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- PDB-2b7n: Crystal structure of quinolinic acid phosphoribosyltransferase fr... -

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Basic information

Entry
Database: PDB / ID: 2b7n
TitleCrystal structure of quinolinic acid phosphoribosyltransferase from Helicobacter pylori
ComponentsProbable nicotinate-nucleotide pyrophosphorylase
KeywordsTRANSFERASE / quinolinate phosphoribosyltransferase / quinolinic acid / Helicobacter pylori
Function / homology
Function and homology information


quinolinate catabolic process / nicotinate-nucleotide diphosphorylase (carboxylating) / nicotinate-nucleotide diphosphorylase (carboxylating) activity / NAD biosynthetic process / 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 / Probable nicotinate-nucleotide pyrophosphorylase [carboxylating]
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsKim, M.K. / Im, Y.J. / Lee, J.H. / Eom, S.H.
CitationJournal: Proteins / Year: 2006
Title: Crystal structure of quinolinic acid phosphoribosyltransferase from Helicobacter pylori
Authors: Kim, M.K. / Im, Y.J. / Lee, J.H. / Eom, S.H.
History
DepositionOct 4, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 14, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Mar 13, 2024Group: 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

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Assembly

Deposited unit
A: Probable nicotinate-nucleotide pyrophosphorylase
B: Probable nicotinate-nucleotide pyrophosphorylase
C: Probable nicotinate-nucleotide pyrophosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,3429
Polymers92,5523
Non-polymers7906
Water3,783210
1
A: Probable nicotinate-nucleotide pyrophosphorylase
B: Probable nicotinate-nucleotide pyrophosphorylase
C: Probable nicotinate-nucleotide pyrophosphorylase
hetero molecules

A: Probable nicotinate-nucleotide pyrophosphorylase
B: Probable nicotinate-nucleotide pyrophosphorylase
C: Probable nicotinate-nucleotide pyrophosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)186,68318
Polymers185,1046
Non-polymers1,57912
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_465y-1,x+1,-z1
Buried area32030 Å2
ΔGint-174 kcal/mol
Surface area60200 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)148.855, 148.855, 145.662
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Probable nicotinate-nucleotide pyrophosphorylase / Quinolinate phosphoribosyltransferase / decarboxylating / QAPRTase


Mass: 30850.717 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Production host: Escherichia coli (E. coli)
References: UniProt: O25909, nicotinate-nucleotide diphosphorylase (carboxylating)
#2: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 167.119 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C7H5NO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 210 / 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: 4.36 Å3/Da / Density % sol: 71.8 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 100mM HEPES-NaOH, 1.5M LiSO4, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 6B / Wavelength: 1.12714 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 22, 2002
RadiationMonochromator: Ni MIRROR + Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12714 Å / Relative weight: 1
ReflectionResolution: 2.3→29.17 Å / Num. all: 73432 / Num. obs: 68675 / % possible obs: 93.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Biso Wilson estimate: 25.8 Å2
Reflection shellResolution: 2.3→2.38 Å / % possible all: 81.6

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Processing

Software
NameVersionClassification
CNS1.1refinement
MAR345data collection
AUTOMARdata reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→29.17 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 1039705.55 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.256 6947 10.1 %RANDOM
Rwork0.224 ---
all0.231 73432 --
obs0.224 68675 94.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 39.2517 Å2 / ksol: 0.373019 e/Å3
Displacement parametersBiso mean: 38.85 Å2
Baniso -1Baniso -2Baniso -3
1--3.54 Å20 Å20 Å2
2---3.54 Å20 Å2
3---7.08 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.27 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 2.3→29.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6483 0 51 210 6744
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.02
X-RAY DIFFRACTIONc_angle_deg2
X-RAY DIFFRACTIONc_dihedral_angle_d22.1
X-RAY DIFFRACTIONc_improper_angle_d1.99
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.29 1034 9.9 %
Rwork0.247 9385 -
obs--86.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water.paramwater.top
X-RAY DIFFRACTION3ntm_sul.paramntm_sul.top

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