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

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Basic information

Entry
Database: PDB / ID: 5ktp
TitleCrystal structure of Pyrococcus horikoshii quinolinate synthase (NadA) with bound itaconate and Fe4S4 cluster
ComponentsQuinolinate synthase A
KeywordsTRANSFERASE / Dehydratase / iron-sulfur cluster / substrate analog 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
2-methylidenebutanedioic acid / AMMONIUM ION / IRON/SULFUR CLUSTER / Quinolinate synthase
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.542 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)35,1185
Polymers34,5821
Non-polymers5354
Water5,477304
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area570 Å2
ΔGint-26 kcal/mol
Surface area12560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.477, 52.671, 55.686
Angle α, β, γ (deg.)90.00, 112.41, 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, 308 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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-ITN / 2-methylidenebutanedioic acid


Mass: 130.099 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H6O4
#5: Chemical ChemComp-NH4 / AMMONIUM ION


Mass: 18.038 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H4N
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 304 / 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: 1.86 Å3/Da / Density % sol: 33.92 % / 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. Itaconic acid, pH 6.0, was added to the cryopreservation solution to a final concentration of 7 mM
PH range: 5.5 - 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.9779 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 26, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9779 Å / Relative weight: 1
ReflectionResolution: 1.54→20 Å / Num. obs: 36334 / % possible obs: 96.8 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.046 / Net I/av σ(I): 23.8 / Net I/σ(I): 16.3
Reflection shellResolution: 1.54→1.6 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.216 / Mean I/σ(I) obs: 4.9 / % possible all: 91.8

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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: 1.542→19.625 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.06
RfactorNum. reflection% reflection
Rfree0.1977 1861 5.12 %
Rwork0.1549 --
obs0.1571 36334 96.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.542→19.625 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2329 0 19 304 2652
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112434
X-RAY DIFFRACTIONf_angle_d1.8423305
X-RAY DIFFRACTIONf_dihedral_angle_d17.216930
X-RAY DIFFRACTIONf_chiral_restr0.056377
X-RAY DIFFRACTIONf_plane_restr0.006420
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.542-1.58370.22811460.14972466X-RAY DIFFRACTION91
1.5837-1.63030.24051600.15132562X-RAY DIFFRACTION94
1.6303-1.68280.22381360.14542585X-RAY DIFFRACTION96
1.6828-1.7430.19741400.14232670X-RAY DIFFRACTION97
1.743-1.81270.22571520.14512619X-RAY DIFFRACTION97
1.8127-1.89510.22131310.14512683X-RAY DIFFRACTION98
1.8951-1.9950.22171590.14582645X-RAY DIFFRACTION98
1.995-2.11980.20341530.14122648X-RAY DIFFRACTION98
2.1198-2.28330.18671300.14282697X-RAY DIFFRACTION98
2.2833-2.51260.2051210.16072747X-RAY DIFFRACTION99
2.5126-2.87520.21641320.17942723X-RAY DIFFRACTION99
2.8752-3.61880.20821570.16372730X-RAY DIFFRACTION99
3.6188-19.62680.14591440.15552698X-RAY DIFFRACTION96

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