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- PDB-5f33: Structure of quinolinate synthase in complex with phosphoglycoloh... -

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Basic information

Entry
Database: PDB / ID: 5f33
TitleStructure of quinolinate synthase in complex with phosphoglycolohydroxamate
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
PHOSPHOGLYCOLOHYDROXAMIC ACID / IRON/SULFUR CLUSTER / Quinolinate synthase
Similarity search - Component
Biological speciesThermotoga maritima MSB8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsVolbeda, A. / Fontecilla-Camps, J.C.
Funding support France, 2items
OrganizationGrant numberCountry
French National Research AgencyANR-12-BS07-0018-01 France
French National Research AgencyANR-11-LABX-0003-01 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. / Darnaux, C. / Reichmann, D. / Amara, P. / Ollagnier de Choudens, S. / Fontecilla-Camps, J.C.
History
DepositionDec 2, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 7, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 14, 2016Group: Database references
Revision 1.2Sep 21, 2016Group: Database references
Revision 1.3Sep 6, 2017Group: Author supporting evidence / Data collection / Category: diffrn_radiation_wavelength / 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)35,4516
Polymers34,6411
Non-polymers8115
Water5,080282
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1280 Å2
ΔGint-64 kcal/mol
Surface area13130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.094, 49.160, 60.221
Angle α, β, γ (deg.)90.00, 104.10, 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 / Mutation: Y107F, K219R
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


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4
#3: Chemical ChemComp-PGH / PHOSPHOGLYCOLOHYDROXAMIC ACID


Mass: 171.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6NO6P
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: 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: 2.16 Å3/Da / Density % sol: 43.03 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.8 / Details: PEG3350, Tris, LiSO4, KCl, PGH 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: 1.45→49.16 Å / Num. obs: 51724 / % possible obs: 98.6 % / Redundancy: 2.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.04 / Rpim(I) all: 0.034 / Net I/σ(I): 12 / Num. measured all: 143402 / Scaling rejects: 3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsCC1/2Diffraction-ID% possible all
1.45-1.52.80.5551.70.556198.7
5.62-49.162.70.02934.50.997196.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0151refinement
Aimless0.5.15data scaling
PDB_EXTRACT3.15data extraction
XDSNovember 3, 2014data reduction
PHASER2.5.7phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4P3X

4p3x


Resolution: 1.45→30 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.966 / Cross valid method: THROUGHOUT / ESU R: 0.072 / ESU R Free: 0.066 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18627 2574 5 %RANDOM
Rwork0.14141 ---
obs0.14369 49128 98.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 22.337 Å2
Baniso -1Baniso -2Baniso -3
1-0.47 Å20 Å2-0.65 Å2
2---0.22 Å20 Å2
3---0.06 Å2
Refinement stepCycle: LAST / Resolution: 1.45→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2400 0 33 282 2715
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0192615
X-RAY DIFFRACTIONr_bond_other_d00.022610
X-RAY DIFFRACTIONr_angle_refined_deg1.512.0043561
X-RAY DIFFRACTIONr_angle_other_deg3.493.0016080
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3035339
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.25424.954109
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.9115514
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5591513
X-RAY DIFFRACTIONr_chiral_restr0.0950.2411
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212846
X-RAY DIFFRACTIONr_gen_planes_other0.0090.02518
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7841.941256
X-RAY DIFFRACTIONr_mcbond_other1.7721.9361255
X-RAY DIFFRACTIONr_mcangle_it2.3173.6521579
X-RAY DIFFRACTIONr_mcangle_other2.3183.6561580
X-RAY DIFFRACTIONr_scbond_it2.1332.3051359
X-RAY DIFFRACTIONr_scbond_other2.092.2921347
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.5064.1381933
X-RAY DIFFRACTIONr_long_range_B_refined3.4325.7043067
X-RAY DIFFRACTIONr_long_range_B_other3.11224.5252920
X-RAY DIFFRACTIONr_rigid_bond_restr8.77135225
X-RAY DIFFRACTIONr_sphericity_free24.485568
X-RAY DIFFRACTIONr_sphericity_bonded8.78955367
LS refinement shellResolution: 1.45→1.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 180 -
Rwork0.254 3650 -
obs--98.64 %

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