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- PDB-1xdi: Crystal structure of LpdA (Rv3303c) from Mycobacterium tuberculosis -

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Basic information

Entry
Database: PDB / ID: 1xdi
TitleCrystal structure of LpdA (Rv3303c) from Mycobacterium tuberculosis
ComponentsRv3303c-lpdA
KeywordsUNKNOWN FUNCTION / Mycobacterium tuberculosis / reductase / FAD / NAD / NADP
Function / homology
Function and homology information


NADPH dehydrogenase (quinone) activity / NAD(P)H dehydrogenase (quinone) / NADH:ubiquinone reductase (non-electrogenic) activity / NAD(P)H dehydrogenase (quinone) activity / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / NADP+ binding / : / cell redox homeostasis / flavin adenine dinucleotide binding
Similarity search - Function
Tryptophan halogenase / Pyridine nucleotide-disulphide oxidoreductase / Pyridine nucleotide-disulphide oxidoreductase, class I / FAD/NAD-linked reductase, C-terminal dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / FAD/NAD-linked reductase, dimerisation domain superfamily / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / Enolase-like; domain 1 ...Tryptophan halogenase / Pyridine nucleotide-disulphide oxidoreductase / Pyridine nucleotide-disulphide oxidoreductase, class I / FAD/NAD-linked reductase, C-terminal dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / FAD/NAD-linked reductase, dimerisation domain superfamily / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / Enolase-like; domain 1 / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / NAD(P)H dehydrogenase (quinone) / NAD(P)H dehydrogenase (quinone)
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2.81 Å
AuthorsArgyrou, A. / Vetting, M.W. / Blanchard, J.S.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Characterization of a New Member of the Flavoprotein Disulfide Reductase Family of Enzymes from Mycobacterium tuberculosis
Authors: Argyrou, A. / Vetting, M.W. / Blanchard, J.S.
History
DepositionSep 6, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 19, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / 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 / 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

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Assembly

Deposited unit
A: Rv3303c-lpdA
B: Rv3303c-lpdA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,3144
Polymers104,7432
Non-polymers1,5712
Water1,928107
1
A: Rv3303c-lpdA
B: Rv3303c-lpdA
hetero molecules

A: Rv3303c-lpdA
B: Rv3303c-lpdA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)212,6298
Polymers209,4874
Non-polymers3,1424
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10020 Å2
ΔGint-67 kcal/mol
Surface area34140 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)244.200, 244.200, 104.800
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
DetailsThe biological assymbly is a tetramer generated from the dimer in the assymetric unit by the operation: y,x,-z

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Components

#1: Protein Rv3303c-lpdA


Mass: 52371.652 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: Rv3303c - lpdA / Plasmid: pET23a(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O53355, UniProt: P9WHH7*PLUS
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / 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: 2.92 Å3/Da / Density % sol: 58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: Peg 6000, Tri-sodium Citrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 22, 2003 / Details: Osmic Blue Optics
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. all: 29136 / Num. obs: 29136 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.6 % / Biso Wilson estimate: 35 Å2 / Rmerge(I) obs: 0.102 / Rsym value: 0.102 / Net I/σ(I): 18.3
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.249 / Mean I/σ(I) obs: 5.1 / Num. unique all: 2896 / Rsym value: 0.249 / % possible all: 99.7

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNS1refinement
RefinementMethod to determine structure: MIR / Resolution: 2.81→50 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2763 1431 -random
Rwork0.1944 ---
all0.1944 29120 --
obs0.1944 29120 98.9 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.315 Å2-8.832 Å20 Å2
2--2.315 Å20 Å2
3----4.63 Å2
Refinement stepCycle: LAST / Resolution: 2.81→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6712 0 106 107 6925
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0193
X-RAY DIFFRACTIONc_angle_deg2.22
LS refinement shellResolution: 2.81→2.93 Å
RfactorNum. reflection% reflection
Rfree0.3043 173 -
Rwork0.226 --
obs-3386 99.7 %

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