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- PDB-1jpz: Crystal structure of a complex of the heme domain of P450BM-3 wit... -

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Basic information

Entry
Database: PDB / ID: 1jpz
TitleCrystal structure of a complex of the heme domain of P450BM-3 with N-Palmitoylglycine
ComponentsBIFUNCTIONAL P-450:NADPH-P450 REDUCTASE
KeywordsOXIDOREDUCTASE / Protein-substrate complex / hemeprotein
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 / response to hormone / FMN binding / flavin adenine dinucleotide binding / iron ion 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 / metabolic process / response to hormone / FMN binding / flavin adenine dinucleotide binding / iron ion binding / heme binding / identical protein binding / cytosol
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
N-PALMITOYLGLYCINE / PROTOPORPHYRIN IX CONTAINING FE / Bifunctional cytochrome P450/NADPH--P450 reductase
Similarity search - Component
Biological speciesBacillus megaterium (bacteria)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.65 Å
AuthorsHaines, D.C. / Tomchick, D.R. / Machius, M. / Peterson, J.A.
Citation
Journal: Biochemistry / Year: 2001
Title: Pivotal role of water in the mechanism of P450BM-3.
Authors: Haines, D.C. / Tomchick, D.R. / Machius, M. / Peterson, J.A.
#1: 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.
#2: 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.
#3: Journal: Proc.Natl.Acad.Sci.USA / Year: 1999
Title: Structure of a cytochrome P450-redox partner electron-transfer complex
Authors: Sevrioukova, I.F. / Li, H. / Zang, H. / Peterson, J.A. / Poulos, T.L.
History
DepositionAug 3, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2001Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 2023Group: 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 / pdbx_initial_refinement_model / 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

Downloads & links

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Assembly

Deposited unit
A: BIFUNCTIONAL P-450:NADPH-P450 REDUCTASE
B: BIFUNCTIONAL P-450:NADPH-P450 REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,6576
Polymers107,7972
Non-polymers1,8604
Water17,204955
1
A: BIFUNCTIONAL P-450:NADPH-P450 REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,8283
Polymers53,8981
Non-polymers9302
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: BIFUNCTIONAL P-450:NADPH-P450 REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,8283
Polymers53,8981
Non-polymers9302
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.190, 148.356, 64.134
Angle α, β, γ (deg.)90.00, 98.82, 90.00
Int Tables number4
Cell settingmonoclinic
Space group name H-MP1211

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Components

#1: Protein BIFUNCTIONAL P-450:NADPH-P450 REDUCTASE / E.C.1.14.14.1 / P450BM-3 / CYTOCHROME P450(BM-3) [INCLUDES: CYTOCHROME P450 102 / NADPH-CYTOCHROME P450 REDUCTASE / ...P450BM-3 / CYTOCHROME P450(BM-3) [INCLUDES: CYTOCHROME P450 102 / NADPH-CYTOCHROME P450 REDUCTASE / cytochrome P450 BM-3/NADPH--ferrihemoprotein reductase / cytochrome P-450:NADPH-P-450 reductase


Mass: 53898.422 Da / Num. of mol.: 2 / Fragment: CYTOCHROME P450 102 DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus megaterium (bacteria) / Plasmid: pProEx-1 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5(alpha)F'IQ / References: UniProt: P14779, unspecific monooxygenase
#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-140 / N-PALMITOYLGLYCINE / N-HEXADECANOYLGLYCINE


Mass: 313.475 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H35NO3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 955 / Source method: isolated from a natural source / Formula: H2O

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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: 2.8 Å3/Da / Density % sol: 55 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 6% PEG 3350, 25 mM potassium phosphate, 50 mM magnesium chloride, 50 mM Morpholinoethanesulfonic acid pH 6.0, VAPOR DIFFUSION, HANGING DROP at 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
112 %(w/v)PEG33501reservoir
2150 mM1reservoirMgCl2
3100 mMMES1reservoir
412.5 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 31, 2000
RadiationMonochromator: OSMIC MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.65→30 Å / Num. all: 259395 / Num. obs: 218743 / % possible obs: 84.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.2 % / Biso Wilson estimate: 26.6 Å2 / Rmerge(I) obs: 0.031 / Net I/σ(I): 23.1
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.284 / Mean I/σ(I) obs: 1.9 / Num. unique all: 4962 / % possible all: 38.3
Reflection
*PLUS
Lowest resolution: 30 Å
Reflection shell
*PLUS
% possible obs: 38.3 %

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 1FAG

1fag


Resolution: 1.65→30 Å / Isotropic thermal model: ANISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER
Details: THE PHI, PSI TORSION ANGLES OF LEUCINE 437 IN BOTH MONOMERS FALL IN THE DISALLOWED REGIONS, BUT THE DENSITY FOR THESE RESIDUES IS QUITE CLEAR. THEY OCCUR IN A TIGHT TURN NEAR THE SUBSTRATE BINDING CAVITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.193 10378 4.7 %RANDOM
Rwork0.177 ---
all0.178 259395 --
obs0.178 218743 84.3 %-
Solvent computationBsol: 49.7 Å2 / ksol: 0.369 e/Å3
Displacement parametersBiso mean: 25.4 Å2
Baniso -1Baniso -2Baniso -3
1-3.88 Å20 Å2-0.38 Å2
2--0.184 Å20 Å2
3----4.07 Å2
Refine analyzeLuzzati coordinate error obs: 0.23 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.15 Å
Refinement stepCycle: LAST / Resolution: 1.65→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7440 0 130 955 8525
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.52
X-RAY DIFFRACTIONc_dihedral_angle_d21.3
X-RAY DIFFRACTIONc_improper_angle_d1.02
X-RAY DIFFRACTIONc_mcbond_it1.53
X-RAY DIFFRACTIONc_mcangle_it2.04
X-RAY DIFFRACTIONc_scbond_it2.59
X-RAY DIFFRACTIONc_scangle_it3.6
LS refinement shellResolution: 1.65→1.71 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.474 501 1.94 %
Rwork0.439 --
all-11319 -
obs-10818 44 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3LIGANDS.PARAMLIGANDS.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 30 Å / σ(F): 0 / % reflection Rfree: 4.7 % / Rfactor obs: 0.177
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 25.4 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.02
LS refinement shell
*PLUS
Rfactor Rfree: 0.474 / Rfactor Rwork: 0.439

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