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- PDB-6i0k: Structure of quinolinate synthase in complex with 4-mercaptophtha... -

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Basic information

Entry
Database: PDB / ID: 6i0k
TitleStructure of quinolinate synthase in complex with 4-mercaptophthalic acid
ComponentsQuinolinate synthase A
KeywordsTRANSFERASE / NAD BIOSYNTHESIS / IRON SULFUR CLUSTER
Function / homology
Function and homology information


quinolinate synthase / quinolinate synthetase A activity / 'de novo' NAD+ biosynthetic process from L-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-GZ8 / PHOSPHATE ION / IRON/SULFUR CLUSTER / Quinolinate synthase
Similarity search - Component
Biological speciesThermotoga maritima MSB8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 Å
AuthorsVolbeda, A. / Fontecilla-Camps, J.C.
Funding support France, 1items
OrganizationGrant numberCountry
ANR-16-CE18-0026 France
CitationJournal: Chem.Commun.(Camb.) / Year: 2019
Title: Design of specific inhibitors of quinolinate synthase based on [4Fe-4S] cluster coordination.
Authors: Saez Cabodevilla, J. / Volbeda, A. / Hamelin, O. / Latour, J.M. / Gigarel, O. / Clemancey, M. / Darnault, C. / Reichmann, D. / Amara, P. / Fontecilla-Camps, J.C. / Ollagnier de Choudens, S.
History
DepositionOct 26, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 20, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 24, 2024Group: 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)35,3215
Polymers34,6411
Non-polymers6804
Water4,810267
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area730 Å2
ΔGint-38 kcal/mol
Surface area12900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.700, 48.380, 60.640
Angle α, β, γ (deg.)90.000, 107.660, 90.000
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: 34640.598 Da / Num. of mol.: 1 / Mutation: K219R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima MSB8 (bacteria) / Gene: nadA, TM_1644 / Plasmid: PT7 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9X1X7, quinolinate synthase

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Non-polymers , 5 types, 271 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-GZ8 / 4-mercaptoidenecyclohexa-2,5-diene-1,2-dicarboxylic acid


Mass: 198.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H6O4S / 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
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 267 / 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: 2.28 Å3/Da / Density % sol: 46.13 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7 / Details: PEG33500, NaCl, Na2HPO4, MES, anaerobic

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.07438 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07438 Å / Relative weight: 1
ReflectionResolution: 1.6→46.8 Å / Num. obs: 40160 / % possible obs: 98.7 % / Redundancy: 4.4 % / CC1/2: 0.997 / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.045 / Rrim(I) all: 0.096 / Net I/σ(I): 8.7 / Num. measured all: 176966 / Scaling rejects: 15
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.6-1.664.61.47639360.3140.771.66999.5
6.2-46.840.0557060.9970.0290.06295.5

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.5.32data scaling
REFMAC5.8.0232refinement
PDB_EXTRACT3.24data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6F48

6f48


Resolution: 1.64→46.8 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.962 / SU B: 6.584 / SU ML: 0.094 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.131 / ESU R Free: 0.096
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.206 1845 5 %RANDOM
Rwork0.1564 ---
obs0.1589 35414 98.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 92.15 Å2 / Biso mean: 32.414 Å2 / Biso min: 18.98 Å2
Baniso -1Baniso -2Baniso -3
1--0.4 Å20 Å2-1.03 Å2
2--0.33 Å20 Å2
3---0.61 Å2
Refinement stepCycle: final / Resolution: 1.64→46.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2384 0 27 267 2678
Biso mean--29.03 44.46 -
Num. residues----301
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0132506
X-RAY DIFFRACTIONr_bond_other_d0.0040.0172446
X-RAY DIFFRACTIONr_angle_refined_deg1.381.6643405
X-RAY DIFFRACTIONr_angle_other_deg1.3181.5815720
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6535316
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.49823.478115
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.54815486
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6361512
X-RAY DIFFRACTIONr_chiral_restr0.0830.2337
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022715
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02452
X-RAY DIFFRACTIONr_rigid_bond_restr1.58234952
X-RAY DIFFRACTIONr_sphericity_free20.6325141
X-RAY DIFFRACTIONr_sphericity_bonded9.83855022
LS refinement shellResolution: 1.64→1.683 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.366 123 -
Rwork0.315 2622 -
all-2745 -
obs--98.81 %

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