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- PDB-6or8: An Unexpected Intermediate in the Reaction Catalyzed by Quinolina... -

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Basic information

Entry
Database: PDB / ID: 6or8
TitleAn Unexpected Intermediate in the Reaction Catalyzed by Quinolinate Synthase
ComponentsQuinolinate synthase A
KeywordsTRANSFERASE / biosynthesis of nicotinamide adenine dinucleotide
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
Chem-5XR / PHOSPHATE ION / IRON/SULFUR CLUSTER / Quinolinate synthase
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsEsakova, O.A. / Grove, T.L. / Yennawar, N.H. / Booker, S.J.
Funding support United States, 4items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB - 1716686 to sjb United States
National Science Foundation (NSF, United States)CHE - 1659679 United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)GM - 122595 United States
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: J.Am.Chem.Soc. / Year: 2019
Title: An Unexpected Species Determined by X-ray Crystallography that May Represent an Intermediate in the Reaction Catalyzed by Quinolinate Synthase.
Authors: Esakova, O.A. / Silakov, A. / Grove, T.L. / Warui, D.M. / Yennawar, N.H. / Booker, S.J.
History
DepositionApr 29, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / reflns_shell
Item: _pdbx_audit_support.funding_organization / _reflns_shell.d_res_high / _reflns_shell.d_res_low
Revision 1.2Oct 11, 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

Downloads & links

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Assembly

Deposited unit
A: Quinolinate synthase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8584
Polymers34,1901
Non-polymers6683
Water5,134285
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.393, 52.527, 53.393
Angle α, β, γ (deg.)90.00, 114.39, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Quinolinate synthase A


Mass: 34190.027 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 / Production host: Escherichia coli (E. coli) / 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 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-5XR / 2-hydroxy-N-[(1S)-1-hydroxy-3-oxopropyl]-L-aspartic acid


Mass: 221.165 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H11NO7 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 285 / 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: 1.77 Å3/Da / Density % sol: 30.52 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M MES, pH 6.5, 12% PEG 20000, 0.2 mM FAD, 5 mM Asp

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 23, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.65→48.65 Å / Num. obs: 28922 / % possible obs: 100 % / Redundancy: 3.7 % / Net I/σ(I): 9.93
Reflection shellResolution: 1.65→1.69 Å

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
HKL-2000data reduction
HKL-2000data scaling
MLPHAREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WZU

1wzu


Resolution: 1.65→48.627 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.57
RfactorNum. reflection% reflection
Rfree0.208 2005 6.93 %
Rwork0.1661 --
obs0.169 28922 99.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.65→48.627 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2375 0 28 285 2688
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082472
X-RAY DIFFRACTIONf_angle_d1.5673352
X-RAY DIFFRACTIONf_dihedral_angle_d12.2431544
X-RAY DIFFRACTIONf_chiral_restr0.062379
X-RAY DIFFRACTIONf_plane_restr0.007423
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.68780.24661330.18051806X-RAY DIFFRACTION94
1.6878-1.73350.28651380.18051930X-RAY DIFFRACTION100
1.7335-1.78450.28931390.18051896X-RAY DIFFRACTION100
1.7845-1.84210.22811520.18051927X-RAY DIFFRACTION100
1.8421-1.90790.20121440.18051920X-RAY DIFFRACTION100
1.9079-1.98430.23161420.17351912X-RAY DIFFRACTION100
1.9843-2.07460.20821430.16881934X-RAY DIFFRACTION100
2.0746-2.1840.23081480.15361918X-RAY DIFFRACTION100
2.184-2.32080.20911430.15791928X-RAY DIFFRACTION100
2.3208-2.50.20911440.15761949X-RAY DIFFRACTION100
2.5-2.75160.20721390.16731929X-RAY DIFFRACTION100
2.7516-3.14970.19131490.16171927X-RAY DIFFRACTION100
3.1497-3.9680.18451460.13841952X-RAY DIFFRACTION100
3.968-48.6270.18051450.14671989X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
18.23151.1818-5.3496.3832-3.62227.99610.0508-0.4367-0.64850.2255-0.6482-1.43740.02461.32880.42830.1049-0.0036-0.06170.28850.0670.35880.8214-10.443284.6068
21.69960.390.8561.6403-1.00268.8629-0.0815-0.1038-0.0029-0.0427-0.1005-0.16090.22150.2720.15090.08130.02640.03450.07240.00010.0894-9.681-11.675678.5611
36.00281.0553-0.10332.75560.554.1312-0.09930.2947-0.447-0.07820.1242-0.21640.21290.0338-0.00250.16720.02130.03030.0667-0.02880.1077-11.2228-13.838472.0323
42.1225-0.22380.3412.8947-1.55633.37710.0102-0.0407-0.0406-0.1820.06870.16120.3498-0.2401-0.07460.0939-0.0076-0.00360.0661-0.01220.0541-18.3704-8.748178.6709
57.25050.51433.9964-0.11130.34361.6327-0.23-0.14710.4525-0.0037-0.02250.0561-0.1515-0.0670.2410.09020.0005-0.00190.0976-0.01250.1159-30.51033.261465.2481
64.5238-0.17650.63032.74340.30595.35830.0615-0.4553-0.47510.0239-0.134-0.21550.05820.29640.04720.0898-0.01350.00150.16910.10750.1869-30.1203-8.715162.8167
75.29251.63640.15633.86691.42232.5775-0.11560.3836-0.0586-0.24230.108-0.0767-0.02560.13840.01960.06970.0006-0.00040.09280.00930.0729-31.5428-5.031753.5504
85.7623-2.8326-2.94752.511.72562.95860.23820.28590.5004-0.32110.0088-0.2809-0.30830.0222-0.21510.1286-0.03280.00730.10360.02290.1048-10.2651-0.666148.8588
94.366-2.23810.24354.90910.23812.24970.07170.12-0.2852-0.1731-0.01810.25190.141-0.1424-0.05340.0699-0.0245-0.00860.0781-0.00430.0568-12.7878-11.086650.4555
101.8875-0.5939-1.16543.1941.75993.0534-0.0826-0.1487-0.00790.10990.0867-0.08180.03660.2242-0.00920.0482-0.0081-0.01470.0720.01020.0541-4.3075-7.902159.3187
114.1511-1.613-1.0122.8222-0.66514.66810.0133-0.21050.18660.3641-0.0284-0.3122-0.17050.3516-0.02510.114-0.0232-0.04450.0749-0.02150.1119-8.0691-2.283.3406
122.6168-0.29450.46053.49733.36497.61930.0676-0.7984-0.84190.2748-0.36050.40470.5423-0.39140.17020.1828-0.0671-0.00610.53310.28840.3949-32.0579-11.29573.0089
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 1:11)
2X-RAY DIFFRACTION2(chain A and resid 12:23)
3X-RAY DIFFRACTION3(chain A and resid 24:48)
4X-RAY DIFFRACTION4(chain A and resid 49:77)
5X-RAY DIFFRACTION5(chain A and resid 78:104)
6X-RAY DIFFRACTION6(chain A and resid 105:135)
7X-RAY DIFFRACTION7(chain A and resid 136:165)
8X-RAY DIFFRACTION8(chain A and resid 166:191)
9X-RAY DIFFRACTION9(chain A and resid 192:229)
10X-RAY DIFFRACTION10(chain A and resid 230:261)
11X-RAY DIFFRACTION11(chain A and resid 262:278)
12X-RAY DIFFRACTION12(chain A and resid 279:299)

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