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- PDB-6f4l: Structure of quinolinate synthase with inhibitor-derived quinolinate -

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Basic information

Entry
Database: PDB / ID: 6f4l
TitleStructure of quinolinate synthase with inhibitor-derived quinolinate
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 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
QUINOLINIC ACID / IRON/SULFUR CLUSTER / Quinolinate synthase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsVolbeda, A. / Fontecilla-Camps, J.C.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research AgencyANR-16-CE18-0026 France
Citation
Journal: ACS Chem. Biol. / Year: 2018
Title: Crystallographic Trapping of Reaction Intermediates in Quinolinic Acid Synthesis by NadA.
Authors: Volbeda, A. / Saez Cabodevilla, J. / Darnault, C. / Gigarel, O. / Han, T.H. / Renoux, O. / Hamelin, O. / Ollagnier-de-Choudens, S. / Amara, P. / Fontecilla-Camps, J.C.
#1: Journal: J. Am. Chem. Soc. / Year: 2016
Title: Crystal Structures of Quinolinate Synthase in Complex with a Substrate Analogue, the Condensation Intermediate, and Substrate-Derived Product.
Authors: Volbeda, A. / Darnault, C. / Renoux, O. / Reichmann, D. / Amara, P. / Ollagnier de Choudens, S. / Fontecilla-Camps, J.C.
#2: Journal: J. Am. Chem. Soc. / Year: 2014
Title: The crystal structure of Fe4S4 quinolinate synthase unravels an enzymatic dehydration mechanism that uses tyrosine and a hydrolase-type triad.
Authors: Cherrier, M.V. / Chan, A. / Darnault, C. / Reichmann, D. / Amara, P. / Ollagnier de Choudens, S. / Fontecilla-Camps, J.C.
History
DepositionNov 29, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 25, 2018Provider: repository / Type: Initial release
Revision 1.1May 30, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.name
Revision 1.2Jan 17, 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)35,4185
Polymers34,6571
Non-polymers7624
Water66737
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1230 Å2
ΔGint-28 kcal/mol
Surface area12970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.440, 49.310, 61.900
Angle α, β, γ (deg.)90.000, 107.210, 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: 34656.598 Da / Num. of mol.: 1 / Mutation: K219R
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, 41 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
#3: Chemical ChemComp-NTM / QUINOLINIC ACID / Quinolinic acid


Mass: 167.119 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H5NO4
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-NHE / 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID / N-CYCLOHEXYLTAURINE / CHES / CHES (buffer)


Mass: 207.290 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H17NO3S / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 2.33 Å3/Da / Density % sol: 47.26 % / Mosaicity: 0 °
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 9.1 / Details: PEG33500, Na2HPO4, CHES, anaerobic

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Dec 9, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.3→46.95 Å / Num. obs: 14259 / % possible obs: 99.1 % / Redundancy: 5.4 % / CC1/2: 0.996 / Rmerge(I) obs: 0.137 / Rpim(I) all: 0.064 / Rrim(I) all: 0.152 / Net I/σ(I): 8.9 / Num. measured all: 77646
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.3-2.385.71.775800614120.3750.8251.962199.7
8.91-46.954.90.04913162670.9970.0240.05545.598.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0158refinement
XDSdata reduction
Aimless0.5.27data scaling
PHASERphasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4P3X

4p3x


Resolution: 2.3→46.95 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.954 / SU B: 24.078 / SU ML: 0.241 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.391 / ESU R Free: 0.221 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2204 720 5.1 %RANDOM
Rwork0.2019 ---
obs0.2029 13514 98.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 138.25 Å2 / Biso mean: 55.07 Å2 / Biso min: 31.74 Å2
Baniso -1Baniso -2Baniso -3
1-1.13 Å20 Å2-1.75 Å2
2---0.56 Å20 Å2
3---0.43 Å2
Refinement stepCycle: final / Resolution: 2.3→46.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2379 0 34 38 2451
Biso mean--75.6 54.33 -
Num. residues----302
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.022485
X-RAY DIFFRACTIONr_angle_refined_deg1.3732.0213364
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0495309
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.45225100
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.05915474
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.5641512
X-RAY DIFFRACTIONr_chiral_restr0.0860.2389
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211797
LS refinement shellResolution: 2.3→2.36 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 50 -
Rwork0.363 986 -
all-1036 -
obs--98.01 %
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)
10.48040.13820.06840.7094-0.57861.17570.0105-0.01920.0319-0.03650.0566-0.02160.0355-0.2416-0.06710.007-0.00710.00060.07720.0020.05912.5078-5.832824.412
20.445-0.18660.10970.5020.15232.0471-0.01610.0534-0.02880.0134-0.04260.00450.0919-0.03720.05870.0584-0.00290.00850.0126-0.0210.067223.73227.282216.809
31.5197-0.38380.22310.9908-0.31590.86960.00910.0192-0.0289-0.1032-0.00080.0822-0.02830.0255-0.00830.06660.0065-0.02470.0226-0.02030.02816.2857-0.1954-0.7452
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-3 - 80
2X-RAY DIFFRACTION1A254 - 279
3X-RAY DIFFRACTION2A81 - 167
4X-RAY DIFFRACTION2A280 - 298
5X-RAY DIFFRACTION3A168 - 253

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