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- PDB-1t0i: YLR011wp, a Saccharomyces cerevisiae NA(D)PH-dependent FMN reductase -

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Basic information

Entry
Database: PDB / ID: 1t0i
TitleYLR011wp, a Saccharomyces cerevisiae NA(D)PH-dependent FMN reductase
ComponentsYLR011wp
KeywordsOXIDOREDUCTASE / Saccharomyces cerevisiae / FMN binding protein / Flavodoxin / Azoreductase
Function / homology
Function and homology information


cytoplasmic sequestering of transcription factor / FMN reductase [NAD(P)H] / FMN reductase (NADH) activity / FMN reductase (NADPH) activity / NAD(P)H dehydrogenase (quinone) activity / transcription factor binding / FMN binding / cellular response to oxidative stress / apoptotic process / nucleus ...cytoplasmic sequestering of transcription factor / FMN reductase [NAD(P)H] / FMN reductase (NADH) activity / FMN reductase (NADPH) activity / NAD(P)H dehydrogenase (quinone) activity / transcription factor binding / FMN binding / cellular response to oxidative stress / apoptotic process / nucleus / cytosol / cytoplasm
Similarity search - Function
NADPH-dependent FMN reductase-like / NADPH-dependent FMN reductase / Flavodoxin domain / Flavoprotein-like superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / NAD(P)H-dependent FMN reductase LOT6
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsLiger, D. / Graille, M. / Zhou, C.-Z. / Leulliot, N. / Quevillon-Cheruel, S. / Blondeau, K. / Janin, J. / van Tilbeurgh, H.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Crystal Structure and Functional Characterization of Yeast YLR011wp, an Enzyme with NAD(P)H-FMN and Ferric Iron Reductase Activities
Authors: Liger, D. / Graille, M. / Zhou, C.-Z. / Leulliot, N. / Quevillon-Cheruel, S. / Blondeau, K. / Janin, J. / Van Tilbeurgh, H.
History
DepositionApr 9, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 22, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: 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: YLR011wp
B: YLR011wp
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,6046
Polymers42,6112
Non-polymers9934
Water1,946108
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4550 Å2
ΔGint-29 kcal/mol
Surface area15120 Å2
MethodPISA
2
A: YLR011wp
B: YLR011wp
hetero molecules

A: YLR011wp
B: YLR011wp
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,20812
Polymers85,2224
Non-polymers1,9868
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_675-x+1,-y+2,z1
Buried area11300 Å2
ΔGint-95 kcal/mol
Surface area28280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.801, 109.957, 49.951
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-201-

CA

DetailsThe biological assembly is the homodimer present in the asymmetric unit.

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Components

#1: Protein YLR011wp


Mass: 21305.557 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: YLR011w / Plasmid: pet 9 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / References: UniProt: Q07923
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 108 / 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: 2.06 Å3/Da / Density % sol: 40 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 10% PEG 3000, 30% PEG 400, 0.1M Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.979678 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 9, 2003
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979678 Å / Relative weight: 1
ReflectionResolution: 1.9→35 Å / Num. obs: 27164 / % possible obs: 96.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.35 % / Biso Wilson estimate: 40 Å2 / Rsym value: 0.063 / Net I/σ(I): 21.9
Reflection shellResolution: 1.9→1.94 Å / % possible all: 95.5

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2→10 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.933 / SU B: 5.432 / SU ML: 0.151 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.223 / ESU R Free: 0.193 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25436 1156 5 %RANDOM
Rwork0.19894 ---
all0.258 23174 --
obs0.20175 22018 97.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 40.579 Å2
Baniso -1Baniso -2Baniso -3
1--1.14 Å20 Å20 Å2
2---1.61 Å20 Å2
3---2.75 Å2
Refinement stepCycle: LAST / Resolution: 2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2823 0 64 108 2995
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0212944
X-RAY DIFFRACTIONr_bond_other_d0.0010.022719
X-RAY DIFFRACTIONr_angle_refined_deg0.7431.9894014
X-RAY DIFFRACTIONr_angle_other_deg0.93236349
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.225359
X-RAY DIFFRACTIONr_chiral_restr0.1320.2461
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.023177
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02503
X-RAY DIFFRACTIONr_nbd_refined0.230.3712
X-RAY DIFFRACTIONr_nbd_other0.2730.33182
X-RAY DIFFRACTIONr_nbtor_other0.1010.51706
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2170.5212
X-RAY DIFFRACTIONr_metal_ion_refined0.0780.53
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3480.316
X-RAY DIFFRACTIONr_symmetry_vdw_other0.350.335
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2390.513
X-RAY DIFFRACTIONr_mcbond_it2.16221803
X-RAY DIFFRACTIONr_mcangle_it3.28832932
X-RAY DIFFRACTIONr_scbond_it2.09621141
X-RAY DIFFRACTIONr_scangle_it3.19431082
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.278 73
Rwork0.239 1530

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