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- PDB-4x0e: Structure of M. tuberculosis nicotinate mono nucleotide adenylylt... -

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Basic information

Entry
Database: PDB / ID: 4x0e
TitleStructure of M. tuberculosis nicotinate mono nucleotide adenylyltransferase
ComponentsProbable nicotinate-nucleotide adenylyltransferase
KeywordsTRANSFERASE / enzyme inhibitors
Function / homology
Function and homology information


nicotinamide-nucleotide adenylyltransferase activity / nicotinate-nucleotide adenylyltransferase / nicotinate-nucleotide adenylyltransferase activity / NAD biosynthetic process / ATP binding
Similarity search - Function
Nicotinate/nicotinamide nucleotide adenylyltransferase / Cytidylyltransferase-like / Cytidyltransferase-like domain / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Probable nicotinate-nucleotide adenylyltransferase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.41 Å
AuthorsZuccola, H.J. / Ostermna, A.L.
CitationJournal: J. Biol. Chem. / Year: 2015
Title: Mycobacterial nicotinate mononucleotide adenylyltransferase: structure, mechanism, and implications for drug discovery.
Authors: Rodionova, I.A. / Zuccola, H.J. / Sorci, L. / Aleshin, A.E. / Kazanov, M.D. / Ma, C.T. / Sergienko, E. / Rubin, E.J. / Locher, C.P. / Osterman, A.L.
History
DepositionNov 21, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 28, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 1, 2016Group: Data collection
Revision 1.2Dec 13, 2017Group: Database references / Derived calculations
Category: citation / citation_author / pdbx_struct_oper_list
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable nicotinate-nucleotide adenylyltransferase
B: Probable nicotinate-nucleotide adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,2634
Polymers47,9722
Non-polymers2912
Water1448
1
A: Probable nicotinate-nucleotide adenylyltransferase


Theoretical massNumber of molelcules
Total (without water)23,9861
Polymers23,9861
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Probable nicotinate-nucleotide adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2773
Polymers23,9861
Non-polymers2912
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.650, 67.650, 187.366
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Probable nicotinate-nucleotide adenylyltransferase / Deamido-NAD(+) diphosphorylase / Deamido-NAD(+) pyrophosphorylase / Nicotinate mononucleotide ...Deamido-NAD(+) diphosphorylase / Deamido-NAD(+) pyrophosphorylase / Nicotinate mononucleotide adenylyltransferase / NaMN adenylyltransferase


Mass: 23986.092 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: ATCC 25618 / H37Rv / Gene: nadD, Rv2421c, MTCY428.26 / Production host: Escherichia coli (E. coli)
References: UniProt: P9WJJ5, nicotinate-nucleotide adenylyltransferase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.58 Å3/Da / Density % sol: 52.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 1.2-1.5M magnesium sulfate, 0.1M MES buffer / PH range: 6-6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9774 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 30, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.629
11-h,-k,l20.371
ReflectionResolution: 2.41→93.68 Å / Num. obs: 19922 / % possible obs: 99.8 % / Redundancy: 4.7 % / Net I/σ(I): 14.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
PROCESSdata reduction
PROCESSdata scaling
PHASERphasing
RefinementResolution: 2.41→62.46 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.935 / SU B: 6.073 / SU ML: 0.149 / Cross valid method: THROUGHOUT / ESU R: 0.073 / ESU R Free: 0.053 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25744 1030 5.2 %RANDOM
Rwork0.22149 ---
obs0.22324 18841 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 65.183 Å2
Baniso -1Baniso -2Baniso -3
1-23.13 Å20 Å20 Å2
2--23.13 Å20 Å2
3----46.27 Å2
Refinement stepCycle: 1 / Resolution: 2.41→62.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2877 0 17 8 2902
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0192964
X-RAY DIFFRACTIONr_bond_other_d0.0010.022751
X-RAY DIFFRACTIONr_angle_refined_deg1.0881.9564036
X-RAY DIFFRACTIONr_angle_other_deg0.7536309
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8595364
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.57422.782133
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.94115450
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5681524
X-RAY DIFFRACTIONr_chiral_restr0.0630.2452
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213320
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02694
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.3596.4611471
X-RAY DIFFRACTIONr_mcbond_other2.3556.4611470
X-RAY DIFFRACTIONr_mcangle_it3.759.6861830
X-RAY DIFFRACTIONr_mcangle_other3.7499.6861831
X-RAY DIFFRACTIONr_scbond_it2.1526.7391493
X-RAY DIFFRACTIONr_scbond_other2.1526.7381493
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.50310.0122207
X-RAY DIFFRACTIONr_long_range_B_refined5.94452.4013360
X-RAY DIFFRACTIONr_long_range_B_other5.94352.413361
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.41→2.476 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.649 61 -
Rwork0.609 1363 -
obs--99.72 %

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