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- PDB-6ofc: Crystal structure of M. tuberculosis glutamine-dependent NAD+ syn... -

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Basic information

Entry
Database: PDB / ID: 6ofc
TitleCrystal structure of M. tuberculosis glutamine-dependent NAD+ synthetase complexed with Sulfonamide derivative 1, pyrophosphate, and glutamine
ComponentsGlutamine-dependent NAD(+) synthetase
KeywordsLIGASE / GLUTAMINE-AMIDO TRANSFERASE / GAT / NAD+ SYNTHETASE / GLUTAMINE-DEPENDENT NAD+ SYNTHETASE / NAD SYNTHETASE 1 / GLUTAMINASE / AMMONIA TUNNELING / ENZYME / ATP-BINDING / NUCLEOTIDE-BINDING / INHIBITOR COMPLEX / TUBERCULOSIS
Function / homology
Function and homology information


NAD+ synthase (glutamine-hydrolysing) / NAD+ synthase activity / NAD+ synthase (glutamine-hydrolyzing) activity / NAD+ biosynthetic process / glutaminase activity / ATP binding / 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 / PYROPHOSPHATE 2- / 5'-O-[(pyridine-3-carbonyl)sulfamoyl]adenosine / Glutamine-dependent NAD(+) synthetase
Similarity search - Component
Biological speciesMycobacterium tuberculosis CDC1551 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.14 Å
AuthorsChuenchor, W. / Doukov, T.I. / Gerratana, B.
CitationJournal: Nat Commun / Year: 2020
Title: Different ways to transport ammonia in human and Mycobacterium tuberculosis NAD+synthetases.
Authors: Chuenchor, W. / Doukov, T.I. / Chang, K.T. / Resto, M. / Yun, C.S. / Gerratana, B.
History
DepositionMar 28, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 8, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Feb 1, 2023Group: Advisory / Database references / Category: database_2 / pdbx_database_PDB_obs_spr
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_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)303,49722
Polymers298,9454
Non-polymers4,55218
Water75742
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)606,99444
Polymers597,8908
Non-polymers9,10336
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area77190 Å2
ΔGint-309 kcal/mol
Surface area143100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)179.270, 179.270, 208.180
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111METMETHISHIS(chain 'A' and (resid 1 through 454 or (resid 455...AA1 - 4411 - 441
121VALVALTHRTHR(chain 'A' and (resid 1 through 454 or (resid 455...AA452 - 543452 - 543
131GLUGLULYSLYS(chain 'A' and (resid 1 through 454 or (resid 455...AA553 - 678553 - 678
211METMETHISHIS(chain 'B' and (resid 1 through 407 or (resid 408...BB1 - 4411 - 441
221VALVALTHRTHR(chain 'B' and (resid 1 through 407 or (resid 408...BB452 - 543452 - 543
231GLUGLULYSLYS(chain 'B' and (resid 1 through 407 or (resid 408...BB553 - 678553 - 678
112METMETPHEPHE(chain 'C' and (resid 1 through 166 or (resid 167...CC1 - 4021 - 402
122HISHISTHRTHR(chain 'C' and (resid 1 through 166 or (resid 167...CC407 - 543407 - 543
132GLUGLULYSLYS(chain 'C' and (resid 1 through 166 or (resid 167...CC558 - 678558 - 678
212METMETPHEPHE(chain 'D' and (resid 1 through 524 or (resid 525...DD1 - 4021 - 402
222HISHISTHRTHR(chain 'D' and (resid 1 through 524 or (resid 525...DD407 - 543407 - 543
232GLUGLULYSLYS(chain 'D' and (resid 1 through 524 or (resid 525...DD558 - 678558 - 678

NCS ensembles :
ID
1
2

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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: 74736.273 Da / Num. of mol.: 4 / Mutation: C176A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis CDC1551 (bacteria)
Strain: CDC 1551 / Oshkosh / Gene: nadE, MT2513 / Plasmid: PSMT3 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P9WJJ2, NAD+ synthase (glutamine-hydrolysing)

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Non-polymers , 6 types, 60 molecules

#2: Chemical
ChemComp-SFH / 5'-O-[(pyridine-3-carbonyl)sulfamoyl]adenosine


Mass: 451.414 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C16H17N7O7S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-POP / PYROPHOSPHATE 2-


Mass: 175.959 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2O7P2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-GLN / GLUTAMINE


Type: L-peptide linking / Mass: 146.144 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C5H10N2O3 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 42 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.79 Å3/Da / Density % sol: 55.87 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 1.6 M AMMONIUM CITRATE TRIBASIC DIHYDRATE, 10 % GLYCEROL

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.98 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Mar 16, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.14→39.56 Å / Num. obs: 58806 / % possible obs: 99 % / Redundancy: 11.2 % / Biso Wilson estimate: 51.38 Å2 / Rmerge(I) obs: 0.181 / Rsym value: 0.187 / Net I/σ(I): 12.9
Reflection shellResolution: 3.14→3.31 Å / Redundancy: 8.7 % / Mean I/σ(I) obs: 3.5 / Num. unique obs: 8258 / Rsym value: 0.43 / % possible all: 96.4

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
PHENIX1.16_3549refinement
XDSdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3DLA

3dla


Resolution: 3.14→36.09 Å / SU ML: 0.3021 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.5145
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2353 2962 5.05 %
Rwork0.1861 55658 -
obs0.1886 58620 98.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 52.01 Å2
Refinement stepCycle: LAST / Resolution: 3.14→36.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20517 0 303 42 20862
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006821348
X-RAY DIFFRACTIONf_angle_d0.946629042
X-RAY DIFFRACTIONf_chiral_restr0.05193178
X-RAY DIFFRACTIONf_plane_restr0.0063797
X-RAY DIFFRACTIONf_dihedral_angle_d12.184412551
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.14-3.20.29071190.27682356X-RAY DIFFRACTION88.71
3.2-3.250.33091290.25792628X-RAY DIFFRACTION99.03
3.25-3.310.32621450.24652617X-RAY DIFFRACTION99.57
3.31-3.370.28071320.22052660X-RAY DIFFRACTION99.61
3.37-3.440.31271450.21272621X-RAY DIFFRACTION99.71
3.44-3.520.27911440.20612657X-RAY DIFFRACTION99.64
3.52-3.60.25191360.19082619X-RAY DIFFRACTION99.49
3.6-3.690.24481300.1942661X-RAY DIFFRACTION99.82
3.69-3.790.2281320.17382663X-RAY DIFFRACTION99.4
3.79-3.90.2221490.17852650X-RAY DIFFRACTION99.64
3.9-4.030.2211560.18062630X-RAY DIFFRACTION99.39
4.03-4.170.21581530.16222653X-RAY DIFFRACTION99.36
4.17-4.340.20051370.15012638X-RAY DIFFRACTION99.46
4.34-4.530.20351320.1442685X-RAY DIFFRACTION99.44
4.53-4.770.18751470.14862661X-RAY DIFFRACTION99.08
4.77-5.070.19911330.15462677X-RAY DIFFRACTION99.15
5.07-5.460.23541470.16542668X-RAY DIFFRACTION98.98
5.46-6.010.22691290.18542703X-RAY DIFFRACTION98.81
6.01-6.870.22981570.18992696X-RAY DIFFRACTION98.69
6.87-8.640.19981500.18042701X-RAY DIFFRACTION97.84
8.64-36.090.24671600.21812814X-RAY DIFFRACTION96.9

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