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- PDB-1fag: STRUCTURE OF CYTOCHROME P450 -

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Basic information

Entry
Database: PDB / ID: 1fag
TitleSTRUCTURE OF CYTOCHROME P450
ComponentsCYTOCHROME P450 BM-3
KeywordsELECTRON TRANSPORT / MONOOXYGENASE / HEME
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 / PALMITOLEIC ACID / Bifunctional cytochrome P450/NADPH--P450 reductase
Similarity search - Component
Biological speciesBacillus megaterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsLi, H.Y. / Poulos, T.L.
Citation
Journal: Nat.Struct.Biol. / Year: 1997
Title: The structure of the cytochrome p450BM-3 haem domain complexed with the fatty acid substrate, palmitoleic acid.
Authors: Li, H. / Poulos, T.L.
#1: Journal: To be Published
Title: Comformational Dynamics in Cytochrome P450-Substrate Interactions
Authors: Li, H.Y. / Poulos, T.L.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 1995
Title: Modeling Protein-Substrate Interactions in the Heme Domain of Cytochrome P450Bm-3
Authors: Li, H.Y. / Poulos, T.L.
#3: 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. / Hasemann, C.A. / Peterson, J.A. / Deisenhofer, J.
History
DepositionAug 1, 1996Processing site: BNL
Revision 1.0Feb 12, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / software / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name / _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_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
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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
C: CYTOCHROME P450 BM-3
D: CYTOCHROME P450 BM-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)218,66912
Polymers215,1854
Non-polymers3,4848
Water0
1
A: CYTOCHROME P450 BM-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,6673
Polymers53,7961
Non-polymers8712
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: CYTOCHROME P450 BM-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,6673
Polymers53,7961
Non-polymers8712
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: CYTOCHROME P450 BM-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,6673
Polymers53,7961
Non-polymers8712
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: CYTOCHROME P450 BM-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,6673
Polymers53,7961
Non-polymers8712
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)106.200, 165.200, 223.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.736383, 0.000575, -0.676565), (-0.015594, -0.99972, -0.017822), (-0.676386, 0.023674, -0.736167)157.8562, -32.3265, 133.2411
2given(-0.917437, 0.327136, 0.226477), (0.338133, 0.341034, 0.877133), (0.209705, 0.881293, -0.423493)125.7098, -95.4045, 97.5033
3given(-0.838017, -0.356511, 0.41307), (-0.298673, -0.333839, -0.894062), (0.456642, -0.872612, 0.173283)189.3315, 58.3471, -23.694

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Components

#1: Protein
CYTOCHROME P450 BM-3 / P450 102 / FATTY ACID HYDROXYLASE


Mass: 53796.293 Da / Num. of mol.: 4 / Fragment: HEME DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus megaterium (bacteria) / Strain: 14581 / Production host: Escherichia coli (E. coli) / References: UniProt: P14779, unspecific monooxygenase
#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical
ChemComp-PAM / PALMITOLEIC ACID / Palmitoleic acid


Mass: 254.408 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H30O2

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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: 2.28 Å3/Da / Density % sol: 46 %
Crystal growpH: 6 / Details: SEE REFERENCE 1, pH 6.0
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
17.5-9 mg/mlprotein1drop
20.05 %(v/v)palmitoleic1drop
39 %PEG33501drop
480 mM1dropMgCl2
550 mMMES1drop
618 %PEG33501reservoir
7160 mM1reservoirMgCl2
8100 mMMES1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.008
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 16, 1996
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.008 Å / Relative weight: 1
ReflectionResolution: 2.6→48.8 Å / Num. obs: 60630 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 7 % / Rmerge(I) obs: 0.071 / Rsym value: 0.071 / Net I/σ(I): 8.3
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 1.4 / Rsym value: 0.5 / % possible all: 97

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.1refinement
DENZOdata reduction
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
TRUNCATEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: SUBSTRATE-FREE P450BM-3 HEME DOMAIN

Resolution: 2.7→10 Å / σ(F): 2
Details: THE F/G AND G/H LOOP REGIONS IN FOUR MOLECULES SHOWED QUITE DIFFERENT CONFORMATIONS. A FEW RESIDUES IN THESE SURFACE LOOP REGIONS ARE NOT WELL DEFINED IN THE STRUCTURE WITH RATHER HIGH B ...Details: THE F/G AND G/H LOOP REGIONS IN FOUR MOLECULES SHOWED QUITE DIFFERENT CONFORMATIONS. A FEW RESIDUES IN THESE SURFACE LOOP REGIONS ARE NOT WELL DEFINED IN THE STRUCTURE WITH RATHER HIGH B FACTORS, E.G. GLU 228 IN MOLECULES A AND C, GLN 229 IN MOLECULE D, ASP 195 IN MOLECULE C. THE PHI, PSI TORTION ANGLES OF LEUCINE 437 IN ALL FOUR MOLECULES FALL IN THE DISALLOWED REGION, BUT THE ODD CONFORMER MIGHT RESULT FROM THE NON-BONDING INTERACTION BETWEEN THE SUBSTRATE AND ENZYME.
RfactorNum. reflection% reflection
Rfree0.353 -10 %
Rwork0.246 --
obs0.246 52300 98.38 %
Refine analyzeLuzzati coordinate error obs: 0.4 Å
Refinement stepCycle: LAST / Resolution: 2.7→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14684 0 244 0 14928
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
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_deg1.496
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d22.97
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.5
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
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg22.976
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.5

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