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- PDB-3dla: X-ray crystal structure of glutamine-dependent NAD+ synthetase fr... -

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Basic information

Entry
Database: PDB / ID: 3dla
TitleX-ray crystal structure of glutamine-dependent NAD+ synthetase from Mycobacterium tuberculosis bound to NaAD+ and DON
ComponentsGlutamine-dependent NAD(+) synthetase
KeywordsLIGASE / glutaminase / NAD+ synthetase / ammonia tunneling / enzyme / glutamine-dependent NAD+ synthetase / Glutamine-amido transferase / 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
NICOTINIC ACID ADENINE DINUCLEOTIDE / 5-OXO-L-NORLEUCINE / Glutamine-dependent NAD(+) synthetase / Glutamine-dependent NAD(+) synthetase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.35 Å
AuthorsLaRonde-LeBlanc, N.A. / Resto, M. / Gerratana, B.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2009
Title: Regulation of active site coupling in glutamine-dependent NAD(+) synthetase.
Authors: LaRonde-LeBlanc, N. / Resto, M. / Gerratana, B.
History
DepositionJun 26, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 2.0Oct 23, 2019Group: Advisory / Atomic model ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_ref_seq_dif
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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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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)304,04527
Polymers299,4224
Non-polymers4,62423
Water25,9961443
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)608,09154
Polymers598,8438
Non-polymers9,24746
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area90380 Å2
ΔGint-246 kcal/mol
Surface area140250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)178.130, 178.130, 215.177
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-1055-

HOH

21C-959-

HOH

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Components

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


Mass: 74855.414 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: nadE, Rv2438c, MT2513, MTCY428.08 / Plasmid: pSMT3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P0A5L6, UniProt: P9WJJ3*PLUS, NAD+ synthase (glutamine-hydrolysing)
#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-ONL / 5-OXO-L-NORLEUCINE


Type: L-peptide linking / Mass: 145.156 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H11NO3
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1443 / 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: 56.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7
Details: 1.8 M ammonium citrate tribasic dihydrate, 5 % glycerol, pH 7.0, VAPOR DIFFUSION, 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
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.35→29.7 Å / Num. all: 143290 / Num. obs: 142287 / % possible obs: 99.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 11.4 % / Biso Wilson estimate: 42.2 Å2 / Rsym value: 0.139
Reflection shellResolution: 2.35→2.41 Å / Redundancy: 5.3 % / Num. unique all: 9636 / Rsym value: 0.56 / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.35→29.7 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.918 / SU B: 16.514 / SU ML: 0.194 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.301 / ESU R Free: 0.237 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24566 7144 5 %RANDOM
Rwork0.18439 ---
obs0.18743 135143 99.4 %-
all-143290 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 6.71 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å20 Å20 Å2
2---0.05 Å20 Å2
3---0.09 Å2
Refinement stepCycle: LAST / Resolution: 2.35→29.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20221 0 306 1443 21970
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.02121027
X-RAY DIFFRACTIONr_angle_refined_deg1.6591.96928557
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0252604
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.35722.588962
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.929153231
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.98215204
X-RAY DIFFRACTIONr_chiral_restr0.110.23131
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0216201
X-RAY DIFFRACTIONr_nbd_refined0.2380.211463
X-RAY DIFFRACTIONr_nbtor_refined0.3120.214256
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2030.21715
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2640.2318
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2120.295
X-RAY DIFFRACTIONr_mcbond_it0.5821.513308
X-RAY DIFFRACTIONr_mcangle_it0.968220801
X-RAY DIFFRACTIONr_scbond_it1.63638719
X-RAY DIFFRACTIONr_scangle_it2.6694.57756
LS refinement shellResolution: 2.35→2.411 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.347 512 -
Rwork0.288 9636 -
obs-9636 99 %
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)
10.83790.2954-0.0360.5141-0.06770.22110.0087-0.0694-0.20880.1318-0.0007-0.2230.1090.0462-0.008-0.04050.0483-0.0518-0.09150.0032-0.0279112.719862.467265.5445
24.16230.157-0.3011.96770.09080.02710.0479-0.203-0.21210.0571-0.0627-0.21810.09140.30370.0148-0.07830.095-0.07010.1547-0.00770.1141157.026673.961858.4795
31.14010.3752-0.1780.7437-0.48730.78320.0016-0.1948-0.20580.1849-0.024-0.45750.0830.17910.0224-0.05420.0734-0.1270.01180.00920.1859137.754673.554373.6612
40.5212-0.07380.15470.882-0.07970.2249-0.0033-0.09140.11580.0821-0.019-0.231-0.02470.06910.0222-0.0608-0.0238-0.0297-0.025-0.0263-0.1396114.0464113.354268.7945
50.9975-0.59070.06531.1589-0.18890.322-0.0662-0.04590.48140.15770.0094-0.1668-0.23320.07730.05680.0935-0.0782-0.0904-0.0784-0.03380.2927103.5337157.612660.0307
60.8091-0.04960.47410.95720.0180.8853-0.049-0.17850.35270.1571-0.0447-0.0617-0.17380.03020.09370.019-0.0397-0.0546-0.0567-0.08950.0407102.0518138.698975.4491
70.54740.31910.14441.16320.30560.265-0.03130.1150.2566-0.0896-0.02320.1775-0.0344-0.07390.0545-0.02870.021-0.0555-0.0240.0053-0.258163.3832115.130241.9282
80.57450.402-0.08951.18290.19520.317-0.0511-0.00970.5237-0.1243-0.00660.2625-0.2174-0.06830.05770.10380.0681-0.0799-0.1089-0.0270.380474.4148158.971155.2875
90.71740.33980.41711.10890.30910.8942-0.07110.13970.4559-0.22640.00510.0842-0.1932-0.03830.06590.05210.031-0.0731-0.06190.06410.005975.1941140.660238.4473
100.9694-0.15270.15670.3439-0.06830.1671-0.04270.10330.1931-0.09310.0059-0.3105-0.07410.06980.0367-0.0311-0.02550.004-0.0216-0.0024-0.1599114.4101116.230745.3271
111.397-0.5361-0.02360.60020.05790.2047-0.03180.08580.199700.0109-0.4286-0.05420.2410.0209-0.1046-0.0527-0.04450.1607-0.02970.3936158.2745103.534557.2914
121.1131-0.05190.15260.6091-0.31250.7764-0.02710.22180.1119-0.0808-0.0104-0.4067-0.05660.22190.0375-0.0843-0.04550.05520.0841-0.00420.1625140.1222104.94740.4057
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 401
2X-RAY DIFFRACTION2A407 - 543
3X-RAY DIFFRACTION3A559 - 679
4X-RAY DIFFRACTION4B1 - 401
5X-RAY DIFFRACTION5B409 - 543
6X-RAY DIFFRACTION6B557 - 679
7X-RAY DIFFRACTION7C0 - 402
8X-RAY DIFFRACTION8C410 - 541
9X-RAY DIFFRACTION9C559 - 679
10X-RAY DIFFRACTION10D1 - 402
11X-RAY DIFFRACTION11D410 - 541
12X-RAY DIFFRACTION12D558 - 679

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