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

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Basic information

Entry
Database: PDB / ID: 5ktr
TitleCrystal structure of Pyrococcus horikoshii quinolinate synthase (NadA) with bound maleate 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 aspartate / 4 iron, 4 sulfur cluster binding / metal ion binding / cytosol
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
MALEIC ACID / AMMONIUM ION / IRON/SULFUR CLUSTER / Quinolinate synthase
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / 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)35,1757
Polymers34,5821
Non-polymers5926
Water8,791488
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1140 Å2
ΔGint-45 kcal/mol
Surface area13490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.256, 52.605, 55.510
Angle α, β, γ (deg.)90.00, 111.70, 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, 494 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-MAE / MALEIC ACID


Mass: 116.072 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H4O4
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#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.: 488 / 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: 33.65 % / 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. Maleic 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: F1 / Wavelength: 0.9181 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 18, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9181 Å / Relative weight: 1
ReflectionResolution: 1.34→35 Å / Num. obs: 56427 / % possible obs: 98.7 % / Redundancy: 3 % / Rmerge(I) obs: 0.062 / Net I/av σ(I): 21.9 / Net I/σ(I): 15.2
Reflection shellResolution: 1.34→1.39 Å / Redundancy: 2 % / Rmerge(I) obs: 0.205 / Mean I/σ(I) obs: 4.7 / % possible all: 94.1

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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: FOURIER SYNTHESIS
Starting model: 5KTN

5ktn


Resolution: 1.34→28.615 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 14.34
RfactorNum. reflection% reflection
Rfree0.1564 2850 5.05 %
Rwork0.1249 --
obs0.1265 56405 98.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.34→28.615 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2417 0 20 488 2925
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112750
X-RAY DIFFRACTIONf_angle_d1.7843745
X-RAY DIFFRACTIONf_dihedral_angle_d18.1291088
X-RAY DIFFRACTIONf_chiral_restr0.086413
X-RAY DIFFRACTIONf_plane_restr0.007488
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3366-1.35960.1831150.14642348X-RAY DIFFRACTION86
1.3596-1.38440.19861290.13682634X-RAY DIFFRACTION96
1.3844-1.4110.19311640.13152592X-RAY DIFFRACTION97
1.411-1.43980.17771320.1332637X-RAY DIFFRACTION98
1.4398-1.47110.19361240.13092702X-RAY DIFFRACTION98
1.4711-1.50530.17521440.12432651X-RAY DIFFRACTION98
1.5053-1.5430.17391460.11812675X-RAY DIFFRACTION99
1.543-1.58470.15831580.11292685X-RAY DIFFRACTION100
1.5847-1.63130.15511630.1082710X-RAY DIFFRACTION100
1.6313-1.68390.15031430.10822698X-RAY DIFFRACTION100
1.6839-1.74410.13881460.11092707X-RAY DIFFRACTION100
1.7441-1.81390.16141530.11372724X-RAY DIFFRACTION100
1.8139-1.89650.13841360.11732704X-RAY DIFFRACTION100
1.8965-1.99640.14611520.11782701X-RAY DIFFRACTION100
1.9964-2.12150.14241600.1182723X-RAY DIFFRACTION100
2.1215-2.28520.14981280.11962726X-RAY DIFFRACTION100
2.2852-2.51510.1691240.13092773X-RAY DIFFRACTION100
2.5151-2.87870.16711320.1432724X-RAY DIFFRACTION100
2.8787-3.62570.15731560.12922743X-RAY DIFFRACTION100
3.6257-28.62140.14091450.13052698X-RAY DIFFRACTION96

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