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- PDB-6i0r: Structure of quinolinate synthase in complex with 5-mercaptopyrid... -

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Basic information

Entry
Database: PDB / ID: 6i0r
TitleStructure of quinolinate synthase in complex with 5-mercaptopyridine-2,3-dicarboxylic acid
ComponentsQuinolinate synthase A
KeywordsTRANSFERASE / NAD BIOSYNTHESIS / IRON SULFUR CLUSTER
Function / homology
Function and homology information


'de novo' NAD biosynthetic process from aspartate / quinolinate synthase / quinolinate synthetase A activity / 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
: / HYDROSULFURIC ACID / 5-mercaptopyridine-2,3-dicarboxylic acid / Quinolinate synthase
Similarity search - Component
Biological speciesThermotoga maritima MSB8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsVolbeda, A. / Fontecilla-Camps, J.C.
Funding support France, 1items
OrganizationGrant numberCountry
ANR-16-CE18-0026 France
CitationJournal: Chem.Commun.(Camb.) / Year: 2019
Title: Design of specific inhibitors of quinolinate synthase based on [4Fe-4S] cluster coordination.
Authors: Saez Cabodevilla, J. / Volbeda, A. / Hamelin, O. / Latour, J.M. / Gigarel, O. / Clemancey, M. / Darnault, C. / Reichmann, D. / Amara, P. / Fontecilla-Camps, J.C. / Ollagnier de Choudens, S.
History
DepositionOct 26, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 20, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 24, 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Quinolinate synthase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,19910
Polymers34,6411
Non-polymers5599
Water1,982110
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1260 Å2
ΔGint-81 kcal/mol
Surface area12700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.900, 48.500, 60.500
Angle α, β, γ (deg.)90.000, 107.100, 90.000
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: Y21F, 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-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#3: Chemical
ChemComp-H2S / HYDROSULFURIC ACID / HYDROGEN SULFIDE / Hydrogen sulfide


Mass: 34.081 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: H2S
#4: Chemical ChemComp-QAT / 5-mercaptopyridine-2,3-dicarboxylic acid


Mass: 199.184 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H5NO4S
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 110 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.24 Å3/Da / Density % sol: 45.19 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.7 / Details: PEG33500, dioxane, Na2HPO4, MES, anaerobic

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 1.00394 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 28, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00394 Å / Relative weight: 1
ReflectionResolution: 2.1→37.16 Å / Num. obs: 17011 / % possible obs: 95.3 % / Redundancy: 3 % / CC1/2: 0.982 / Rmerge(I) obs: 0.143 / Rpim(I) all: 0.091 / Rrim(I) all: 0.171 / Net I/σ(I): 8.5 / Num. measured all: 50636
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.1-2.172.90.88716700.5360.5761.06496.7
8.13-37.162.70.0862880.9860.0550.10387.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.5.32data scaling
PHASERphasing
REFMAC5.8.0232refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6F48

6f48


Resolution: 2.1→37.16 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.932 / SU B: 15.437 / SU ML: 0.197 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.28 / ESU R Free: 0.206
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2393 830 4.9 %RANDOM
Rwork0.1978 ---
obs0.1999 16177 94.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 124.58 Å2 / Biso mean: 43.712 Å2 / Biso min: 21.98 Å2
Baniso -1Baniso -2Baniso -3
1--0.82 Å20 Å2-0.77 Å2
2--0.18 Å20 Å2
3---0.94 Å2
Refinement stepCycle: final / Resolution: 2.1→37.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2397 0 21 110 2528
Biso mean--40.27 44.35 -
Num. residues----303
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0132474
X-RAY DIFFRACTIONr_bond_other_d0.0160.0172431
X-RAY DIFFRACTIONr_angle_refined_deg1.5431.6563344
X-RAY DIFFRACTIONr_angle_other_deg1.5581.5825677
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4995308
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.63423.363113
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.41315481
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5371512
X-RAY DIFFRACTIONr_chiral_restr0.1050.2330
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022686
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02449
LS refinement shellResolution: 2.1→2.154 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 60 -
Rwork0.321 1197 -
all-1257 -
obs--96.25 %
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)
10.7846-0.1978-0.14630.6902-0.79611.66210.0012-0.06290.017-0.07350.04570.03350.055-0.1638-0.04690.02010.0054-0.02870.05560.00150.06782.486-5.07824.028
21.17280.83750.67120.70910.79892.2632-0.0840.1238-0.0301-0.02550.09460.002-0.09140.1108-0.01060.0481-0.0055-0.01020.0437-0.00880.060523.6427.71816.181
31.9484-0.20380.34290.4753-0.21730.9222-0.00390.17770.0416-0.10190.04430.11-0.00840.1134-0.04040.07320.0077-0.06350.0678-0.0040.06016.262-0.312-1.412
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-4 - 80
2X-RAY DIFFRACTION1A254 - 279
3X-RAY DIFFRACTION2A81 - 167
4X-RAY DIFFRACTION2A280 - 298
5X-RAY DIFFRACTION3A168 - 253

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