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

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Basic information

Entry
Database: PDB / ID: 5ktn
TitleCrystal structure of Pyrococcus horikoshii quinolinate synthase (NadA) with bound dihydroxyacetone phosphate (DHAP) and Fe4S4 cluster
ComponentsQuinolinate synthase A
KeywordsTRANSFERASE / Dehydratase / iron-sulfur cluster / substrate complex / 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
1,3-DIHYDROXYACETONEPHOSPHATE / AMMONIUM ION / IRON/SULFUR CLUSTER / Quinolinate synthase
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.34 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)35,1936
Polymers34,5821
Non-polymers6115
Water9,404522
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1070 Å2
ΔGint-39 kcal/mol
Surface area13490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.303, 52.522, 55.544
Angle α, β, γ (deg.)90.00, 112.20, 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, 527 molecules

#2: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4
#3: Chemical ChemComp-13P / 1,3-DIHYDROXYACETONEPHOSPHATE / Dihydroxyacetone phosphate


Mass: 170.058 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7O6P
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-NH4 / AMMONIUM ION / Ammonium


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


Mass: 18.015 Da / Num. of mol.: 522 / 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: 1.85 Å3/Da / Density % sol: 33.42 % / Description: Rod
Crystal growTemperature: 296 K / Method: vapor diffusion
Details: 210 mM ammonium chloride, 8 - 15% polyethylene glycol 4000, and 40 mM HEPES, pH 5.5 - 7.5. DHAP was added to the protein solution to a final concentration of 7-10 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: 0.97925 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: 0.97925 Å / Relative weight: 1
ReflectionResolution: 1.34→35 Å / Num. obs: 56267 / % possible obs: 99.4 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.047 / Net I/av σ(I): 29.4 / Net I/σ(I): 19.3
Reflection shellResolution: 1.34→1.39 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.242 / Mean I/σ(I) obs: 5 / % possible all: 95.1

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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: MOLECULAR REPLACEMENT
Starting model: Crystal structure of Pyrococcus horikoshii NadA with bound malate and lacking Fe4S4 cluster (PDB entry 1WZU)

1wzu


Resolution: 1.34→33.636 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 14.12
RfactorNum. reflection% reflection
Rfree0.1546 2850 5.07 %
Rwork0.1227 --
obs0.1243 56248 99.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.34→33.636 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2419 0 21 522 2962
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122795
X-RAY DIFFRACTIONf_angle_d1.7283809
X-RAY DIFFRACTIONf_dihedral_angle_d18.1511123
X-RAY DIFFRACTIONf_chiral_restr0.084412
X-RAY DIFFRACTIONf_plane_restr0.006498
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3401-1.36320.21571310.16482396X-RAY DIFFRACTION90
1.3632-1.3880.18291300.1442657X-RAY DIFFRACTION98
1.388-1.41470.16521560.12852648X-RAY DIFFRACTION100
1.4147-1.44350.15761450.12362704X-RAY DIFFRACTION100
1.4435-1.47490.19371250.12422659X-RAY DIFFRACTION100
1.4749-1.50920.1791400.11542652X-RAY DIFFRACTION100
1.5092-1.5470.17241430.11112674X-RAY DIFFRACTION100
1.547-1.58880.15181630.10642682X-RAY DIFFRACTION100
1.5888-1.63550.15031530.10382666X-RAY DIFFRACTION100
1.6355-1.68830.15861470.10442677X-RAY DIFFRACTION100
1.6883-1.74870.16251430.10752691X-RAY DIFFRACTION100
1.7487-1.81870.14961510.11212680X-RAY DIFFRACTION100
1.8187-1.90140.12751330.1182672X-RAY DIFFRACTION100
1.9014-2.00170.15391530.1172689X-RAY DIFFRACTION100
2.0017-2.12710.1471560.11512687X-RAY DIFFRACTION100
2.1271-2.29130.14221270.11912708X-RAY DIFFRACTION100
2.2913-2.52180.16491190.13172734X-RAY DIFFRACTION100
2.5218-2.88650.17391330.14262710X-RAY DIFFRACTION100
2.8865-3.6360.1541550.12222704X-RAY DIFFRACTION100
3.636-33.6470.13481470.12942708X-RAY DIFFRACTION98

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