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- PDB-4hhe: Quinolinate synthase from Pyrococcus furiosus -

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Basic information

Entry
Database: PDB / ID: 4hhe
TitleQuinolinate synthase from Pyrococcus furiosus
ComponentsQuinolinate synthase A
KeywordsTRANSFERASE / QUINOLINATE SYNTHASE / NAD BIOSYNTHESIS / NADA / PYRIDINE NUCLEOTIDE BIOSYNTHESIS / BIOSYNTHETIC PROTEIN
Function / homology
Function and homology information


quinolinate synthase / quinolinate synthetase A activity / NAD biosynthetic process / 4 iron, 4 sulfur cluster binding / metal ion binding / cytoplasm
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
Quinolinate synthase A
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.797 Å
AuthorsSoriano, E.V. / Zhang, Y. / Settembre, E.C. / Colabroy, K. / Sanders, J.M. / Dorrestein, P.C. / Begley, T.P. / Ealick, S.E.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2013
Title: Active-site models for complexes of quinolinate synthase with substrates and intermediates.
Authors: Soriano, E.V. / Zhang, Y. / Colabroy, K.L. / Sanders, J.M. / Settembre, E.C. / Dorrestein, P.C. / Begley, T.P. / Ealick, S.E.
History
DepositionOct 9, 2012Deposition site: RCSB / Processing site: RCSB
SupersessionAug 28, 2013ID: 2QS0
Revision 1.0Aug 28, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 18, 2013Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_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)36,7023
Polymers36,6321
Non-polymers712
Water00
1
A: Quinolinate synthase A
hetero molecules

A: Quinolinate synthase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,4056
Polymers73,2632
Non-polymers1424
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area4930 Å2
ΔGint-68 kcal/mol
Surface area26590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.915, 80.717, 141.042
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Quinolinate synthase A


Mass: 36631.566 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q8TZL3, quinolinate synthase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl

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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: 2.99 Å3/Da / Density % sol: 58.83 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 4.4 M NaCl, 50 mM Tris, 5% ethylene glycol, pH 7.5, vapor diffusion, hanging drop, temperature 291K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 8-BM10.9795
SYNCHROTRONAPS 8-BM20.9792
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDJul 14, 2004
ADSC QUANTUM 3152CCDDec 1, 2003
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.97951
20.97921
ReflectionResolution: 2.8→50 Å / Num. all: 11147 / Num. obs: 11147 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 8.9 % / Rmerge(I) obs: 0.105 / Χ2: 1.769 / Net I/σ(I): 16.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.8-2.99.10.40511041.5691,2100
2.9-3.029.10.30910871.7011,2100
3.02-3.159.10.24710961.7711,2100
3.15-3.329.10.18711041.8111,2100
3.32-3.5390.15211061.8111,2100
3.53-3.890.12611042.3021,299.9
3.8-4.188.80.09611091.991,2100
4.18-4.798.80.08111281.851,299.8
4.79-6.038.40.0711361.5951,299.8
6.03-508.10.05411731.2561,297.8

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
SnBphasing
RefinementMethod to determine structure: SAD / Resolution: 2.797→25.225 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7561 / SU ML: 0.36 / σ(F): 1.35 / Phase error: 29.82 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2698 531 4.78 %Random
Rwork0.2077 ---
obs0.2107 11117 99.49 %-
all-11147 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 132.56 Å2 / Biso mean: 39.245 Å2 / Biso min: 1.98 Å2
Refinement stepCycle: LAST / Resolution: 2.797→25.225 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2281 0 2 0 2283
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052312
X-RAY DIFFRACTIONf_angle_d0.8473137
X-RAY DIFFRACTIONf_chiral_restr0.058371
X-RAY DIFFRACTIONf_plane_restr0.004402
X-RAY DIFFRACTIONf_dihedral_angle_d13.53855
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7971-3.07810.34751330.26782592272599
3.0781-3.52250.31521450.228126022747100
3.5225-4.4340.27291150.18526592774100
4.434-25.2260.2251380.19632733287199
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)
12.03140.16420.17691.7582-0.31830.78260.4111-0.01820.54420.0781-0.27270.3758-0.1676-0.23210.2382-0.0036-0.0967-0.0484-0.0791-0.1596-0.046234.073511.281139.394
20.76950.15170.11580.59650.05451.1222-0.09820.96360.9871-0.38680.02650.2153-1.66980.7302-0.05550.856-0.1534-0.01770.81820.08340.407447.509112.1210.4054
30.78890.94090.68451.14490.80991.1265-0.23230.03110.3303-0.4277-0.10440.2717-0.5253-0.3294-0.52980.0614-0.09910.07350.00890.01140.41436.790120.296839.8805
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 1:174)A1 - 174
2X-RAY DIFFRACTION2(chain A and resid 175:261)A175 - 261
3X-RAY DIFFRACTION3(chain A and resid 262:303)A262 - 303

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