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- PDB-5f3d: Structure of quinolinate synthase in complex with reaction interm... -

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Basic information

Entry
Database: PDB / ID: 5f3d
TitleStructure of quinolinate synthase in complex with reaction intermediate W
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
2-IMINO,3-CARBOXY,5-OXO,6-HYDROXY HEXANOIC ACID / IRON/SULFUR CLUSTER / Quinolinate synthase
Similarity search - Component
Biological speciesThermotoga maritima MSB8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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: STRUCTURE OF THE FE4S4 QUINOLINATE SYNTHASE NADA FROM THERMOTOGA MARITIMA
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 1.0Aug 31, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 7, 2016Group: Database references
Revision 1.2Sep 21, 2016Group: Database references
Revision 1.3Aug 16, 2017Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.type
Revision 1.4Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Jan 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)35,4846
Polymers34,6411
Non-polymers8435
Water4,252236
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area790 Å2
ΔGint-44 kcal/mol
Surface area13140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.902, 49.029, 60.520
Angle α, β, γ (deg.)90.00, 105.40, 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 / Plasmid: PT7 / 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-5UK / 2-IMINO,3-CARBOXY,5-OXO,6-HYDROXY HEXANOIC ACID


Mass: 203.149 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H9NO6
#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.: 236 / 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: 2.23 Å3/Da / Density % sol: 44.8 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG3350, Tris, LiSO4, NH4SO4, KCl, DHAP, oxaloacetic acid, 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 PILATUS 6M-F / Detector: PIXEL / Date: Jun 29, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 1.9→45.2 Å / Num. obs: 23542 / % possible obs: 97 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 9.5
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.893 / Mean I/σ(I) obs: 1.4 / % possible all: 89.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0151refinement
XDSNovember 3, 2014data reduction
Aimless0.5.9data scaling
PHASER2.5.7phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4P3X

4p3x


Resolution: 1.9→45 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.957 / SU B: 10.543 / SU ML: 0.142 / Cross valid method: THROUGHOUT / ESU R: 0.164 / ESU R Free: 0.145 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21082 1182 5 %RANDOM
Rwork0.16991 ---
obs0.17202 22317 96.94 %-
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: 36.946 Å2
Baniso -1Baniso -2Baniso -3
1-2.01 Å20 Å2-2.57 Å2
2---0.53 Å20 Å2
3----0.05 Å2
Refinement stepCycle: LAST / Resolution: 1.9→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2396 0 37 236 2669
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0192592
X-RAY DIFFRACTIONr_bond_other_d0.0020.022572
X-RAY DIFFRACTIONr_angle_refined_deg1.5441.9993526
X-RAY DIFFRACTIONr_angle_other_deg0.9513.0015980
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5475332
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.65224.954109
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.74115500
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3591512
X-RAY DIFFRACTIONr_chiral_restr0.0890.2406
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212832
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02521
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_it2.7142.7771247
X-RAY DIFFRACTIONr_mcbond_other2.7072.7731246
X-RAY DIFFRACTIONr_mcangle_it3.8865.191567
X-RAY DIFFRACTIONr_mcangle_other3.8895.1931568
X-RAY DIFFRACTIONr_scbond_it3.7743.2971345
X-RAY DIFFRACTIONr_scbond_other3.6693.2581332
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.585.8821911
X-RAY DIFFRACTIONr_long_range_B_refined8.5236.3363041
X-RAY DIFFRACTIONr_long_range_B_other8.33835.0272928
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.403 72 -
Rwork0.428 1508 -
obs--88.17 %
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)
10.4863-0.14480.13560.2094-0.10991.1467-0.0026-0.07180.0257-0.04450.05120.02860.1042-0.1274-0.04860.0266-0.0066-0.02350.03580.00170.05392.4826-4.383624.3062
20.44020.2369-0.06190.45250.43772.1206-0.06390.1217-0.04530.02540.0253-0.0119-0.06560.02290.03860.0381-0.02830.00020.056-0.02770.023623.72958.928416.8389
31.5547-0.77560.34080.4553-0.45951.45620.0390.10760.027-0.0405-0.0599-0.00010.01580.12170.0210.0775-0.0093-0.04480.01630.00920.02725.74841.0552-1.4331
42.68860.3998-0.76071.06980.22354.85690.07280.1311-0.00070.02690.0694-0.01530.09020.1214-0.14220.01660.0171-0.01590.0208-0.0150.017315.7396-6.942411.5445
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-4 - 78
2X-RAY DIFFRACTION1A257 - 279
3X-RAY DIFFRACTION2A84 - 165
4X-RAY DIFFRACTION2A280 - 298
5X-RAY DIFFRACTION3A171 - 251
6X-RAY DIFFRACTION4A79 - 83
7X-RAY DIFFRACTION4A166 - 170
8X-RAY DIFFRACTION4A252 - 256
9X-RAY DIFFRACTION4A301 - 302

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