→19 Å / Data cutoff high absF: 10000000 / Cross valid method: THROUGHOUT / σ(F): 0 / Details: N-TERMINUS IS DISORDERED
RfactorNum. reflection% reflectionSelection details
Rfree0.2363 3395 4.7 %RANDOM
Rwork0.1964 ---
obs0.1964 67892 94.5 %-
Solvent computationBsol: 36.16 Å2
Refinement stepCycle: LAST / Resolution: 1.8→19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6406 0 123 951 7480
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01073
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_deg1.93348
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refinement
*PLUS
Lowest resolution: 20 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.236 / Rfactor Rwork: 0.196
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0107
X-RAY DIFFRACTIONc_angle_deg1.93

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