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- PDB-6f48: Structure of quinolinate synthase with reaction intermediates X and Y -

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Basic information

Entry
Database: PDB / ID: 6f48
TitleStructure of quinolinate synthase with reaction intermediates X and Y
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
IRON/SULFUR CLUSTER / 2-imino,3-carboxy,5-hydroxy,6-oxo hexanoic acid / 5-hydroxy,-4,5-dihydroquinolinate / Quinolinate synthase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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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)35,5447
Polymers34,6411
Non-polymers9036
Water5,657314
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area880 Å2
ΔGint-41 kcal/mol
Surface area12820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.500, 48.950, 61.250
Angle α, β, γ (deg.)90.000, 107.270, 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: Y21F, K219R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: nadA, TM_1644 / Plasmid: PT7 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9X1X7, quinolinate synthase

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Non-polymers , 6 types, 320 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-XQB / 2-imino,3-carboxy,5-hydroxy,6-oxo hexanoic acid


Mass: 203.149 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H9NO6 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-YQA / 5-hydroxy,-4,5-dihydroquinolinate


Mass: 185.134 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H7NO5 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 314 / 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: 2.29 Å3/Da / Density % sol: 46.37 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7.1
Details: PEG33500, ammonium sulfate, oxaloacetate, DHAP, NaF, Bis Tris propane, 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: 1.5→37.54 Å / Num. obs: 49728 / % possible obs: 98.8 % / Redundancy: 4.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.028 / Rrim(I) all: 0.059 / Net I/σ(I): 16.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.5-1.554.40.90748440.7190.4881.03299.3
5.81-37.5440.0348760.9990.020.03994.5

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Processing

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

4p3x


Resolution: 1.5→37.5 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.973 / SU B: 4.812 / SU ML: 0.07 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.074 / ESU R Free: 0.067
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1789 2499 5 %RANDOM
Rwork0.1343 ---
obs0.1365 47225 98.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 95.8 Å2 / Biso mean: 27.231 Å2 / Biso min: 10.66 Å2
Baniso -1Baniso -2Baniso -3
1-2.21 Å20 Å2-1.27 Å2
2---1.34 Å20 Å2
3----0.07 Å2
Refinement stepCycle: final / Resolution: 1.5→37.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2387 0 43 317 2747
Biso mean--27.43 40.47 -
Num. residues----302
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0192555
X-RAY DIFFRACTIONr_bond_other_d0.0020.022498
X-RAY DIFFRACTIONr_angle_refined_deg1.4972.013464
X-RAY DIFFRACTIONr_angle_other_deg1.1423.0015845
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.225323
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.48625.192104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.38815497
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5471512
X-RAY DIFFRACTIONr_chiral_restr0.0980.2399
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212760
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02447
X-RAY DIFFRACTIONr_rigid_bond_restr1.7535053
X-RAY DIFFRACTIONr_sphericity_free27.2555194
X-RAY DIFFRACTIONr_sphericity_bonded13.53555117
LS refinement shellResolution: 1.5→1.539 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.374 201 -
Rwork0.346 3497 -
all-3698 -
obs--99.33 %

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