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- PDB-2cp4: CRYSTAL STRUCTURE OF THE CYTOCHROME P450-CAM ACTIVE SITE MUTANT T... -

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Basic information

Entry
Database: PDB / ID: 2cp4
TitleCRYSTAL STRUCTURE OF THE CYTOCHROME P450-CAM ACTIVE SITE MUTANT THR252ALA
ComponentsCYTOCHROME P450-CAM
KeywordsOXIDOREDUCTASE(OXYGENASE)
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 / Camphor 5-monooxygenase
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.1 Å
AuthorsRaag, R. / Poulos, T.L.
Citation
Journal: Biochemistry / Year: 1991
Title: Crystal structure of the cytochrome P-450CAM active site mutant Thr252Ala.
Authors: Raag, R. / Martinis, S.A. / Sligar, S.G. / Poulos, T.L.
#1: Journal: To be Published
Title: X-Ray Crystallographic Structural Studies of Cytochrome P450-Cam+
Authors: Raag, R. / Poulos, T.L.
#2: Journal: Biochemistry / Year: 1991
Title: Crystal Structures of Cytochrome P450-Cam Complexed with Camphane, Thiocamphor, and Adamantane: Factors Controlling P450 Substrate Hydroxylation
Authors: Raag, R. / Poulos, T.L.
#3: Journal: Biochemistry / Year: 1989
Title: Crystal Structure of the Carbon Monoxy-Substrate-Cytochrome P450-Cam Ternary Complex
Authors: Raag, R. / Poulos, T.L.
#4: Journal: Biochemistry / Year: 1989
Title: The Structural Basis for Substrate-Induced Changes in Redox Potential and Spin Equilibrium in Cytochrome P450(Cam)
Authors: Raag, R. / Poulos, T.L.
History
DepositionJun 4, 1991Processing site: BNL
Revision 1.0Jan 15, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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-CAM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,3283
Polymers46,5591
Non-polymers7692
Water4,179232
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)108.670, 103.900, 36.380
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: RESIDUES PRO 89, PRO 100, AND PRO 106 ARE CIS PROLINES.

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Components

#1: Protein CYTOCHROME P450-CAM


Mass: 46558.855 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: POTENTIAL / References: UniProt: P00183, camphor 5-monooxygenase
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-CAM / CAMPHOR


Mass: 152.233 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 232 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 44.2 %
Crystal grow
*PLUS
pH: 7 / Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.05 mlprotein11
20.05 mlammonium sulfate11
350 mMpotassium phosphate11
4250 mM11KCl
550 mMdithiotheitol11

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Data collection

Reflection
*PLUS
Highest resolution: 2.1 Å / Num. obs: 106045 / Observed criterion σ(I): 0.5 / Rmerge(I) obs: 0.086
Reflection shell
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 2.2 Å / % possible obs: 65 %

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Processing

SoftwareName: PROFFT / Classification: refinement
RefinementRfactor obs: 0.179 / Highest resolution: 2.1 Å
Refinement stepCycle: LAST / Highest resolution: 2.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3233 0 54 232 3519
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.02
X-RAY DIFFRACTIONp_angle_d0.034
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
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
Refinement
*PLUS
Lowest resolution: 10 Å / Num. reflection all: 22942 / Num. reflection obs: 16775 / σ(I): 2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: p_dihedral_angle_d / Dev ideal: 0.034

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