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

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Basic information

Entry
Database: PDB / ID: 6nso
TitleAn Unexpected Intermediate in the Reaction Catalyzed by Quinolinate Synthase
ComponentsQuinolinate synthase A
KeywordsTRANSFERASE / quinolinic acid / biosynthesis
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 / IRON/SULFUR CLUSTER / Quinolinate synthase
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsEsakova, O.A. / Grove, T.L. / Silakov, A. / Yennawar, N.H. / Booker, S.J.
Funding support United States, 4items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB - 1716686 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
DepositionJan 25, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
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)34,7123
Polymers34,1901
Non-polymers5222
Water5,386299
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)47.400, 52.790, 55.640
Angle α, β, γ (deg.)90.00, 112.07, 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) / Strain (production host): ROSETTA 2 (DE3) / References: UniProt: O57767, quinolinate synthase
#2: Chemical ChemComp-13P / 1,3-DIHYDROXYACETONEPHOSPHATE / Dihydroxyacetone phosphate


Mass: 170.058 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7O6P
#3: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 299 / 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: 34.92 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.2 M AMMONIUM ACETATE, 0.1 M SODIUM ACETATE, PH 4.6, 30% PEG 4000, 5 MM ASP, 10 MM DHAP, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 295K
PH range: 4.6

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Data collection

DiffractionMean temperature: 80 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
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→33.77 Å / Num. obs: 31790 / % possible obs: 94.2 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.076 / Rsym value: 0.063 / Net I/σ(I): 10.2
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.667 / Mean I/σ(I) obs: 1.3 / % possible all: 62.9

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Processing

Software
NameVersionClassification
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
PHENIX1.10.1_2155refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WZU

1wzu


Resolution: 1.6→33.77 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.09
RfactorNum. reflection% reflection
Rfree0.221 2004 6.31 %
Rwork0.184 --
obs0.186 31775 94.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.6→33.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2383 0 18 299 2700
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072518
X-RAY DIFFRACTIONf_angle_d1.4663418
X-RAY DIFFRACTIONf_dihedral_angle_d14.2771592
X-RAY DIFFRACTIONf_chiral_restr0.056384
X-RAY DIFFRACTIONf_plane_restr0.006435
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.640.3175960.27121438X-RAY DIFFRACTION64
1.64-1.68440.32431190.25831642X-RAY DIFFRACTION74
1.6844-1.73390.26321210.24151924X-RAY DIFFRACTION85
1.7339-1.78990.25011380.22252128X-RAY DIFFRACTION95
1.7899-1.85390.25951500.21912236X-RAY DIFFRACTION100
1.8539-1.92810.26881580.20962263X-RAY DIFFRACTION100
1.9281-2.01580.20761420.19152251X-RAY DIFFRACTION100
2.0158-2.12210.23131540.1852256X-RAY DIFFRACTION100
2.1221-2.2550.2171560.17652253X-RAY DIFFRACTION100
2.255-2.42910.22491520.17442254X-RAY DIFFRACTION100
2.4291-2.67340.22631480.192263X-RAY DIFFRACTION100
2.6734-3.06010.23431550.19292269X-RAY DIFFRACTION100
3.0601-3.85450.20871580.16252275X-RAY DIFFRACTION100
3.8545-33.77340.17221570.15522319X-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)
15.3178-0.96574.1345.71144.63118.44480.45320.00080.15240.288-0.27380.59320.0666-1.2904-0.1780.15830.02070.05970.33590.06730.2052-20.9819.682437.4983
21.7826-0.2728-0.06591.43750.59297.18650.1155-0.04850.19770.07810.07360.1169-0.2096-0.2593-0.18750.1210.01380.03170.09290.0250.1215-12.324711.211828.3726
31.861-0.0219-0.98580.5783-0.47537.82690.2519-0.0303-0.03930.131-0.0578-0.1624-0.54170.1035-0.17860.317-0.0142-0.07950.24190.03120.4695-0.773416.663625.211
45.26231.45160.97521.9244-0.37244.8090.1314-0.0096-0.00620.0328-0.0012-0.2208-0.02950.052-0.12120.10150.01890.0040.08220.0140.1073-1.33747.277229.6707
53.26770.0179-0.8842.56020.09114.75870.02340.01130.15030.00260.1591-0.2641-0.16920.3259-0.1370.0876-0.009-0.00070.09730.0040.1199-1.76362.645929.3637
63.82720.425-0.81931.7221-0.13573.6541-0.1930.064-0.3523-0.0119-0.0293-0.20610.25360.02650.19770.15290.01170.00880.1237-0.00410.228213.4373.617515.2381
74.68431.2925-0.59322.6946-0.99992.7738-0.25980.3034-0.254-0.2991-0.0335-0.45350.28580.39370.26470.1580.02820.03560.17130.01320.15525.9182.08486.8669
89.2022-1.89393.02536.1712-0.68422.01230.40040.6999-0.4281-0.5685-0.12550.0990.7287-0.2906-0.24640.24860.0077-0.00010.2055-0.05390.1193-11.8950.7953-1.5042
94.7849-0.84571.22782.7156-0.41773.2133-0.05460.47860.1321-0.3949-0.1095-0.09680.08990.17150.14770.15-0.01830.01990.14070.0160.0688-8.04988.37740.6859
103.6839-0.99220.05394.0444-0.21823.2933-0.06860.02620.0432-0.126-0.03150.0588-0.05480.00230.09130.0782-0.0126-0.0130.07930.01220.0418-14.682112.29849.0744
111.9109-0.7079-0.26611.65710.67443.1321-0.0084-0.1242-0.00970.14760.05480.00010.1547-0.241-0.03670.1186-0.0085-0.00380.07720.04530.0877-9.82741.23132.7221
124.51831.3357-0.97885.8349-4.04942.02160.0826-0.0547-0.03580.4264-0.1567-0.448-0.94290.47170.09850.25740.0013-0.03980.2429-0.09310.323312.503110.991725.6268
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 1:11)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 12:36)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 37:49)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 50:68)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 69:86)
6X-RAY DIFFRACTION6(CHAIN A AND RESID 87:143)
7X-RAY DIFFRACTION7(CHAIN A AND RESID 144:173)
8X-RAY DIFFRACTION8(CHAIN A AND RESID 174:185)
9X-RAY DIFFRACTION9(CHAIN A AND RESID 186:212)
10X-RAY DIFFRACTION10(CHAIN A AND RESID 213:255)
11X-RAY DIFFRACTION11(CHAIN A AND RESID 256:281)
12X-RAY DIFFRACTION12(CHAIN A AND RESID 282:299)

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