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- PDB-3dv2: Crystal Structure of nicotinic acid mononucleotide adenylyltransf... -

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Basic information

Entry
Database: PDB / ID: 3dv2
TitleCrystal Structure of nicotinic acid mononucleotide adenylyltransferase from Bacillus anthracis
ComponentsNicotinate (Nicotinamide) nucleotide adenylyltransferase
KeywordsTRANSFERASE / alpha and beta protein / Rossmann fold / NAD / Nucleotidyltransferase / Pyridine nucleotide biosynthesis
Function / homologyHUPs / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / :
Function and homology information
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsLu, S. / Smith, C.D. / Yang, Z. / Pruett, P.S. / Nagy, L. / McCombs, D.P. / DeLucas, L.J. / Brouillette, W.J. / Brouillette, C.G.
CitationJournal: ACTA CRYSTALLOGR.,SECT.F / Year: 2008
Title: Structure of nicotinic acid mononucleotide adenylyltransferase from Bacillus anthracis.
Authors: Lu, S. / Smith, C.D. / Yang, Z. / Pruett, P.S. / Nagy, L. / McCombs, D. / Delucas, L.J. / Brouillette, W.J. / Brouillette, C.G.
History
DepositionJul 18, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 4, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 12, 2014Group: Structure summary
Revision 1.3Oct 25, 2017Group: Refinement description / Category: software
Revision 1.4Aug 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 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: 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)94,28812
Polymers93,5194
Non-polymers7698
Water2,324129
1
C: Nicotinate (Nicotinamide) nucleotide adenylyltransferase
D: Nicotinate (Nicotinamide) nucleotide adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,1446
Polymers46,7602
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2640 Å2
ΔGint-72 kcal/mol
Surface area19510 Å2
MethodPISA
2
A: Nicotinate (Nicotinamide) nucleotide adenylyltransferase
B: Nicotinate (Nicotinamide) nucleotide adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,1446
Polymers46,7602
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2600 Å2
ΔGint-73 kcal/mol
Surface area19630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.073, 100.586, 73.068
Angle α, β, γ (deg.)90.00, 110.42, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Nicotinate (Nicotinamide) nucleotide adenylyltransferase


Mass: 23379.869 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Gene: nadD / Plasmid: pET21b / Production host: Escherichia coli (E. coli)
References: UniProt: Q6HT60, nicotinate-nucleotide adenylyltransferase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 129 / 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: 2.33 Å3/Da / Density % sol: 47.3 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 2.1M ammonium sulfate, 0.1M HEPES, 2% PEG400, 10mM magnesium chloride, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 12, 2007
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→25.15 Å / Num. all: 38428 / Num. obs: 37472 / % possible obs: 97.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.7 % / Rmerge(I) obs: 0.059 / Rsym value: 0.059 / Net I/σ(I): 10.5
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.285 / Mean I/σ(I) obs: 3.2 / Rsym value: 0.285 / % possible all: 88.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
CNS1.2refinement
PDB_EXTRACT3.006data extraction
MAR345dtbdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1KAM

1kam


Resolution: 2.3→25.15 Å / Rfactor Rfree error: 0.006 / Occupancy max: 1 / Occupancy min: 1 / Data cutoff high absF: 566579 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.264 1775 5 %RANDOM
Rwork0.227 ---
obs0.227 35501 93.4 %-
all-38021 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 42.93 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 44.44 Å2
Baniso -1Baniso -2Baniso -3
1--12.22 Å20 Å2-2.43 Å2
2--11.03 Å20 Å2
3---1.19 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.37 Å0.23 Å
Refinement stepCycle: LAST / Resolution: 2.3→25.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6164 0 40 129 6333
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.79
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it3.571.5
X-RAY DIFFRACTIONc_mcangle_it5.032
X-RAY DIFFRACTIONc_scbond_it5.192
X-RAY DIFFRACTIONc_scangle_it6.892.5
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.339 235 4.4 %
Rwork0.275 5078 -
obs--84.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER_REP.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP

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