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- PDB-5kto: Crystal structure of Pyrococcus horikoshii quinolinate synthase (... -

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Basic information

Entry
Database: PDB / ID: 5kto
TitleCrystal structure of Pyrococcus horikoshii quinolinate synthase (NadA) with bound quinolinate and Fe4S4 cluster
ComponentsQuinolinate synthase A
KeywordsTRANSFERASE / Dehydratase / iron-sulfur cluster / product complex / biosynthetic enzyme
Function / homology
Function and homology information


quinolinate synthase / quinolinate synthetase A activity / 'de novo' NAD+ biosynthetic process from L-aspartate / 4 iron, 4 sulfur cluster binding / metal ion binding / cytoplasm
Similarity search - Function
NadA-like / Quinolinate synthetase A / Quinolinate synthase A, type 2 / Quinolinate synthetase A superfamily / Quinolinate synthetase A protein / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
QUINOLINIC ACID / IRON/SULFUR CLUSTER / Quinolinate synthase
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.442 Å
AuthorsFenwick, M.K. / Ealick, S.E.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM103403 United States
Department of Energy (DOE, United States)DE-AC02-06CH11357 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM103485 United States
CitationJournal: Biochemistry / Year: 2016
Title: Crystal Structures of the Iron-Sulfur Cluster-Dependent Quinolinate Synthase in Complex with Dihydroxyacetone Phosphate, Iminoaspartate Analogues, and Quinolinate.
Authors: Fenwick, M.K. / Ealick, S.E.
History
DepositionJul 12, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 27, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2016Group: Database references
Revision 1.2Aug 17, 2016Group: Database references
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Quinolinate synthase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4467
Polymers34,5821
Non-polymers8636
Water6,936385
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1580 Å2
ΔGint-41 kcal/mol
Surface area12580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.900, 52.424, 55.313
Angle α, β, γ (deg.)90.00, 115.79, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Quinolinate synthase A


Mass: 34582.434 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3) (archaea)
Strain: ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3
Gene: nadA, PH0013 / Plasmid: pDESTF1
Details (production host): Gateway-adapted vector based on the pET system (Novagen)
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O57767, quinolinate synthase

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Non-polymers , 5 types, 391 molecules

#2: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4
#3: Chemical ChemComp-NTM / QUINOLINIC ACID


Mass: 167.119 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H5NO4
#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 385 / 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: 1.88 Å3/Da / Density % sol: 34.7 % / Description: Rod
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop
Details: 210 mM ammonium chloride, 8 - 15% polyethylene glycol 4000, and 40 mM HEPES, pH 5.5 - 7.5. Quinolinic acid, pH 7.5, was added to the protein solution to a final concentration of 5 mM.
PH range: 5.5 - 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97924 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 6, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97924 Å / Relative weight: 1
ReflectionResolution: 1.44→35 Å / Num. obs: 44518 / % possible obs: 95.9 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.045 / Net I/av σ(I): 30.2 / Net I/σ(I): 18.5
Reflection shellResolution: 1.44→1.49 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.406 / Mean I/σ(I) obs: 3.3 / % possible all: 81.8

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: 000)refinement
PHENIX(1.10_2155: 000)phasing
HKL-2000data scaling
HKL-2000data reduction
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5KTN

5ktn


Resolution: 1.442→34.114 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.01
RfactorNum. reflection% reflection
Rfree0.189 2288 5.14 %
Rwork0.1401 --
obs0.1426 44515 95.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.442→34.114 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2344 0 38 385 2767
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122557
X-RAY DIFFRACTIONf_angle_d1.7333485
X-RAY DIFFRACTIONf_dihedral_angle_d14.577994
X-RAY DIFFRACTIONf_chiral_restr0.08393
X-RAY DIFFRACTIONf_plane_restr0.006449
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4418-1.47320.23831210.17322000X-RAY DIFFRACTION73
1.4732-1.50750.24151440.16792559X-RAY DIFFRACTION93
1.5075-1.54520.22551520.14972612X-RAY DIFFRACTION96
1.5452-1.58690.22561570.13972630X-RAY DIFFRACTION97
1.5869-1.63360.20231430.13432654X-RAY DIFFRACTION97
1.6336-1.68640.1751550.13222639X-RAY DIFFRACTION97
1.6864-1.74660.19761380.13152673X-RAY DIFFRACTION97
1.7466-1.81660.18361230.13032717X-RAY DIFFRACTION98
1.8166-1.89920.18541550.13342666X-RAY DIFFRACTION98
1.8992-1.99940.21391480.13532688X-RAY DIFFRACTION98
1.9994-2.12460.17481550.13862711X-RAY DIFFRACTION98
2.1246-2.28860.16751310.13622709X-RAY DIFFRACTION98
2.2886-2.51890.1931270.1452757X-RAY DIFFRACTION99
2.5189-2.88320.21451380.15842760X-RAY DIFFRACTION99
2.8832-3.63190.19631610.14272751X-RAY DIFFRACTION99
3.6319-34.12370.15571400.13022701X-RAY DIFFRACTION95

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