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- PDB-2b7q: Crystal structure of quinolinic acid phosphoribosyltransferase fr... -

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Basic information

Entry
Database: PDB / ID: 2b7q
TitleCrystal structure of quinolinic acid phosphoribosyltransferase from Helicobacter pylori with nicotinate mononucleotide
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
NICOTINATE MONONUCLEOTIDE / Probable nicotinate-nucleotide pyrophosphorylase [carboxylating]
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.31 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 5, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 21, 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 1.4Sep 19, 2018Group: Data collection / Structure summary / Category: struct / Item: _struct.title
Revision 1.5Mar 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

Downloads & links

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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)93,5586
Polymers92,5523
Non-polymers1,0063
Water32418
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)187,11612
Polymers185,1046
Non-polymers2,0116
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_553-y,-x,-z-3/21
Buried area32070 Å2
ΔGint-120 kcal/mol
Surface area62580 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-NCN / NICOTINATE MONONUCLEOTIDE / NAMN


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


Mass: 18.015 Da / Num. of mol.: 18 / 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: 0.1M HEPES-NaOH, 1.5M Li2SO4, 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: 0.97941 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: 0.97941 Å / Relative weight: 1
ReflectionResolution: 3.3→29.95 Å / Num. obs: 24834 / % possible obs: 91.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 3.3→20 Å / % possible all: 91.3

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Processing

Software
NameVersionClassification
CNS1.1refinement
MAR345data collection
AUTOMARdata reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.31→29.95 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 471356.03 / 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
Rfree0.286 2249 10 %RANDOM
Rwork0.221 ---
all0.268 ---
obs0.221 22603 90.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 45.3175 Å2 / ksol: 0.298977 e/Å3
Displacement parametersBiso mean: 56.6 Å2
Baniso -1Baniso -2Baniso -3
1--7.85 Å20 Å20 Å2
2---7.85 Å20 Å2
3---15.69 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.48 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.87 Å0.55 Å
Refinement stepCycle: LAST / Resolution: 3.31→29.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6480 0 66 18 6564
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.031
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg2.8
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d2.78
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 3.3→3.51 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.352 317 10.5 %
Rwork0.285 2695 -
obs--73.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water.paramwater.top
X-RAY DIFFRACTION3ncn.paramncn.top

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