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- PDB-2h29: Crystal structure of Nicotinic acid mononucleotide Adenylyltransf... -

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Basic information

Entry
Database: PDB / ID: 2h29
TitleCrystal structure of Nicotinic acid mononucleotide Adenylyltransferase from Staphylococcus aureus: product bound form 1
ComponentsProbable nicotinate-nucleotide adenylyltransferase
KeywordsTRANSFERASE / NadD / NaMNAT / NMNAT
Function / homology
Function and homology information


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
NICOTINIC ACID ADENINE DINUCLEOTIDE / Probable nicotinate-nucleotide adenylyltransferase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsHan, S.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Crystal Structure of Nicotinic Acid Mononucleotide Adenylyltransferase from Staphyloccocus aureus: Structural Basis for NaAD Interaction in Functional Dimer.
Authors: Han, S. / Forman, M.D. / Loulakis, P. / Rosner, M.H. / Xie, Z. / Wang, H. / Danley, D.E. / Yuan, W. / Schafer, J. / Xu, Z.
History
DepositionMay 18, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 8, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

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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)45,6414
Polymers44,3112
Non-polymers1,3312
Water4,576254
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)118.217, 81.972, 61.942
Angle α, β, γ (deg.)90.00, 116.39, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1087-

HOH

21B-1016-

HOH

31B-1032-

HOH

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Components

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


Mass: 22155.312 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: nadD / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): M15[pREP4]
References: UniProt: Q5HFG7, nicotinate-nucleotide adenylyltransferase
#2: Chemical ChemComp-DND / NICOTINIC ACID ADENINE DINUCLEOTIDE / DEAMIDO-NAD+


Mass: 665.418 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N6O15P2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 254 / 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: 3.03 Å3/Da / Density % sol: 59.44 %
Crystal growDetails: 10mg/ml protein, 50mM Hepes pH 7.2, 300mM KCl, 0.5mM TCEP, 1mM EDTA mixed with equal volume of 10%(w/v) PEG3000, 100mM phosphate-citrate buffer pH4.2, 0.2M NaCl

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.542 Å
DetectorDate: Dec 1, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 31473 / % possible obs: 87.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.1999 / Mean I/σ(I) obs: 4.6 / Num. unique all: 102150 / % possible all: 44.3

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Processing

SoftwareName: REFMAC / Version: 5.2.0005 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→30 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.888 / SU B: 3.453 / SU ML: 0.101 / Cross valid method: THROUGHOUT / ESU R: 0.198 / ESU R Free: 0.177 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.246 1577 5 %RANDOM
Rwork0.20166 ---
all0.20391 ---
obs0.20391 29895 87.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.853 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å2-0.12 Å2
2--0.1 Å20 Å2
3----0.2 Å2
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3094 0 88 254 3436
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0223259
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4061.9824410
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7285374
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.92625.062162
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.77115590
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.411512
X-RAY DIFFRACTIONr_chiral_restr0.0810.2476
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022434
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2090.21529
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3050.22261
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.2274
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1830.251
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1770.229
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8921.51960
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.41123056
X-RAY DIFFRACTIONr_scbond_it2.21131519
X-RAY DIFFRACTIONr_scangle_it3.3064.51354
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 64 -
Rwork0.224 1056 -
obs--42.94 %

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