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- PDB-7p4q: Structure of the quinolinate synthase S124A variant complexed wit... -

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Basic information

Entry
Database: PDB / ID: 7p4q
TitleStructure of the quinolinate synthase S124A variant complexed with citrate
ComponentsQuinolinate synthase A
KeywordsTRANSFERASE / NAD biosynthesis / Iron Sulfur cluster / active site cavity
Function / homology
Function and homology information


'de novo' NAD biosynthetic process from aspartate / quinolinate synthase / quinolinate synthetase A activity / 4 iron, 4 sulfur cluster binding / metal ion binding / cytosol
Similarity search - Function
Quinolinate synthetase A / Quinolinate synthase A, type 2 / Quinolinate synthetase A superfamily / Quinolinate synthetase A protein
Similarity search - Domain/homology
FE3-S4 CLUSTER / CITRATE ANION / IRON/SULFUR CLUSTER / Quinolinate synthase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsVolbeda, A.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-16-CE18-0026 France
CitationJournal: Acs Chem.Biol. / Year: 2021
Title: Transient Formation of a Second Active Site Cavity during Quinolinic Acid Synthesis by NadA.
Authors: Basbous, H. / Volbeda, A. / Amara, P. / Rohac, R. / Martin, L. / Ollagnier de Choudens, S. / Fontecilla-Camps, J.C.
History
DepositionJul 12, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 29, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 20, 2021Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Dec 1, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)36,10112
Polymers34,6411
Non-polymers1,46011
Water5,134285
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2680 Å2
ΔGint-54 kcal/mol
Surface area13250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.740, 49.330, 62.240
Angle α, β, γ (deg.)90.000, 108.140, 90.000
Int Tables number4
Space group name H-MP1211
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Quinolinate synthase A


Mass: 34640.598 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8) (bacteria)
Strain: ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8
Gene: nadA, TM_1644
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q9X1X7, quinolinate synthase

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Non-polymers , 6 types, 296 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 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-FLC / CITRATE ANION / Citric acid


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#4: Chemical ChemComp-F3S / FE3-S4 CLUSTER / Iron–sulfur cluster


Mass: 295.795 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe3S4
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 285 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.35 Å3/Da / Density % sol: 47.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: PEG4000, ammonium acetate, NaCl, trisodium citrate, pH 5.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9999 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 14, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 2.2→59.15 Å / Num. obs: 16403 / % possible obs: 99.2 % / Redundancy: 5 % / Biso Wilson estimate: 27.59 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.083 / Net I/σ(I): 14.2
Reflection shellResolution: 2.2→2.28 Å / Rmerge(I) obs: 0.351 / Num. unique obs: 1585 / CC1/2: 0.897

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6i0p

6i0p


Resolution: 2.2→59.15 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 26.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.223 802 4.89 %
Rwork0.1792 15601 -
obs0.1815 16403 99.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 122.58 Å2 / Biso mean: 34.9661 Å2 / Biso min: 14.25 Å2
Refinement stepCycle: final / Resolution: 2.2→59.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2400 0 66 285 2751
Biso mean--48.42 43.05 -
Num. residues----303
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2-2.340.34371110.24872596270799
2.34-2.520.28191390.2292542268199
2.52-2.770.29821250.21762596272199
2.77-3.170.22711370.18992569270699
3.17-40.21451420.150526192761100
4-59.150.16191480.152726792827100
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)
10.4529-0.1965-0.16690.457-0.42960.8866-0.0346-0.00320.0539-0.09460.06190.0029-0.0366-0.1879-00.0776-0.003500.125-0.00350.10821.154-3.799923.8439
20.38020.083-0.45620.55040.54931.0748-0.1220.0929-0.0986-0.07990.0705-0.01070.01170.021700.1209-0.03220.01870.104-0.02030.108424.95946.719714.3159
30.34970.2525-0.02760.7173-0.16150.23270.05990.0287-0.0683-0.06840.00050.0366-0.03410.0114-00.17610.0347-0.0370.1475-0.00980.14096.1181-0.1328-0.7568
40.1755-0.4261-0.08620.2236-0.21320.1674-0.1229-0.08390.1885-0.11930.19430.19160.3124-0.078200.1425-0.03460.04370.1529-0.0080.1314.4387-11.957725.7566
50.02770.08080.08560.07630.10390.02570.3612-0.72920.17780.408-0.8805-0.195-0.503-0.777800.14720.00970.04080.0759-0.18090.078316.639711.667726.9821
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -4 through 81 )A-4 - 81
2X-RAY DIFFRACTION2chain 'A' and (resid 82 through 168 )A82 - 168
3X-RAY DIFFRACTION3chain 'A' and (resid 169 through 254 )A169 - 254
4X-RAY DIFFRACTION4chain 'A' and (resid 255 through 278 )A255 - 278
5X-RAY DIFFRACTION5chain 'A' and (resid 279 through 298)A279 - 298

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