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- PDB-6i0p: Structure of quinolinate synthase in complex with 6-mercaptopyrid... -

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Basic information

Entry
Database: PDB / ID: 6i0p
TitleStructure of quinolinate synthase in complex with 6-mercaptopyridine-2,3-dicarboxylic 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
PHOSPHATE ION / 6-mercaptopyridine-2,3-dicarboxylic acid / IRON/SULFUR CLUSTER / Quinolinate synthase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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

Downloads & links

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Assembly

Deposited unit
A: Quinolinate synthase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,3225
Polymers34,6411
Non-polymers6814
Water5,585310
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area660 Å2
ΔGint-35 kcal/mol
Surface area12800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.500, 48.700, 60.600
Angle α, β, γ (deg.)90.000, 107.000, 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, Y21F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099) (bacteria)
Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099 / 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, 314 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-QAS / 6-mercaptopyridine-2,3-dicarboxylic acid


Mass: 199.184 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H5NO4S
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 310 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.28 Å3/Da / Density % sol: 46.13 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7.3 / Details: PEG33500, dioxane, Na2HPO4, HEPES, anaerobic

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 21, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.9→46.49 Å / Num. obs: 24522 / % possible obs: 99.7 % / Redundancy: 5.8 % / CC1/2: 0.995 / Rmerge(I) obs: 0.125 / Rpim(I) all: 0.055 / Rrim(I) all: 0.137 / Net I/σ(I): 9 / Num. measured all: 141788 / Scaling rejects: 2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.9-1.975.21.13323900.5730.5451.26399.7
7.36-46.495.60.0794570.9910.0360.08899.3

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Processing

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

6f48


Resolution: 1.9→46.49 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.954 / SU B: 8.79 / SU ML: 0.125 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.156 / ESU R Free: 0.133
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2003 1227 5 %RANDOM
Rwork0.1699 ---
obs0.1714 23281 99.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 92.02 Å2 / Biso mean: 34.929 Å2 / Biso min: 12.2 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20 Å2-1.22 Å2
2---0.19 Å20 Å2
3---0.75 Å2
Refinement stepCycle: final / Resolution: 1.9→46.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2382 0 27 310 2719
Biso mean--29.3 43.67 -
Num. residues----301
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0132506
X-RAY DIFFRACTIONr_bond_other_d0.0110.0172457
X-RAY DIFFRACTIONr_angle_refined_deg1.5371.6663397
X-RAY DIFFRACTIONr_angle_other_deg1.511.5825743
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8165314
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.25923.509114
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.02515491
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7651512
X-RAY DIFFRACTIONr_chiral_restr0.1140.2337
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022702
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02449
LS refinement shellResolution: 1.9→1.949 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 99 -
Rwork0.306 1698 -
all-1797 -
obs--98.84 %
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)
11.14310.090.34471.022-0.88522.2466-0.0231-0.22720.0318-0.05080.17260.16630.0394-0.3087-0.14950.01190.0030.00980.13010.02420.07192.92-5.26124.117
20.82270.63211.10861.34771.29473.4682-0.19590.13950.0219-0.10950.11430.046-0.30040.26270.08160.0565-0.04310.01090.1151-0.01520.042523.9057.68415.959
31.7387-0.92060.64060.9974-0.3511.99340.08950.2433-0.0622-0.1812-0.05150.15090.07050.1221-0.0380.07640.0132-0.03790.07710.00230.03116.344-0.009-1.239
426.7231-3.93411.624824.3261-22.777321.48960.21670.4784-0.0219-0.1209-0.09640.13430.09840.0593-0.12040.0330.0180.00750.0756-0.01740.009914.913-5.23112.098
516.83050.3975-2.12520.0094-0.05010.26880.1595-0.18780.31990.0052-0.05830.0065-0.02560.0293-0.10120.10540.03280.02420.1491-0.03470.121511.0170.93911.898
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-2 - 81
2X-RAY DIFFRACTION1A255 - 279
3X-RAY DIFFRACTION2A82 - 168
4X-RAY DIFFRACTION2A280 - 298
5X-RAY DIFFRACTION3A169 - 254
6X-RAY DIFFRACTION4A301
7X-RAY DIFFRACTION5A302

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