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- PDB-3sdb: Crystal structure of C176A mutant of glutamine-dependent NAD+ syn... -

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Basic information

Entry
Database: PDB / ID: 3sdb
TitleCrystal structure of C176A mutant of glutamine-dependent NAD+ synthetase from M. tuberculosis in apo form
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 / NAD+ biosynthetic process / glutaminase activity / 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 / NAD/GMP synthase / NAD synthase / Nitrilase/N-carbamoyl-D-aminoacid amidohydrolase / Carbon-nitrogen hydrolase / 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 / NAD/GMP synthase / NAD synthase / Nitrilase/N-carbamoyl-D-aminoacid amidohydrolase / Carbon-nitrogen hydrolase / 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
Glutamine-dependent NAD(+) synthetase / Glutamine-dependent NAD(+) synthetase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.0017 Å
AuthorsChuenchor, W. / 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
DepositionJun 9, 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 1.2Sep 13, 2023Group: 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glutamine-dependent NAD(+) synthetase


Theoretical massNumber of molelcules
Total (without water)74,8231
Polymers74,8231
Non-polymers00
Water6,539363
1
A: Glutamine-dependent NAD(+) synthetase
x 8


Theoretical massNumber of molelcules
Total (without water)598,5878
Polymers598,5878
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
crystal symmetry operation5_555-x,y,-z1
crystal symmetry operation6_555x,-y,-z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation8_555-y,-x,-z1
Buried area70530 Å2
ΔGint-210 kcal/mol
Surface area138680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)179.937, 179.937, 98.716
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-991-

HOH

21A-1009-

HOH

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Components

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


Mass: 74823.352 Da / Num. of mol.: 1 / Mutation: C176A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: MT2513, MTCY428.08, nadE, Rv2438c / Plasmid: pSMT3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P0A5L6, UniProt: P9WJJ3*PLUS, NAD+ synthase (glutamine-hydrolysing)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 363 / 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: 2.67 Å3/Da / Density % sol: 53.93 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 7
Details: 1.6 M ammonium citrate tribasic dihydrate, 5 % glycerol, pH 7.0, EVAPORATION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97949 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 29, 2008
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 54362 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 8.1 % / Rsym value: 0.055 / Net I/σ(I): 34.7
Reflection shellResolution: 2→2.07 Å / Redundancy: 8.2 % / Mean I/σ(I) obs: 4.9 / Num. unique all: 5372 / Rsym value: 0.404 / % possible all: 100

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Processing

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

3dla


Resolution: 2.0017→44.538 Å / SU ML: 0.37 / Isotropic thermal model: anisotropic / σ(F): 1.34 / Phase error: 20.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1955 2717 5 %RANDOM
Rwork0.1627 ---
obs0.1644 54342 99.77 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.473 Å2 / ksol: 0.341 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--6.7862 Å2-0 Å20 Å2
2---6.7862 Å20 Å2
3---13.5723 Å2
Refinement stepCycle: LAST / Resolution: 2.0017→44.538 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4980 0 0 363 5343
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.025089
X-RAY DIFFRACTIONf_angle_d1.7246916
X-RAY DIFFRACTIONf_dihedral_angle_d13.6891831
X-RAY DIFFRACTIONf_chiral_restr0.14768
X-RAY DIFFRACTIONf_plane_restr0.009908
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0017-2.03810.28231380.22552630X-RAY DIFFRACTION98
2.0381-2.07730.25141420.20462683X-RAY DIFFRACTION100
2.0773-2.11970.22121410.1972694X-RAY DIFFRACTION100
2.1197-2.16580.22571420.18672692X-RAY DIFFRACTION100
2.1658-2.21620.25921410.18492673X-RAY DIFFRACTION100
2.2162-2.27160.21991430.17622707X-RAY DIFFRACTION100
2.2716-2.3330.20551400.16982683X-RAY DIFFRACTION100
2.333-2.40170.20761430.16442702X-RAY DIFFRACTION100
2.4017-2.47920.23511420.16212711X-RAY DIFFRACTION100
2.4792-2.56780.20891430.15682696X-RAY DIFFRACTION100
2.5678-2.67060.21481420.16622720X-RAY DIFFRACTION100
2.6706-2.79210.2081420.16222696X-RAY DIFFRACTION100
2.7921-2.93930.20031430.16372710X-RAY DIFFRACTION100
2.9393-3.12340.18771430.16622715X-RAY DIFFRACTION100
3.1234-3.36450.21531450.15962749X-RAY DIFFRACTION100
3.3645-3.70290.19551440.15232742X-RAY DIFFRACTION100
3.7029-4.23840.15831440.13532757X-RAY DIFFRACTION100
4.2384-5.33850.14751460.13492774X-RAY DIFFRACTION100
5.3385-44.54860.20141530.19162891X-RAY DIFFRACTION99
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)
11.07630.16110.02370.7577-0.15520.3577-0.004-0.1164-0.05040.1198-0.0151-0.05580.03040.0359-00.2670.0199-0.00330.24750.02270.218916.2698-27.506116.1258
20.6629-0.2286-0.07091.1668-0.01250.9562-0.016-0.03910.0162-0.0109-0.0521-0.40280.07720.3046-0.0140.16720.0391-0.02330.35050.05260.470958.5396-16.46835.9247
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 0:320)
2X-RAY DIFFRACTION2(chain A and resid 321:679)

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