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Yorodumi- PDB-2hpd: CRYSTAL STRUCTURE OF HEMOPROTEIN DOMAIN OF P450BM-3, A PROTOTYPE ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2hpd | ||||||
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Title | CRYSTAL STRUCTURE OF HEMOPROTEIN DOMAIN OF P450BM-3, A PROTOTYPE FOR MICROSOMAL P450'S | ||||||
Components | CYTOCHROME P450 BM-3 | ||||||
Keywords | OXIDOREDUCTASE(OXYGENASE) | ||||||
Function / homology | Function and homology information NADPH-hemoprotein reductase / NADPH-hemoprotein reductase activity / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen / unspecific monooxygenase / aromatase activity / response to hormone / FMN binding / flavin adenine dinucleotide binding / iron ion binding / heme binding ...NADPH-hemoprotein reductase / NADPH-hemoprotein reductase activity / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen / unspecific monooxygenase / aromatase activity / response to hormone / FMN binding / flavin adenine dinucleotide binding / iron ion binding / heme binding / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | Bacillus megaterium (bacteria) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2 Å | ||||||
Authors | Ravichandran, K.G. / Boddupalli, S.S. / Hasemann, C.A. / Peterson, J.A. / Deisenhofer, J. | ||||||
Citation | Journal: Science / Year: 1993 Title: Crystal structure of hemoprotein domain of P450BM-3, a prototype for microsomal P450's. Authors: Ravichandran, K.G. / Boddupalli, S.S. / Hasermann, C.A. / Peterson, J.A. / Deisenhofer, J. #1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1992 Title: Crystallization and Preliminary X-Ray Diffraction Analysis of P450Terp and the Hemoprotein Domain of P450Bm-3, Enzymes Belonging to Two Distinct Classes of the Cytochrome P450 Superfamily Authors: Boddupalli, S.S. / Hasemann, C.A. / Ravichandran, K.G. / Lu, J.-Y. / Goldsmith, E.J. / Deisenhofer, J. / Peterson, J.A. #2: Journal: Annu.Rev.Pharmacol.Toxicol. / Year: 1991 Title: P450Bm-3 and Other Inducible Bacterial P450 Cytochromes: Biochemistry and Regulation Authors: Fulco, A.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2hpd.cif.gz | 205.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2hpd.ent.gz | 162.7 KB | Display | PDB format |
PDBx/mmJSON format | 2hpd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2hpd_validation.pdf.gz | 545 KB | Display | wwPDB validaton report |
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Full document | 2hpd_full_validation.pdf.gz | 566.3 KB | Display | |
Data in XML | 2hpd_validation.xml.gz | 21.2 KB | Display | |
Data in CIF | 2hpd_validation.cif.gz | 33.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hp/2hpd ftp://data.pdbj.org/pub/pdb/validation_reports/hp/2hpd | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Atom site foot note | 1: RESIDUES ALA 191 - ALA 197 OF BOTH MOLECULES HAVE LARGE B VALUES (B > 80 ANGSTROMS**2). 2: ASP A 195 - PRO A 196 OMEGA =104.96 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION FTNOTE 1 ALSO APPLIES. | ||||||||||||
Noncrystallographic symmetry (NCS) | NCS oper:
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Details | THE TRANSFORMATION PRESENTED ON *MTRIX 1* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN *B* WHEN APPLIED TO CHAIN *A*, WITH AN RMSD = 0.779480. THE TRANSFORMATION PRESENTED ON *MTRIX 2* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN *A* WHEN APPLIED TO CHAIN *B*, WITH AN RMSD = 0.785550. |
-Components
#1: Protein | Mass: 53796.293 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus megaterium (bacteria) / References: UniProt: P14779, unspecific monooxygenase #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.63 Å3/Da / Density % sol: 53.3 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 4 ℃ / pH: 7.4 / Method: vapor diffusion, hanging dropDetails: Boddupalli, S.S., (1992) Proc.Nat.Acad.Sci.USA, 89, 5567. | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Reflection | *PLUS Highest resolution: 2 Å / Num. obs: 55129 / % possible obs: 73.6 % / Observed criterion σ(I): 2 / Num. measured all: 251913 / Rmerge(I) obs: 0.058 |
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-Processing
Software |
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Refinement | Resolution: 2→20 Å / Rfactor Rwork: 0.167 / Rfactor obs: 0.167 Details: THE ELECTRON DENSITY FOR THE LOOP REGION BETWEEN THE F AND G HELICES (RESIDUES 190 - 196) IS POORLY DEFINED FOR BOTH MOLECULES A AND B. THIS COULD ACCOUNT FOR THE HIGH B FACTORS OF RESIDUES ...Details: THE ELECTRON DENSITY FOR THE LOOP REGION BETWEEN THE F AND G HELICES (RESIDUES 190 - 196) IS POORLY DEFINED FOR BOTH MOLECULES A AND B. THIS COULD ACCOUNT FOR THE HIGH B FACTORS OF RESIDUES IN THIS REGION AND FOR THE BAD CONFORMATION OF THE 195 - 196 PEPTIDE PLANE. DIHEDRAL ANGLES OF RESIDUES THR A 436 AND THR B 436 LIE OUTSIDE THE ALLOWED REGIONS IN THE RAMACHANDRAN PLOT. THIS MAY BE DUE TO THEIR ROLE IN SUBSTRATE INTERACTIONS. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→20 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 2 Å / Lowest resolution: 20 Å / Num. reflection obs: 7895 / σ(F): 2 / Rfactor obs: 0.167 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 25 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_angle_d / Dev ideal: 3.1 |