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- PDB-3szg: Crystal structure of C176A glutamine-dependent NAD+ synthetase fr... -

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Basic information

Entry
Database: PDB / ID: 3szg
TitleCrystal structure of C176A glutamine-dependent NAD+ synthetase from M. tuberculosis bound to AMP/PPi and NaAD+
ComponentsGlutamine-dependent NAD(+) synthetase
KeywordsLIGASE / Glutamine-amidotransferase / Glutaminase / Glutamine-dependent NAD+ synthetase / Ammonia tunneling / ATP binding / NAD / Nucleotide binding
Function / homology
Function and homology information


NAD+ synthase (glutamine-hydrolysing) / NAD+ synthase activity / NAD+ synthase (glutamine-hydrolyzing) activity / glutaminase activity / NAD biosynthetic process / peptidoglycan-based cell wall / ATP binding / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
Glutamine-dependent NAD+ synthetase, C-terminal domain / Glutamine-dependent NAD+ synthetase, C-terminal / Glutamine-dependent NAD(+) synthetase / NAD(+) synthetase / Nitrilase/N-carbamoyl-D-aminoacid amidohydrolase / Carbon-nitrogen hydrolase / NAD/GMP synthase / NAD synthase / Carbon-nitrogen hydrolase superfamily / Carbon-nitrogen hydrolase ...Glutamine-dependent NAD+ synthetase, C-terminal domain / Glutamine-dependent NAD+ synthetase, C-terminal / Glutamine-dependent NAD(+) synthetase / NAD(+) synthetase / Nitrilase/N-carbamoyl-D-aminoacid amidohydrolase / Carbon-nitrogen hydrolase / NAD/GMP synthase / NAD synthase / Carbon-nitrogen hydrolase superfamily / Carbon-nitrogen hydrolase / Carbon-nitrogen hydrolase domain profile. / Carbon-nitrogen hydrolase / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / 4-Layer Sandwich / Arc Repressor Mutant, subunit A / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / NICOTINIC ACID ADENINE DINUCLEOTIDE / PYROPHOSPHATE 2- / Glutamine-dependent NAD(+) synthetase / Glutamine-dependent NAD(+) synthetase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsChuenchor, W. / Doukov, T. / Gerratana, B.
CitationJournal: Biochem.J. / Year: 2012
Title: Regulation of the intersubunit ammonia tunnel in Mycobacterium tuberculosis glutamine-dependent NAD+ synthetase.
Authors: Chuenchor, W. / Doukov, T.I. / Resto, M. / Chang, A. / Gerratana, B.
History
DepositionJul 19, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 11, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Refinement description / Category: software
Revision 2.0Oct 23, 2019Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / struct_ref_seq_dif / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _struct_ref_seq_dif.details / _struct_site_gen.auth_comp_id / _struct_site_gen.label_comp_id
Revision 2.1Sep 13, 2023Group: 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Glutamine-dependent NAD(+) synthetase
B: Glutamine-dependent NAD(+) synthetase
C: Glutamine-dependent NAD(+) synthetase
D: Glutamine-dependent NAD(+) synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)304,32419
Polymers299,2934
Non-polymers5,03115
Water13,421745
1
A: Glutamine-dependent NAD(+) synthetase
B: Glutamine-dependent NAD(+) synthetase
C: Glutamine-dependent NAD(+) synthetase
D: Glutamine-dependent NAD(+) synthetase
hetero molecules

A: Glutamine-dependent NAD(+) synthetase
B: Glutamine-dependent NAD(+) synthetase
C: Glutamine-dependent NAD(+) synthetase
D: Glutamine-dependent NAD(+) synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)608,64838
Polymers598,5878
Non-polymers10,06130
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/21
Buried area90580 Å2
ΔGint-265 kcal/mol
Surface area140080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)177.940, 177.940, 214.940
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A and (resseq 1:402 or resseq 409:441 or resseq 453:542 or resseq 560:679 )
211chain B and (resseq 1:401 or resseq 409:441 or resseq 453:542 or resseq 560:679 )
311chain C and (resseq 1:402 or resseq 409:441 or resseq 453:542 or resseq 560:679 )
411chain D and (resseq 1:402 or resseq 409:441 or resseq 453:542 or resseq 560:679 )

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Glutamine-dependent NAD(+) synthetase / NAD(+) synthase [glutamine-hydrolyzing]


Mass: 74823.352 Da / Num. of mol.: 4 / Fragment: Glutamine-dependent NAD+ synthetase / Mutation: C176A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: MT2513, MTCY428.08, nadE, Rv2438c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P0A5L6, UniProt: P9WJJ3*PLUS, NAD+ synthase (glutamine-hydrolysing)

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Non-polymers , 5 types, 760 molecules

#2: Chemical
ChemComp-DND / NICOTINIC ACID ADENINE DINUCLEOTIDE / DEAMIDO-NAD+


Mass: 665.418 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N6O15P2
#3: Chemical
ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#4: Chemical
ChemComp-POP / PYROPHOSPHATE 2- / Pyrophosphate


Mass: 175.959 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: H2O7P2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 745 / 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: 2.85 Å3/Da / Density % sol: 56.78 %
Crystal growTemperature: 288 K / Method: evaporation
Details: 1.6 M K2HPO4, 100 mM NaH2PO4, EVAPORATION, temperature 288K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.98 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Feb 14, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.25→39.124 Å / Num. obs: 161605 / % possible obs: 99.4 % / Redundancy: 7.9 % / Rmerge(I) obs: 0.187 / Net I/σ(I): 10.8
Reflection shellResolution: 2.25→2.31 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.823 / Mean I/σ(I) obs: 2.84 / % possible all: 93.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphenixphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3DLA

