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- PDB-7p4m: Structure of the quinolinate synthase Y107F variant in an empty o... -

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Basic information

Entry
Database: PDB / ID: 7p4m
TitleStructure of the quinolinate synthase Y107F variant in an empty open form
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 / IRON/SULFUR CLUSTER / Quinolinate synthase
Similarity search - Component
Biological speciesThermotoga maritima MSB8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 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)35,3595
Polymers34,6411
Non-polymers7184
Water6,720373
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1060 Å2
ΔGint-63 kcal/mol
Surface area13080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.442, 49.051, 60.809
Angle α, β, γ (deg.)90.000, 106.830, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#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 MSB8 (bacteria) / Gene: nadA, TM_1644 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9X1X7, quinolinate synthase
#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-F3S / FE3-S4 CLUSTER / Iron–sulfur cluster


Mass: 295.795 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe3S4
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


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


Mass: 18.015 Da / Num. of mol.: 373 / Source method: isolated from a natural source / Formula: H2O
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: 2.28 Å3/Da / Density % sol: 46.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG3350, NaF, Bis Tris propane, anaerobic, pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.55→49.05 Å / Num. obs: 44673 / % possible obs: 98.1 % / Redundancy: 2.6 % / Biso Wilson estimate: 26.48 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.028 / Net I/σ(I): 14.7
Reflection shellResolution: 1.55→1.6 Å / Rmerge(I) obs: 0.498 / Num. unique obs: 4354 / CC1/2: 0.608

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
PHENIX1.18.2refinement
XDSdata reduction
Aimlessdata scaling
PHASER2.5.7phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5F35

5f35


Resolution: 1.55→46.48 Å / SU ML: 0.1736 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.557
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1775 2220 4.97 %
Rwork0.1332 42435 -
obs0.1355 44655 97.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37.77 Å2
Refinement stepCycle: LAST / Resolution: 1.55→46.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2402 0 17 373 2792
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00552580
X-RAY DIFFRACTIONf_angle_d0.8523515
X-RAY DIFFRACTIONf_chiral_restr0.0582404
X-RAY DIFFRACTIONf_plane_restr0.0057449
X-RAY DIFFRACTIONf_dihedral_angle_d18.70111031
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.580.29881340.26942658X-RAY DIFFRACTION97.52
1.58-1.620.3091570.23212599X-RAY DIFFRACTION97.94
1.62-1.660.23651180.19482632X-RAY DIFFRACTION98.04
1.66-1.710.2251230.16322631X-RAY DIFFRACTION97.52
1.71-1.760.21821540.14322645X-RAY DIFFRACTION98.45
1.76-1.810.20861290.13692673X-RAY DIFFRACTION98.45
1.81-1.880.22791290.12962672X-RAY DIFFRACTION98.7
1.88-1.950.1741540.12112621X-RAY DIFFRACTION98.37
1.95-2.040.1771440.11742660X-RAY DIFFRACTION98.18
2.04-2.150.16571520.10742636X-RAY DIFFRACTION98.9
2.15-2.280.16061160.11312680X-RAY DIFFRACTION98.66
2.28-2.460.19241350.12692702X-RAY DIFFRACTION98.34
2.46-2.710.21571410.13992637X-RAY DIFFRACTION98.27
2.71-3.10.18931360.14062666X-RAY DIFFRACTION97.6
3.1-3.90.16031520.12372650X-RAY DIFFRACTION97.09
3.91-46.480.1481460.13452673X-RAY DIFFRACTION95.72

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