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- PDB-5lqm: Structure of quinolinate synthase Y21F mutant in complex with citrate -

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Basic information

Entry
Database: PDB / ID: 5lqm
TitleStructure of quinolinate synthase Y21F mutant in complex with citrate
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
CITRATE ANION / IRON/SULFUR CLUSTER / Quinolinate synthase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.62 Å
AuthorsVolbeda, A. / Fontecilla-Camps, J.C.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research AgencyANR-12-BS07-0018-01 France
Citation
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.
#1: 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
DepositionAug 17, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 31, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 7, 2016Group: Database references
Revision 1.2Sep 21, 2016Group: Database references
Revision 1.3Aug 30, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jan 10, 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)35,1813
Polymers34,6411
Non-polymers5412
Water5,080282
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area850 Å2
ΔGint-23 kcal/mol
Surface area13030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.807, 48.936, 60.422
Angle α, β, γ (deg.)90.00, 104.62, 90.00
Int Tables number4
Space group name H-MP1211

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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
Details: Specific_mutation = "Y21F " Specific_mutation = "K219R "
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-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q9X1X7, quinolinate synthase
#2: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4
#3: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 282 / 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: 2.18 Å3/Da / Density % sol: 43.7 %
Crystal growTemperature: 298 K / Method: vapor diffusion / Details: PEG3350, sodium citrate, KCl, anaerobic

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.96862 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 31, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96862 Å / Relative weight: 1
ReflectionResolution: 1.62→37.53 Å / Num. obs: 34681 / % possible obs: 91 % / Redundancy: 2.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.044 / Net I/σ(I): 12
Reflection shellResolution: 1.62→1.68 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.454 / Mean I/σ(I) obs: 1.8 / CC1/2: 0.49 / % possible all: 62

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Processing

Software
NameVersionClassification
REFMAC5.8.0123refinement
XDSdata reduction
Aimless0.5.15data scaling
PHASER2.5.7phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4P3X

4p3x


Resolution: 1.62→37.53 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.957 / SU B: 5.674 / SU ML: 0.081 / Cross valid method: THROUGHOUT / ESU R: 0.15 / ESU R Free: 0.099 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20136 1733 5 %RANDOM
Rwork0.14945 ---
obs0.15212 32948 90.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 23.029 Å2
Baniso -1Baniso -2Baniso -3
1-1.33 Å20 Å2-1.16 Å2
2---0.73 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.62→37.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2401 0 21 282 2704
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0192566
X-RAY DIFFRACTIONr_bond_other_d0.0020.022579
X-RAY DIFFRACTIONr_angle_refined_deg1.5351.9993485
X-RAY DIFFRACTIONr_angle_other_deg13.0015999
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.275328
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.1724.952105
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.59415506
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5811512
X-RAY DIFFRACTIONr_chiral_restr0.1020.2403
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212789
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02507
X-RAY DIFFRACTIONr_mcangle_it2.4783.031558
X-RAY DIFFRACTIONr_mcangle_other2.4883.0331559
X-RAY DIFFRACTIONr_scbond_it2.1362.361324
X-RAY DIFFRACTIONr_scbond_other2.1292.361322
X-RAY DIFFRACTIONr_scangle_other2.4763.411900
LS refinement shellResolution: 1.62→1.662 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 85 -
Rwork0.324 1580 -
obs--59.66 %

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