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- PDB-1qpr: QUINOLINATE PHOSPHORIBOSYLTRANSFERASE (QAPRTASE) FROM MYCOBACTERI... -

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Basic information

Entry
Database: PDB / ID: 1qpr
TitleQUINOLINATE PHOSPHORIBOSYLTRANSFERASE (QAPRTASE) FROM MYCOBACTERIUM TUBERCULOSIS IN COMPLEX WITH PHTHALATE AND PRPCP
ComponentsQUINOLINIC ACID PHOSPHORIBOSYLTRANSFERASE
KeywordsTRANSFERASE / PRTASE / DE NOVO NAD BIOSYNTHESIS / PRPP / PHOSPHORIBOSYLTRANSFERASE / 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 / Quinolinate phosphoribosyl transferase, N-terminal domain / Quinolinate phosphoribosyl transferase, N-terminal domain / Quinolinate phosphoribosyl transferase, C-terminal / Quinolinate phosphoribosyl transferase, N-terminal domain superfamily / Quinolinate phosphoribosyl transferase, C-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 / Quinolinate phosphoribosyl transferase, N-terminal domain / Quinolinate phosphoribosyl transferase, N-terminal domain / Quinolinate phosphoribosyl transferase, C-terminal / Quinolinate phosphoribosyl transferase, N-terminal domain superfamily / Quinolinate phosphoribosyl transferase, C-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
: / PHTHALIC ACID / Chem-PPC / Nicotinate-nucleotide pyrophosphorylase [carboxylating] / Nicotinate-nucleotide pyrophosphorylase [carboxylating]
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / MIR / 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
DepositionOct 17, 1998Processing site: BNL
Revision 1.0Oct 21, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 29, 2020Group: Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _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.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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.ptnr2_auth_asym_id / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: QUINOLINIC ACID PHOSPHORIBOSYLTRANSFERASE
B: QUINOLINIC ACID PHOSPHORIBOSYLTRANSFERASE
C: QUINOLINIC ACID PHOSPHORIBOSYLTRANSFERASE
D: QUINOLINIC ACID PHOSPHORIBOSYLTRANSFERASE
E: QUINOLINIC ACID PHOSPHORIBOSYLTRANSFERASE
F: QUINOLINIC ACID PHOSPHORIBOSYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)183,09030
Polymers179,1056
Non-polymers3,98524
Water6,107339
1
A: QUINOLINIC ACID PHOSPHORIBOSYLTRANSFERASE
B: QUINOLINIC ACID PHOSPHORIBOSYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,03010
Polymers59,7022
Non-polymers1,3288
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8290 Å2
ΔGint-43 kcal/mol
Surface area19500 Å2
MethodPISA
2
C: QUINOLINIC ACID PHOSPHORIBOSYLTRANSFERASE
D: QUINOLINIC ACID PHOSPHORIBOSYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,03010
Polymers59,7022
Non-polymers1,3288
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8250 Å2
ΔGint-42 kcal/mol
Surface area19480 Å2
MethodPISA
3
E: QUINOLINIC ACID PHOSPHORIBOSYLTRANSFERASE
F: QUINOLINIC ACID PHOSPHORIBOSYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,03010
Polymers59,7022
Non-polymers1,3288
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8280 Å2
ΔGint-43 kcal/mol
Surface area19440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.448, 100.448, 145.792
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.270176, 0.962029, 0.038789), (0.962281, 0.268473, 0.04401), (0.031925, 0.049217, -0.998278)-35.4497, 26.1166, 23.652
2given(-0.498916, -0.862713, -0.082522), (0.866455, -0.49856, -0.026348), (-0.018411, -0.084647, 0.996241)71.167, 71.1695, 4.8102
3given(0.970634, -0.237359, 0.039116), (-0.235409, -0.970678, -0.048653), (0.049517, 0.038016, -0.99805)12.9055, 114.0924, 24.271
4given(-0.492584, 0.870262, -0.002142), (-0.869339, -0.492172, -0.044903), (-0.040132, -0.020257, 0.998989)-26.7866, 96.4534, 1.4523
5given(-0.692818, -0.721077, 0.007188), (-0.720673, 0.692709, 0.028007), (-0.025174, 0.014223, -0.999582)64.6997, 27.4146, 27.1373

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Components

#1: Protein
QUINOLINIC ACID PHOSPHORIBOSYLTRANSFERASE / NICOTINATE-NUCLEOTIDE PYROPHOSPHORYLASE (CARBOXYLATING)


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 / Cell line: BL21 / Gene: NADC / Plasmid: BL21 / 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-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Mn
#3: Chemical
ChemComp-PHT / PHTHALIC ACID / Phthalic acid


Mass: 166.131 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C8H6O4
#4: Sugar
ChemComp-PPC / 1-O-[(R)-hydroxy(phosphonomethyl)phosphoryl]-5-O-phosphono-alpha-D-ribofuranose / 5-PHOSPHORIBOSYL-1-(BETA-METHYLENE) PYROPHOSPHATE / 1-O-[(R)-hydroxy(phosphonomethyl)phosphoryl]-5-O-phosphono-alpha-D-ribose / 1-O-[(R)-hydroxy(phosphonomethyl)phosphoryl]-5-O-phosphono-D-ribose / 1-O-[(R)-hydroxy(phosphonomethyl)phosphoryl]-5-O-phosphono-ribose


Type: D-saccharide / Mass: 388.097 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H15O13P3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 339 / 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: 2.37 Å3/Da / Density % sol: 48.1 %
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 RUH2R / Wavelength: 1.5418
DetectorType: MACSCIENCE / Detector: IMAGE PLATE / Details: MIRRORS
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.45→30 Å / Num. obs: 58603 / % possible obs: 96.9 % / Redundancy: 4.63 % / Rsym value: 0.079 / Net I/σ(I): 9.6
Reflection shellResolution: 2.45→2.54 Å / Rsym value: 0.252 / % possible all: 94.9
Reflection
*PLUS
Rmerge(I) obs: 0.079
Reflection shell
*PLUS
% possible obs: 94.9 % / Rmerge(I) obs: 0.252

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Processing

Software
NameVersionClassification
PHASESphasing
X-PLOR3.1model building
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MIR / Resolution: 2.45→8 Å / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.251 -10 %RANDOM
Rwork0.186 ---
obs0.186 58602 87.131 %-
Displacement parametersBiso mean: 27.1 Å2
Refinement stepCycle: LAST / Resolution: 2.45→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12570 0 252 303 13125
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.017
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_deg1.834
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
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS

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