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- PDB-1qpq: Structure of Quinolinic Acid Phosphoribosyltransferase from Mycob... -

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Basic information

Entry
Database: PDB / ID: 1qpq
TitleStructure of Quinolinic Acid Phosphoribosyltransferase from Mycobacterium Tuberculosis: A Potential TB Drug Target
ComponentsQUINOLINATE PHOSPHORIBOSYLTRANSFERASE
KeywordsTRANSFERASE / TYPE II PRTASE / DE NOVO NAD BIOSYNTHESIS / PRPP / PHOSPHORIBOSYL TRANSFERASE / QUINOLINIC ACID / Structural Genomics / PSI / Protein Structure Initiative / TB Structural Genomics Consortium / TBSGC
Function / homology
Function and homology information


quinolinate catabolic process / nicotinate-nucleotide diphosphorylase (carboxylating) / nicotinate-nucleotide diphosphorylase (carboxylating) activity / NAD biosynthetic process / peptidoglycan-based cell wall / plasma membrane / cytoplasm
Similarity search - Function
Nicotinate-nucleotide pyrophosphorylase / Nicotinate-nucleotide pyrophosphorylase/Putative pyrophosphorylase ModD / Quinolinate phosphoribosyl transferase, N-terminal domain / Quinolinate phosphoribosyl transferase, C-terminal / Quinolinate phosphoribosyl transferase, N-terminal / Quinolinate phosphoribosyl transferase, N-terminal domain superfamily / Quinolinate phosphoribosyl transferase, C-terminal domain / Quinolinate phosphoribosyl transferase, N-terminal domain / Nicotinate phosphoribosyltransferase-like, C-terminal / Aldehyde Oxidoreductase; domain 3 ...Nicotinate-nucleotide pyrophosphorylase / Nicotinate-nucleotide pyrophosphorylase/Putative pyrophosphorylase ModD / Quinolinate phosphoribosyl transferase, N-terminal domain / Quinolinate phosphoribosyl transferase, C-terminal / Quinolinate phosphoribosyl transferase, N-terminal / Quinolinate phosphoribosyl transferase, N-terminal domain superfamily / Quinolinate phosphoribosyl transferase, C-terminal domain / Quinolinate phosphoribosyl transferase, N-terminal domain / Nicotinate phosphoribosyltransferase-like, C-terminal / Aldehyde Oxidoreductase; domain 3 / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
QUINOLINIC ACID / Nicotinate-nucleotide pyrophosphorylase [carboxylating] / Nicotinate-nucleotide pyrophosphorylase [carboxylating]
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsSharma, V. / Grubmeyer, C. / Sacchettini, J.C. / TB Structural Genomics Consortium (TBSGC)
CitationJournal: Structure / Year: 1998
Title: Crystal structure of quinolinic acid phosphoribosyltransferase from Mycobacterium tuberculosis: a potential TB drug target.
Authors: Sharma, V. / Grubmeyer, C. / Sacchettini, J.C.
History
DepositionNov 20, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Nov 25, 1998Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: QUINOLINATE PHOSPHORIBOSYLTRANSFERASE
B: QUINOLINATE PHOSPHORIBOSYLTRANSFERASE
C: QUINOLINATE PHOSPHORIBOSYLTRANSFERASE
D: QUINOLINATE PHOSPHORIBOSYLTRANSFERASE
E: QUINOLINATE PHOSPHORIBOSYLTRANSFERASE
F: QUINOLINATE PHOSPHORIBOSYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,68418
Polymers179,1056
Non-polymers1,57912
Water4,792266
1
A: QUINOLINATE PHOSPHORIBOSYLTRANSFERASE
B: QUINOLINATE PHOSPHORIBOSYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,2286
Polymers59,7022
Non-polymers5264
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6490 Å2
ΔGint-48 kcal/mol
Surface area20240 Å2
MethodPISA, PQS
2
C: QUINOLINATE PHOSPHORIBOSYLTRANSFERASE
D: QUINOLINATE PHOSPHORIBOSYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,2286
Polymers59,7022
Non-polymers5264
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6480 Å2
ΔGint-50 kcal/mol
Surface area20290 Å2
MethodPISA, PQS
3
E: QUINOLINATE PHOSPHORIBOSYLTRANSFERASE
F: QUINOLINATE PHOSPHORIBOSYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,2286
Polymers59,7022
Non-polymers5264
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6430 Å2
ΔGint-50 kcal/mol
Surface area20310 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)100.340, 100.340, 145.658
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Cell settingtrigonal
Space group name H-MP31
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.270334, 0.961948, 0.039706), (0.962177, 0.268495, 0.046114), (0.033698, 0.05067, -0.998147)-35.4092, 26.015, 23.5619
2given(-0.496997, -0.863751, -0.083236), (0.867566, -0.496584, -0.027072), (-0.01795, -0.085668, 0.996162)71.2225, 70.9641, 4.8584
3given(0.970554, -0.237141, 0.042301), (-0.235211, -0.970856, -0.045982), (0.051972, 0.034678, -0.998046)12.882, 113.9705, 24.4859
4given(-0.494843, 0.868981, -0.001863), (-0.867781, -0.49427, -0.051511), (-0.045683, -0.023873, 0.998671)-26.6146, 96.5453, 1.7693
5given(-0.693384, -0.720555, 0.004418), (-0.720182, 0.6932, 0.028483), (-0.023586, 0.016567, -0.999585)64.7581, 27.2826, 26.9451

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Components

#1: Protein
QUINOLINATE PHOSPHORIBOSYLTRANSFERASE / E.C.2.4.2.19 / NICOTINATE-NUCLEOTIDE PYROPHOSPHORYLASE / QAPRTASE


Mass: 29850.863 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Species: Mycobacterium tuberculosis / Strain: H37RV / Gene: NADC / Species (production host): Escherichia coli / Gene (production host): NADC / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: O06594, UniProt: P9WJJ7*PLUS, nicotinate-nucleotide diphosphorylase (carboxylating)
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-NTM / QUINOLINIC ACID


Mass: 167.119 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C7H5NO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 266 / 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: 2.36 Å3/Da / Density % sol: 47.94 %
Crystal growpH: 8 / Details: pH 8.0
Crystal grow
*PLUS
Temperature: 16 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
125-30 %PEG40001reservoir
20.2 Mammonium sulfate1reservoir
30.1 MTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 291 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MACSCIENCE / Detector: IMAGE PLATE / Details: MIRRORS
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.45→30 Å / Num. obs: 55485 / % possible obs: 97.8 % / Redundancy: 3.55 % / Rsym value: 0.061 / Net I/σ(I): 15
Reflection
*PLUS
Rmerge(I) obs: 0.061

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.45→8 Å / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.253 -10 %RANDOM
Rwork0.178 ---
obs-55992 97.8 %-
Displacement parametersBiso mean: 27 Å2
Refinement stepCycle: LAST / Resolution: 2.45→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12570 0 102 266 12938
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
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_deg1.826
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
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

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