3dla


Resolution: 2.25→39.124 Å / SU ML: 0.55 / σ(F): 1.36 / Phase error: 27.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2294 8064 4.99 %
Rwork0.1917 --
obs0.1937 161514 99.32 %
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.005 Å2 / ksol: 0.398 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--17.9481 Å2-0 Å20 Å2
2---17.9481 Å20 Å2
3---35.8962 Å2
Refinement stepCycle: LAST / Resolution: 2.25→39.124 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20314 0 322 745 21381
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01821125
X-RAY DIFFRACTIONf_angle_d1.73528743
X-RAY DIFFRACTIONf_dihedral_angle_d16.5767657
X-RAY DIFFRACTIONf_chiral_restr0.1073147
X-RAY DIFFRACTIONf_plane_restr0.0083740
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A4999X-RAY DIFFRACTIONPOSITIONAL
12B4999X-RAY DIFFRACTIONPOSITIONAL0.106
13C5010X-RAY DIFFRACTIONPOSITIONAL0.096
14D5010X-RAY DIFFRACTIONPOSITIONAL0.093
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.27560.39512420.34514595X-RAY DIFFRACTION91
2.2756-2.30230.37112540.31254843X-RAY DIFFRACTION95
2.3023-2.33040.362640.29445058X-RAY DIFFRACTION99
2.3304-2.35990.3122680.27915074X-RAY DIFFRACTION100
2.3599-2.3910.33442670.26575088X-RAY DIFFRACTION100
2.391-2.42370.29992660.25215061X-RAY DIFFRACTION100
2.4237-2.45830.31022690.25275122X-RAY DIFFRACTION100
2.4583-2.4950.33242670.24665086X-RAY DIFFRACTION100
2.495-2.5340.28552690.24365117X-RAY DIFFRACTION100
2.534-2.57550.28952670.23485072X-RAY DIFFRACTION100
2.5755-2.61990.28532690.23545128X-RAY DIFFRACTION100
2.6199-2.66760.2662680.22055100X-RAY DIFFRACTION100
2.6676-2.71890.26582680.2215098X-RAY DIFFRACTION100
2.7189-2.77430.27422700.20885133X-RAY DIFFRACTION100
2.7743-2.83460.2492680.21365094X-RAY DIFFRACTION100
2.8346-2.90060.27642690.21965119X-RAY DIFFRACTION100
2.9006-2.97310.24632700.20015139X-RAY DIFFRACTION100
2.9731-3.05340.23922690.19245105X-RAY DIFFRACTION100
3.0534-3.14320.22552690.18755132X-RAY DIFFRACTION100
3.1432-3.24460.24322710.17445163X-RAY DIFFRACTION100
3.2446-3.36060.18622710.16425140X-RAY DIFFRACTION100
3.3606-3.4950.212710.17135153X-RAY DIFFRACTION100
3.495-3.6540.20852700.16375146X-RAY DIFFRACTION100
3.654-3.84650.18612710.14955162X-RAY DIFFRACTION100
3.8465-4.08720.19652730.15425187X-RAY DIFFRACTION100
4.0872-4.40240.17972730.14645184X-RAY DIFFRACTION100
4.4024-4.84470.15192730.13635218X-RAY DIFFRACTION100
4.8447-5.54410.18352760.15595252X-RAY DIFFRACTION100
5.5441-6.97850.21022780.19285282X-RAY DIFFRACTION99
6.9785-39.12980.18092840.18015399X-RAY DIFFRACTION97
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)
10.04760.02570.0230.0881-0.04640.0505-0.03590.05060.0887-0.00940.0130.1155-0.0356-0.0131-00.27080.0050.00020.31930.04940.3652-28.210814.8367-69.0986
20.0692-0.014-0.0110.06820.06260.04770.00520.080.2243-0.0621-0.00870.1469-0.0639-0.023400.39060.03650.01930.30260.06410.6803-16.481458.1314-62.471
30.10720.0054-0.06580.04850.00620.0543-0.01680.00070.1033-0.0034-0.00010.0226-0.0104-0.0217-0.0040.23320.0030.03790.21570.06650.145615.516526.1155-72.5925
40.06670.040.02980.0626-0.05560.0522-0.01660.04160.065-0.0355-0.043-0.2243-0.01040.0503-0.00070.1887-0.03040.04580.22890.05280.341258.783615.4807-64.4237
50.01970.0171-0.00780.0381-0.01160.0698-0.0186-0.0001-0.0244-0.0134-0.0306-0.0315-0.0054-0.0612-0.20390.18880.00510.0440.1990.1039-0.014717.6202-26.7963-36.8902
60.0631-0.0707-0.03160.092-0.01080.0435-0.0023-0.0273-0.03990.0292-0.0406-0.22320.00430.041200.18610.00990.01750.25370.05710.319460.2584-16.0932-50.254
70.2752-0.0088-0.01840.0488-0.00840.0096-0.01680.01370.14330.0203-0.0437-0.0318-0.03570.0006-0.01360.2336-0.0041-0.00560.21540.02650.070528.846516.8517-40.4257
80.08560.0244-0.00540.0847-0.04010.0118-0.0143-0.01670.15790.0361-0.0411-0.0852-0.0431-0.005600.3775-0.00450.02330.24380.02730.620916.56259.5919-52.3306
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 1:320)
2X-RAY DIFFRACTION2(chain A and resid 321:679)
3X-RAY DIFFRACTION3(chain B and resid 1:320)
4X-RAY DIFFRACTION4(chain B and resid 321:679)
5X-RAY DIFFRACTION5(chain C and resid 0:320)
6X-RAY DIFFRACTION6(chain C and resid 321:679)
7X-RAY DIFFRACTION7(chain D and resid 1:320)
8X-RAY DIFFRACTION8(chain D and resid 321:679)

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