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- PDB-2hpd: CRYSTAL STRUCTURE OF HEMOPROTEIN DOMAIN OF P450BM-3, A PROTOTYPE ... -

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Basic information

Entry
Database: PDB / ID: 2hpd
TitleCRYSTAL STRUCTURE OF HEMOPROTEIN DOMAIN OF P450BM-3, A PROTOTYPE FOR MICROSOMAL P450'S
ComponentsCYTOCHROME P450 BM-3
KeywordsOXIDOREDUCTASE(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 / metabolic process / FMN binding / iron ion binding / heme binding / identical protein binding / cytoplasm
Similarity search - Function
Bifunctional cytochrome P450/NADPH--cytochrome P450 reductase / Cytochrome p450 / Cytochrome P450 / Sulfite reductase [NADPH] flavoprotein alpha-component-like, FAD-binding / NADPH-cytochrome p450 reductase, FAD-binding, alpha-helical domain superfamily / FAD binding domain / Flavodoxin-like / Flavoprotein pyridine nucleotide cytochrome reductase / Flavodoxin / Flavodoxin-like domain profile. ...Bifunctional cytochrome P450/NADPH--cytochrome P450 reductase / Cytochrome p450 / Cytochrome P450 / Sulfite reductase [NADPH] flavoprotein alpha-component-like, FAD-binding / NADPH-cytochrome p450 reductase, FAD-binding, alpha-helical domain superfamily / FAD binding domain / Flavodoxin-like / Flavoprotein pyridine nucleotide cytochrome reductase / Flavodoxin / Flavodoxin-like domain profile. / Flavodoxin/nitric oxide synthase / Oxidoreductase FAD/NAD(P)-binding / Oxidoreductase NAD-binding domain / FAD-binding domain, ferredoxin reductase-type / Ferredoxin-NADP reductase (FNR), nucleotide-binding domain / Ferredoxin reductase-type FAD binding domain profile. / Riboflavin synthase-like beta-barrel / Cytochrome P450, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / Flavoprotein-like superfamily / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Bifunctional cytochrome P450/NADPH--P450 reductase
Similarity search - Component
Biological speciesBacillus megaterium (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsRavichandran, 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
DepositionSep 16, 1993Processing site: BNL
Revision 1.0Oct 31, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _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.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 / _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 BM-3
B: CYTOCHROME P450 BM-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,8264
Polymers107,5932
Non-polymers1,2332
Water8,197455
1
A: CYTOCHROME P450 BM-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,4132
Polymers53,7961
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: CYTOCHROME P450 BM-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,4132
Polymers53,7961
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.400, 154.000, 62.200
Angle α, β, γ (deg.)90.00, 94.70, 90.00
Int Tables number4
Space group name H-MP1211
Atom site foot note1: 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:
IDCodeMatrixVector
1given(0.9996, 0.0166, 0.0211), (0.0081, -0.9344, 0.3562), (0.0257, -0.3559, -0.9342)-23.7, 39.9, 21.2
2given(0.9996, 0.0081, 0.0257), (0.0167, -0.9344, -0.3559), (0.0211, 0.3562, -0.9342)22.8, 45.2, 6.18
DetailsTHE 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.

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Components

#1: Protein CYTOCHROME P450 BM-3


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 ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 455 / 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: 2.63 Å3/Da / Density % sol: 53.3 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.4 / Method: vapor diffusion, hanging drop
Details: Boddupalli, S.S., (1992) Proc.Nat.Acad.Sci.USA, 89, 5567.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
15 mMprotein1dropabout 275mg/ml
250 mMpotassium phosphate1drop
3100 mMPIPES1reservoir
420 %(w/v)PEG80001reservoir
515 mMdithiothreitol1reservoir
640 mM1reservoirMgSO4

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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
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 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 stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7358 0 88 453 7899
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.016
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg3.1
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
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

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