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- PDB-1b1c: CRYSTAL STRUCTURE OF THE FMN-BINDING DOMAIN OF HUMAN CYTOCHROME P... -

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Basic information

Entry
Database: PDB / ID: 1b1c
TitleCRYSTAL STRUCTURE OF THE FMN-BINDING DOMAIN OF HUMAN CYTOCHROME P450 REDUCTASE AT 1.93A RESOLUTION
ComponentsPROTEIN (NADPH-CYTOCHROME P450 REDUCTASE)
KeywordsOXIDOREDUCTASE / FLAVOPROTEIN / CYTOCHROME P450 REDUCTASE / P450 REDUCTASE / FMN-BINDING DOMAIN / FMN
Function / homology
Function and homology information


Cytochrome P450 - arranged by substrate type / flavonoid metabolic process / iron-cytochrome-c reductase activity / positive regulation of growth plate cartilage chondrocyte proliferation / positive regulation of steroid hormone biosynthetic process / nitrate catabolic process / demethylation / organofluorine metabolic process / carnitine metabolic process / nitric oxide dioxygenase [NAD(P)H] activity ...Cytochrome P450 - arranged by substrate type / flavonoid metabolic process / iron-cytochrome-c reductase activity / positive regulation of growth plate cartilage chondrocyte proliferation / positive regulation of steroid hormone biosynthetic process / nitrate catabolic process / demethylation / organofluorine metabolic process / carnitine metabolic process / nitric oxide dioxygenase [NAD(P)H] activity / nitric oxide catabolic process / cytochrome-b5 reductase activity, acting on NAD(P)H / P450-containing electron transport chain / positive regulation of chondrocyte differentiation / cellular response to follicle-stimulating hormone stimulus / NADPH-hemoprotein reductase / NADPH-hemoprotein reductase activity / positive regulation of smoothened signaling pathway / cellular response to peptide hormone stimulus / response to dexamethasone / fatty acid oxidation / intracellular membrane-bounded organelle / nitric oxide biosynthetic process / response to hormone / response to nutrient / electron transport chain / enzyme activator activity / NADP binding / FMN binding / flavin adenine dinucleotide binding / electron transfer activity / response to xenobiotic stimulus / hydrolase activity / endoplasmic reticulum membrane / negative regulation of apoptotic process / enzyme binding / membrane / cytosol
Similarity search - Function
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 / Flavodoxin-like / Flavoprotein pyridine nucleotide cytochrome reductase / Flavodoxin / Flavodoxin-like domain profile. / Flavodoxin/nitric oxide synthase ...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 / 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 / Flavoprotein-like superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / NADPH--cytochrome P450 reductase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MIRAS / Resolution: 1.93 Å
AuthorsZhao, Q. / Modi, S. / Smith, G. / Paine, M. / Mcdonagh, P.D. / Wolf, C.R. / Tew, D. / Lian, L.-Y. / Roberts, G.C.K. / Driessen, H.P.C.
Citation
Journal: Protein Sci. / Year: 1999
Title: Crystal structure of the FMN-binding domain of human cytochrome P450 reductase at 1.93 A resolution.
Authors: Zhao, Q. / Modi, S. / Smith, G. / Paine, M. / McDonagh, P.D. / Wolf, C.R. / Tew, D. / Lian, L.Y. / Roberts, G.C. / Driessen, H.P.
#1: Journal: J.Struct.Biol. / Year: 1996
Title: Crystallization and Preliminary X-Ray Diffraction Studies of Human Cytochrome P450 Reductase
Authors: Zhao, Q. / Smith, G. / Modi, S. / Paine, M. / Wolf, R.C. / Tew, D. / Lian, L.Y. / Primrose, W.U. / Roberts, G.C. / Driessen, H.P.
History
DepositionNov 19, 1998Deposition site: PDBE / Processing site: RCSB
Revision 1.0Nov 24, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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.ptnr1_symmetry / _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.ptnr3_symmetry / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _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: PROTEIN (NADPH-CYTOCHROME P450 REDUCTASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,8773
Polymers20,3801
Non-polymers4962
Water1,09961
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.310, 51.440, 47.600
Angle α, β, γ (deg.)90.00, 105.93, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein PROTEIN (NADPH-CYTOCHROME P450 REDUCTASE) / P450R-FMN


Mass: 20380.314 Da / Num. of mol.: 1 / Fragment: FMN-BINDING DOMAIN / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Plasmid: PMP CLONED INTO PET15B / References: UniProt: P16435, NADPH-hemoprotein reductase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


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


Mass: 18.015 Da / Num. of mol.: 61 / 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: 2.27 Å3/Da / Density % sol: 45.82 %
Crystal growpH: 7
Details: 18-20% (W/V) PEG400, 100 MM HEPES (PH6.8-7.2), 200 MM CACL2 4 DEGREES C, pH 7.0
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: batch method / Details: Zhao, Q., (1996) J.Struct.Biol., 116, 320. / PH range low: 7.2 / PH range high: 6.8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
118-20 %(w/v)PEG40011
2100 mMHEPES11
3200 mM11CaCl2

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.93→19.45 Å / Num. obs: 13289 / % possible obs: 89.2 % / Observed criterion σ(I): 3 / Redundancy: 3.9 % / Rmerge(I) obs: 0.082
Reflection shellHighest resolution: 1.93 Å / Rmerge(I) obs: 0.193 / % possible all: 72.9

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Processing

Software
NameVersionClassification
RSPSmodel building
VECREFmodel building
X-PLOR3.1refinement
DENZOdata reduction
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
TRUNCATEdata scaling
RSPSphasing
VECREFphasing
RefinementMethod to determine structure: MIRAS / Resolution: 1.93→19.45 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT, EXCEPT LAST 2 PASSES / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.243 -5 %RANDOM
Rwork0.1973 ---
obs-13282 89.2 %-
Refine analyzeLuzzati coordinate error obs: 0.22 Å
Refinement stepCycle: LAST / Resolution: 1.93→19.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1326 0 32 61 1419
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
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_deg1.45
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.3
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.35
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
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.1973
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.3
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.35

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