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- PDB-1qpn: Quinolinate Phosphoribosyl Transferase from Mycobacterium Tubercu... -

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Basic information

Entry
Database: PDB / ID: 1qpn
TitleQuinolinate Phosphoribosyl Transferase from Mycobacterium Tuberculosis in Complex with NCNN
ComponentsPROTEIN (QUINOLINATE PHOSPHORIBOSYL TRANSFERASE)
KeywordsTRANSFERASE / TYPE II PRTASE / DE NOVO NAD BIOSYNTHESIS / PRPP / PHOSPHORIBOSYL TRANSFERASE / QUINOLINIC ACID / NAMN / 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
NICOTINATE MONONUCLEOTIDE / Nicotinate-nucleotide pyrophosphorylase [carboxylating] / Nicotinate-nucleotide pyrophosphorylase [carboxylating]
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 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: PROTEIN (QUINOLINATE PHOSPHORIBOSYL TRANSFERASE)
B: PROTEIN (QUINOLINATE PHOSPHORIBOSYL TRANSFERASE)
C: PROTEIN (QUINOLINATE PHOSPHORIBOSYL TRANSFERASE)
D: PROTEIN (QUINOLINATE PHOSPHORIBOSYL TRANSFERASE)
E: PROTEIN (QUINOLINATE PHOSPHORIBOSYL TRANSFERASE)
F: PROTEIN (QUINOLINATE PHOSPHORIBOSYL TRANSFERASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)181,11612
Polymers179,1056
Non-polymers2,0116
Water4,738263
1
A: PROTEIN (QUINOLINATE PHOSPHORIBOSYL TRANSFERASE)
B: PROTEIN (QUINOLINATE PHOSPHORIBOSYL TRANSFERASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,3724
Polymers59,7022
Non-polymers6702
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6190 Å2
ΔGint-22 kcal/mol
Surface area20500 Å2
MethodPISA, PQS
2
C: PROTEIN (QUINOLINATE PHOSPHORIBOSYL TRANSFERASE)
D: PROTEIN (QUINOLINATE PHOSPHORIBOSYL TRANSFERASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,3724
Polymers59,7022
Non-polymers6702
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6230 Å2
ΔGint-23 kcal/mol
Surface area20480 Å2
MethodPISA, PQS
3
E: PROTEIN (QUINOLINATE PHOSPHORIBOSYL TRANSFERASE)
F: PROTEIN (QUINOLINATE PHOSPHORIBOSYL TRANSFERASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,3724
Polymers59,7022
Non-polymers6702
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6200 Å2
ΔGint-24 kcal/mol
Surface area20430 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)100.383, 100.383, 144.610
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(-0.270118, 0.962315, 0.031399), (0.962306, 0.268755, 0.041677), (0.031668, 0.041473, -0.998638)-35.1605, 25.9539, 23.8977
2given(-0.497383, -0.864635, -0.070825), (0.867406, -0.497037, -0.023682), (-0.014727, -0.073213, 0.997208)71.1436, 70.8462, 3.9083
3given(0.971233, -0.236218, 0.030118), (-0.234809, -0.971047, -0.043967), (0.039631, 0.03563, -0.998579)12.9509, 113.886, 24.3728
4given(-0.49477, 0.86902, 0.002773), (-0.867886, -0.493956, -0.05273), (-0.044454, -0.028496, 0.998605)-26.5387, 96.6177, 1.9385
5given(-0.693434, -0.720439, -0.010822), (-0.720446, 0.693068, 0.024782), (-0.010353, 0.024982, -0.999634)65.0501, 27.4022, 25.9969

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Components

#1: Protein
PROTEIN (QUINOLINATE PHOSPHORIBOSYL TRANSFERASE) / E.C.2.4.2.19 / NICOTINATE-NUCLEOTIDE PYROPHOSPHORYLASE (CARBOXYLATING) / 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-NCN / NICOTINATE MONONUCLEOTIDE / NAMN


Mass: 335.204 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C11H14NO9P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 263 / 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: 2.35 Å3/Da / Density % sol: 47.61 %
Crystal growpH: 8 / Details: pH 8.00
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: 2.6→30 Å / Num. obs: 48262 / % possible obs: 96.3 % / Redundancy: 2.98 % / Rsym value: 0.075 / Net I/σ(I): 9.5
Reflection
*PLUS
Rmerge(I) obs: 0.075

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Processing

Software
NameVersionClassification
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→8 Å / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.269 -10 %RANDOM
Rwork0.185 ---
obs0.185 46616 96.3 %-
Displacement parametersBiso mean: 30.7 Å2
Refinement stepCycle: LAST / Resolution: 2.6→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12570 0 132 263 12965
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
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_deg1.89
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
Xplor fileSerial no: 1 / Param file: NAM.PAR / Topol file: NAM.TOP

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