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

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Basic information

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


quinolinate synthase / quinolinate synthetase A activity / NAD biosynthetic process / 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
IRON/SULFUR CLUSTER / Quinolinate synthase
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.44 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)34,9703
Polymers34,5821
Non-polymers3872
Water6,251347
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area570 Å2
ΔGint-35 kcal/mol
Surface area12780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.480, 52.877, 55.996
Angle α, β, γ (deg.)90.00, 111.72, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 347 / 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: 1.89 Å3/Da / Density % sol: 34.86 % / 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.
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: 0.97923 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: 0.97923 Å / Relative weight: 1
ReflectionResolution: 1.44→50 Å / Num. obs: 43765 / % possible obs: 93.7 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.04 / Net I/av σ(I): 29.8 / Net I/σ(I): 19.7
Reflection shellResolution: 1.44→1.49 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.269 / Mean I/σ(I) obs: 4.4 / % possible all: 83.6

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Processing

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

5ktn


Resolution: 1.44→42.221 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.88
RfactorNum. reflection% reflection
Rfree0.2148 2210 5.05 %
Rwork0.1708 --
obs0.173 43758 93.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.44→42.221 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2337 0 9 347 2693
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112448
X-RAY DIFFRACTIONf_angle_d1.793332
X-RAY DIFFRACTIONf_dihedral_angle_d14.118938
X-RAY DIFFRACTIONf_chiral_restr0.078382
X-RAY DIFFRACTIONf_plane_restr0.006425
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4402-1.47150.2897990.20922142X-RAY DIFFRACTION78
1.4715-1.50570.3091300.1952595X-RAY DIFFRACTION93
1.5057-1.54340.26161480.18252683X-RAY DIFFRACTION97
1.5434-1.58510.21451560.17022659X-RAY DIFFRACTION98
1.5851-1.63170.23131590.16162657X-RAY DIFFRACTION97
1.6317-1.68440.21791410.16052659X-RAY DIFFRACTION97
1.6844-1.74460.24051450.1592699X-RAY DIFFRACTION97
1.7446-1.81450.18791540.15032653X-RAY DIFFRACTION97
1.8145-1.89710.21511330.15772655X-RAY DIFFRACTION96
1.8971-1.99710.22061520.16032657X-RAY DIFFRACTION97
1.9971-2.12220.22191580.16132632X-RAY DIFFRACTION96
2.1222-2.2860.22441280.16672667X-RAY DIFFRACTION95
2.286-2.51610.22041140.17062651X-RAY DIFFRACTION94
2.5161-2.88010.2261230.18812555X-RAY DIFFRACTION92
2.8801-3.62830.19041480.17932545X-RAY DIFFRACTION91
3.6283-42.23920.18861220.17112439X-RAY DIFFRACTION85

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