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- PDB-1qfj: CRYSTAL STRUCTURE OF NAD(P)H:FLAVIN OXIDOREDUCTASE FROM ESCHERICH... -

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Basic information

Entry
Database: PDB / ID: 1qfj
TitleCRYSTAL STRUCTURE OF NAD(P)H:FLAVIN OXIDOREDUCTASE FROM ESCHERICHIA COLI
ComponentsPROTEIN (FLAVIN REDUCTASE)
KeywordsOXIDOREDUCTASE / RIBOFLAVIN / FLAVIN REDUCTASE / FERREDOXIN REDUCTASE SUPERFAMILY
Function / homology
Function and homology information


riboflavin reductase [NAD(P)H] / riboflavin reductase [NAD(P)H] activity / : / riboflavin reductase (NADPH) activity / protein repair / monoatomic ion transport / iron ion transport / enzyme activator activity / response to oxidative stress / cytosol
Similarity search - Function
Flavoprotein pyridine nucleotide cytochrome reductase-like, FAD-binding domain / Oxidoreductase FAD-binding domain / Nucleotide-binding domain of ferredoxin-NADP reductase (FNR) module / Translation factors / Elongation Factor Tu (Ef-tu); domain 3 / 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. ...Flavoprotein pyridine nucleotide cytochrome reductase-like, FAD-binding domain / Oxidoreductase FAD-binding domain / Nucleotide-binding domain of ferredoxin-NADP reductase (FNR) module / Translation factors / Elongation Factor Tu (Ef-tu); domain 3 / 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 / Beta Barrel / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
NAD(P)H-flavin reductase / NAD(P)H-flavin reductase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsIngelman, M. / Ramaswamy, S. / Niviere, V. / Fontecave, M. / Eklund, H.
CitationJournal: Biochemistry / Year: 1999
Title: Crystal structure of NAD(P)H:flavin oxidoreductase from Escherichia coli.
Authors: Ingelman, M. / Ramaswamy, S. / Niviere, V. / Fontecave, M. / Eklund, H.
History
DepositionApr 12, 1999Deposition site: PDBE / Processing site: RCSB
Revision 1.0Jun 1, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (FLAVIN REDUCTASE)
B: PROTEIN (FLAVIN REDUCTASE)
C: PROTEIN (FLAVIN REDUCTASE)
D: PROTEIN (FLAVIN REDUCTASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,9448
Polymers104,5754
Non-polymers3684
Water5,477304
1
A: PROTEIN (FLAVIN REDUCTASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2362
Polymers26,1441
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PROTEIN (FLAVIN REDUCTASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2362
Polymers26,1441
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: PROTEIN (FLAVIN REDUCTASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2362
Polymers26,1441
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: PROTEIN (FLAVIN REDUCTASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2362
Polymers26,1441
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.200, 96.920, 210.410
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.93394, -0.25934, 0.24595), (-0.25926, -0.96523, -0.03331), (0.246047, -0.03265, -0.9687)-6.86784, 119.95302, 181.00014
2given(0.2874, 0.95283, 0.09745), (-0.92435, 0.30258, -0.2324), (-0.25093, -0.02329, 0.96772)101.64164, -8.0036, 65.1351
3given(0.41069, 0.84529, 0.34177), (0.84839, -0.49159, 0.19636), (0.33399, 0.209315, -0.919)-55.87328, 17.66156, 213.32475

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Components

#1: Protein
PROTEIN (FLAVIN REDUCTASE)


Mass: 26143.791 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: DISULFIDE LINKS BETWEEN MOLECULES A AND D AS WELL AS B AND C RESPECTIVELY
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: JM109 / Cell: BACTERIAL / Cellular location: CYTOPLASM / Gene: FRE / Plasmid: PEE1001 / Cellular location (production host): CYTOPLASM / Gene (production host): FRE / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P23486, UniProt: P0AEN1*PLUS
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 304 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.7 Å3/Da / Density % sol: 51 %
Crystal growpH: 6.5
Details: 15 % PEG 4000, 0.5 M NACL, 100 MM BIS-TRIS PROPANE PH 6.5
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
115 mg/mlprotein1drop
215-20 %PEG40001reservoir
30.5 M1reservoirNaCl
4100 mMbis-tris-propane1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.864
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 1, 1995
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.864 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. all: 54692 / Num. obs: 54692 / % possible obs: 93.2 % / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 9.3
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 6 % / Rmerge(I) obs: 0.235 / Mean I/σ(I) obs: 3.9 / % possible all: 88.2
Reflection
*PLUS
Num. measured all: 626153
Reflection shell
*PLUS
% possible obs: 88.2 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
REFMACrefinement
RefinementMethod to determine structure: MAD / Resolution: 2.2→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.29 1569 10 %RANDOM
Rwork0.239 ---
all0.239 54241 --
obs0.239 54241 93 %-
Displacement parametersBiso mean: 35.4 Å2
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7176 0 24 304 7504
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0070.02
X-RAY DIFFRACTIONp_angle_d0.0270.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0270.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it2.6153
X-RAY DIFFRACTIONp_mcangle_it4.585
X-RAY DIFFRACTIONp_scbond_it4.486
X-RAY DIFFRACTIONp_scangle_it6.0528
X-RAY DIFFRACTIONp_plane_restr0.01840.03
X-RAY DIFFRACTIONp_chiral_restr0.0970.15
X-RAY DIFFRACTIONp_singtor_nbd0.1890.3
X-RAY DIFFRACTIONp_multtor_nbd0.2420.3
X-RAY DIFFRACTIONp_xhyhbond_nbd00.3
X-RAY DIFFRACTIONp_xyhbond_nbd0.1790.3
X-RAY DIFFRACTIONp_planar_tor3.27
X-RAY DIFFRACTIONp_staggered_tor21.515
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor3620
X-RAY DIFFRACTIONp_special_tor15
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS

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