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- PDB-1dz9: Putative oxo complex of P450cam from Pseudomonas putida -

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Basic information

Entry
Database: PDB / ID: 1dz9
TitlePutative oxo complex of P450cam from Pseudomonas putida
ComponentsCYTOCHROME P450-CAM
KeywordsOXIDOREDUCTASE / MONO-OXYGENASE / HEME / REACTION INTERMEDIATE
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 / PROTOPORPHYRIN IX CONTAINING FE / : / OXYGEN ATOM / Camphor 5-monooxygenase
Similarity search - Component
Biological speciesPSEUDOMONAS PUTIDA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.9 Å
AuthorsSchlichting, 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.
Citation
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.
#1: Journal: Biochemistry / Year: 1998
Title: Understanding the Role of the Essential Asp251 in Cytochrome P450Cam Using Site-Directed Mcrystallography, and Kinetic Solvent Isotope Effectutagenesis, N
Authors: Vidakovic, M. / Sligar, S.G. / Li, H. / Poulos, T.L.
#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
DepositionFeb 18, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 30, 2000Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 12, 2017Group: Advisory / Derived calculations
Category: pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_conn
Revision 1.4Apr 3, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp
Revision 1.5May 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.ptnr1_symmetry / _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.ptnr2_symmetry / _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.ptnr3_symmetry / _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.ptnr1_symmetry / _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_symmetry

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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)94,96911
Polymers93,1762
Non-polymers1,7939
Water12,773709
1
A: CYTOCHROME P450-CAM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,5346
Polymers46,5881
Non-polymers9465
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: CYTOCHROME P450-CAM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,4355
Polymers46,5881
Non-polymers8474
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)66.900, 61.700, 94.600
Angle α, β, γ (deg.)90.00, 90.30, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.9735, 0.016, 0.228), (0.021, 0.9996, 0.0193), (-0.2276, 0.0236, -0.9735)
Vector: 32.8111, -29.7222, 47.1946)
DetailsBIOLOGICAL_UNIT: MONOMER

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein CYTOCHROME P450-CAM


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

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Non-polymers , 6 types, 718 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-O / OXYGEN ATOM


Mass: 15.999 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O
#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.: 709 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsN-TERMINUS IS DISORDERED THE ELECTRON DENSITY CORRESPONDING TO THE SIXTH LIGAND AT THE HEME IN ...N-TERMINUS IS DISORDERED THE ELECTRON DENSITY CORRESPONDING TO THE SIXTH LIGAND AT THE HEME IN MOLECULE B WAS NOT MODELED NOR THE WATER MOLECULES CLOSE BY.

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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: 2.1 Å3/Da / Density % sol: 41.3 %
Description: THE CRYSTAL WAS REDUCED BY SOAKING IN NITROGENATED RESERVOIR SOLUTION CONTAINING 50 MM DITHIONATE, 40 MM NAOH UNTIL A CLEAR COLOUR CHANGE OCCURED. THE OXYGEN COMPLEX WAS PREPARED BY ...Description: THE CRYSTAL WAS REDUCED BY SOAKING IN NITROGENATED RESERVOIR SOLUTION CONTAINING 50 MM DITHIONATE, 40 MM NAOH UNTIL A CLEAR COLOUR CHANGE OCCURED. THE OXYGEN COMPLEX WAS PREPARED BY EXPOSING THE CRYSTAL FOR 3 MIN. TO 120 BAR OXYGEN AT 2 DEG. C USING A PRESSURE CELL. 20% GLYCEROL WAS USED AS CRYOPROTECTANT, THE CRYSTALS WERE FREEZE QUENCHED IN LIQUID NITROGEN. AFTER COLLECTION OF A DATASET USING 0.91 A WAVELENGTH X-RAYS, THE CRYSTAL WAS ILLUMINATED FOR 3 HOURS WITH 1.5 A WAVELENGTH X-RAYS AND A SECOND DATASET WAS COLLECTED WITH 0.91 A X-RAYS.
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
Method: vapor diffusion, sitting drop
Details: drop consists of equal volume of protein and reservoir solutions
pH: 7.4
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
130 mg/mlprotein1drop
250 mMTris-HCl1reservoirpH7.4
3250 mM1reservoirKCl
4100 mMDTE1reservoir
51 mMcamphor1reservoir
627-30 %PEG40001reservoir

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Data collection

DiffractionMean temperature: 96 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.91
DetectorType: BRANDEIS / Detector: CCD / Date: Oct 15, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91 Å / Relative weight: 1
ReflectionResolution: 1.8→39 Å / Num. obs: 66465 / % possible obs: 92.9 % / Redundancy: 2.9 % / Biso Wilson estimate: 22 Å2 / Rsym value: 0.1 / Net I/σ(I): 8.4
Reflection shellResolution: 1.8→1.85 Å / Redundancy: 1.6 % / Mean I/σ(I) obs: 1.7 / Rsym value: 0.333 / % possible all: 59.2
Reflection
*PLUS
Rmerge(I) obs: 0.1
Reflection shell
*PLUS
% possible obs: 59.2 % / Rmerge(I) obs: 0.333

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Processing

Software
NameClassification
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: OTHER / Resolution: 1.9→19 Å / SU B: 4.82237 / SU ML: 0.13688 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.17864 / ESU R Free: 0.17393
RfactorNum. reflection% reflectionSelection details
Rfree0.248 4136 6.8 %RANDOM
Rwork0.177 ---
obs-69362 96.6 %-
Refinement stepCycle: LAST / Resolution: 1.9→19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6408 0 120 709 7237
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0140.02
X-RAY DIFFRACTIONp_angle_d0.0330.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0390.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor

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