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- PDB-3e27: Nicotinic acid mononucleotide (NaMN) adenylyltransferase from Bac... -

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Basic information

Entry
Database: PDB / ID: 3.0E+27
TitleNicotinic acid mononucleotide (NaMN) adenylyltransferase from Bacillus anthracis: product complex
ComponentsNicotinate (Nicotinamide) nucleotide adenylyltransferase
KeywordsTRANSFERASE / Rossman-like fold / nucleotide-binding motif / Nucleotidyltransferase
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 speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsMartynowski, D. / Eyobo, Y. / Zhang, H.
CitationJournal: Chem.Biol. / Year: 2009
Title: Targeting NAD biosynthesis in bacterial pathogens: Structure-based development of inhibitors of nicotinate mononucleotide adenylyltransferase NadD.
Authors: Sorci, L. / Pan, Y. / Eyobo, Y. / Rodionova, I. / Huang, N. / Kurnasov, O. / Zhong, S. / MacKerell, A.D. / Zhang, H. / Osterman, A.L.
History
DepositionAug 5, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 9, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 11, 2014Group: Database references
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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

Downloads & links

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Assembly

Deposited unit
A: Nicotinate (Nicotinamide) nucleotide adenylyltransferase
B: Nicotinate (Nicotinamide) nucleotide adenylyltransferase
C: Nicotinate (Nicotinamide) nucleotide adenylyltransferase
D: Nicotinate (Nicotinamide) nucleotide adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,69212
Polymers87,9334
Non-polymers2,7598
Water8,899494
1
A: Nicotinate (Nicotinamide) nucleotide adenylyltransferase
B: Nicotinate (Nicotinamide) nucleotide adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3466
Polymers43,9672
Non-polymers1,3794
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1730 Å2
ΔGint-9 kcal/mol
Surface area18110 Å2
MethodPISA
2
C: Nicotinate (Nicotinamide) nucleotide adenylyltransferase
D: Nicotinate (Nicotinamide) nucleotide adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3466
Polymers43,9672
Non-polymers1,3794
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1760 Å2
ΔGint-11 kcal/mol
Surface area18030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.856, 137.413, 143.972
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Nicotinate (Nicotinamide) nucleotide adenylyltransferase


Mass: 21983.305 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: B. anthracis Ames / Gene: nadD, BT9727_4068 / Plasmid: a pET derived vector / Production host: Escherichia coli (E. coli) / Strain (production host): E. coli BL21/DE3
References: UniProt: A0A2P0HJA8*PLUS, nicotinate-nucleotide adenylyltransferase
#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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 494 / 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: 2.35 Å3/Da / Density % sol: 47.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Details: Osmic VariMax
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 43353 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.085 / Rsym value: 0.085 / Net I/σ(I): 15.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1kam

1kam


Resolution: 2.2→50 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.902 / SU B: 7.551 / SU ML: 0.191 / Cross valid method: THROUGHOUT / ESU R: 0.324 / ESU R Free: 0.252 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2734 2162 5 %RANDOM
Rwork0.20117 ---
obs0.2048 40803 99.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 32.75 Å2
Baniso -1Baniso -2Baniso -3
1-1.53 Å20 Å20 Å2
2---1.95 Å20 Å2
3---0.43 Å2
Refinement stepCycle: LAST / Resolution: 2.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6173 0 180 494 6847
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0226556
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5612.0138933
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9885748
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.76323.649296
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.848151121
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.2251538
X-RAY DIFFRACTIONr_chiral_restr0.1130.2976
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024898
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2090.23143
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3160.24396
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1740.2439
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2290.269
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2010.225
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8611.53908
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.46526158
X-RAY DIFFRACTIONr_scbond_it1.94833073
X-RAY DIFFRACTIONr_scangle_it2.9454.52775
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.37 147 -
Rwork0.266 2827 -
obs--95.53 %

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