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- PDB-1bvy: COMPLEX OF THE HEME AND FMN-BINDING DOMAINS OF THE CYTOCHROME P45... -

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Basic information

Entry
Database: PDB / ID: 1bvy
TitleCOMPLEX OF THE HEME AND FMN-BINDING DOMAINS OF THE CYTOCHROME P450(BM-3)
Components(PROTEIN (CYTOCHROME P450 BM- ...) x 2
KeywordsOXIDOREDUCTASE / FATTY ACID MONOOXYGENASE / HEMOPROTEIN / FLAVOPROTEIN / ELECTRON TRANSFER
Function / homology
Function and homology information


aromatase activity / 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 / 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 / Flavodoxin domain / Sulfite reductase [NADPH] flavoprotein alpha-component-like, FAD-binding / NADPH-cytochrome p450 reductase, FAD-binding, alpha-helical domain superfamily / FAD binding domain / Cytochrome p450 / Cytochrome P450 / Flavodoxin-like / Flavoprotein pyridine nucleotide cytochrome reductase / Flavodoxin ...Bifunctional cytochrome P450/NADPH--cytochrome P450 reductase / Flavodoxin domain / Sulfite reductase [NADPH] flavoprotein alpha-component-like, FAD-binding / NADPH-cytochrome p450 reductase, FAD-binding, alpha-helical domain superfamily / FAD binding domain / Cytochrome p450 / Cytochrome P450 / 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 / Cytochrome P450, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / 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 / Flavoprotein-like superfamily / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450 / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / PROTOPORPHYRIN IX CONTAINING FE / Bifunctional cytochrome P450/NADPH--P450 reductase
Similarity search - Component
Biological speciesBacillus megaterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 Å
AuthorsSevrioukova, I.F. / Li, H. / Zhang, H. / Peterson, J.A. / Poulos, T.L.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 1999
Title: Structure of a cytochrome P450-redox partner electron-transfer complex.
Authors: Sevrioukova, I.F. / Li, H. / Zhang, H. / Peterson, J.A. / Poulos, T.L.
History
DepositionSep 21, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Feb 23, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 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 / 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_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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (CYTOCHROME P450 BM-3)
F: PROTEIN (CYTOCHROME P450 BM-3)
B: PROTEIN (CYTOCHROME P450 BM-3)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,59411
Polymers125,5943
Non-polymers2,0008
Water17,060947
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.840, 94.680, 209.060
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.999966, -0.006037, 0.005567), (-0.004931, 0.983495, 0.18087), (-0.006567, 0.180836, -0.983491)
Vector: 18.3505, -18.3681, 202.85629)

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Components

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PROTEIN (CYTOCHROME P450 BM- ... , 2 types, 3 molecules ABF

#1: Protein PROTEIN (CYTOCHROME P450 BM-3)


Mass: 52396.723 Da / Num. of mol.: 2 / Fragment: HEME-BINDING DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus megaterium (bacteria) / Description: SYNTHETIC GENE; / Plasmid: PPROEX / Cell line (production host): DH5AF'IQ / Production host: Escherichia coli (E. coli) / References: UniProt: P14779, unspecific monooxygenase
#2: Protein PROTEIN (CYTOCHROME P450 BM-3)


Mass: 20800.676 Da / Num. of mol.: 1 / Fragment: FMN-BINDING DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus megaterium (bacteria) / Description: SYNTHETIC GENE / Plasmid: PPROEX / Cell line (production host): DH5AF'IQ / Production host: Escherichia coli (E. coli) / References: UniProt: P14779, unspecific monooxygenase

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Non-polymers , 4 types, 955 molecules

#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 947 / 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: 2.24 Å3/Da / Density % sol: 45 %
Crystal growpH: 6.8
Details: LIQUID-LIQUID FREE INTERFACE DIFFUSION AT ROOM TEMPERATURE IN PEG 8000, PIPES PH 6.8, NH4CL.
Crystal
*PLUS
Crystal grow
*PLUS
Method: free interface diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.450 mMprotein11
250 mMpotassium phosphate11
340 %PEG800012
4100 mMPIPES12
5200 mM12NH4Cl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 15, 1998 / Details: YES
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2.03→50 Å / Num. obs: 63363 / % possible obs: 83 % / Redundancy: 2.7 % / Rsym value: 0.046 / Net I/σ(I): 14.4
Reflection shellResolution: 2.03→2.07 Å / Redundancy: 2.1 % / Mean I/σ(I) obs: 3 / Rsym value: 0.4 / % possible all: 69.9
Reflection
*PLUS
% possible obs: 83 % / Rmerge(I) obs: 0.046

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Processing

Software
NameClassification
AMoREphasing
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: MOLECULE A OF P450(BM3) HEME DOMAIN AND FALVODOXIN(PDB ENDRY 3FX2)

3fx2


Resolution: 2.03→10 Å / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.2754 4412 5 %RANDOM
obs0.1872 -83 %-
all-62655 --
Refinement stepCycle: LAST / Resolution: 2.03→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8240 0 137 947 9324
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.006
X-RAY DIFFRACTIONs_angle_d0.02
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes
X-RAY DIFFRACTIONs_zero_chiral_vol
X-RAY DIFFRACTIONs_non_zero_chiral_vol
X-RAY DIFFRACTIONs_anti_bump_dis_restr
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt
X-RAY DIFFRACTIONs_approx_iso_adps
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 10 Å / Num. reflection obs: 58243 / σ(F): 0 / % reflection Rfree: 5 % / Rfactor Rwork: 0.187
Solvent computation
*PLUS
Displacement parameters
*PLUS

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