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- PDB-6kg3: Crystal structure of Nicotinic acid mononucleotide adenylyltransf... -

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Basic information

Entry
Database: PDB / ID: 6kg3
TitleCrystal structure of Nicotinic acid mononucleotide adenylyltransferase mutant P22K/Y84V/Y118D/C132Q/W176F from Escherichia coli
ComponentsProbable nicotinate-nucleotide adenylyltransferase
KeywordsTRANSFERASE / Nicotinic acid mononucleotide adenylyltransferase
Function / homology
Function and homology information


NAD+ biosynthetic process via the salvage pathway / 'de novo' NAD+ biosynthetic process from L-aspartate / 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 / Nicotinate-nucleotide adenylyltransferase
Similarity search - Component
Biological speciesEscherichia coli NCCP15648 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.08 Å
AuthorsXue, S. / Zhao, Z. / Wang, X. / Feng, Y.
CitationJournal: To Be Published
Title: Crystal structure of Nicotinic acid mononucleotide adenylyltransferase mutant P22K/Y84V/Y118D/C132Q/W176F from Escherichia coli
Authors: Xue, S. / Feng, Y. / Zhao, Z. / Wang, X.
History
DepositionJul 10, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 15, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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
C: Probable nicotinate-nucleotide adenylyltransferase
D: Probable nicotinate-nucleotide adenylyltransferase
E: Probable nicotinate-nucleotide adenylyltransferase
F: Probable nicotinate-nucleotide adenylyltransferase


Theoretical massNumber of molelcules
Total (without water)146,7596
Polymers146,7596
Non-polymers00
Water00
1
A: Probable nicotinate-nucleotide adenylyltransferase
B: Probable nicotinate-nucleotide adenylyltransferase
D: Probable nicotinate-nucleotide adenylyltransferase


Theoretical massNumber of molelcules
Total (without water)73,3793
Polymers73,3793
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Probable nicotinate-nucleotide adenylyltransferase
E: Probable nicotinate-nucleotide adenylyltransferase
F: Probable nicotinate-nucleotide adenylyltransferase


Theoretical massNumber of molelcules
Total (without water)73,3793
Polymers73,3793
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.912, 129.176, 105.320
Angle α, β, γ (deg.)90.000, 103.177, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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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: 24459.758 Da / Num. of mol.: 6 / Mutation: P22K, Y84V, Y118D, C132Q, W176F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli NCCP15648 (bacteria) / Gene: nadD, A610_610 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A222QGJ8, UniProt: P0A752*PLUS, nicotinate-nucleotide adenylyltransferase

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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: 3.82 Å3/Da / Density % sol: 67.76 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop
Details: 1.4M Sodium phosphate monobasic monohydrate-Potassium phosphate dibasic, pH 8.1

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9798 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Dec 27, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 3.08→50 Å / Num. obs: 37906 / % possible obs: 97.48 % / Redundancy: 4.5 % / Biso Wilson estimate: 63.51 Å2 / Rmerge(I) obs: 0.135 / Net I/σ(I): 9.05
Reflection shellResolution: 3.08→3.15 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.557 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 2771 / % possible all: 69.33

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1K4K

1k4k


Resolution: 3.08→45.47 Å / SU ML: 0.4592 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.2449
RfactorNum. reflection% reflection
Rfree0.2676 1855 4.9 %
Rwork0.2409 --
obs0.2422 37872 94.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 56.05 Å2
Refinement stepCycle: LAST / Resolution: 3.08→45.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10158 0 0 0 10158
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012410416
X-RAY DIFFRACTIONf_angle_d1.466914205
X-RAY DIFFRACTIONf_chiral_restr0.07751578
X-RAY DIFFRACTIONf_plane_restr0.01011884
X-RAY DIFFRACTIONf_dihedral_angle_d3.40526366
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.08-3.160.3673920.28841911X-RAY DIFFRACTION65.84
3.16-3.260.33741110.29162318X-RAY DIFFRACTION80.03
3.26-3.360.36661290.29942629X-RAY DIFFRACTION89.49
3.36-3.480.35181550.29982869X-RAY DIFFRACTION98.02
3.48-3.620.31431470.28062908X-RAY DIFFRACTION99.61
3.62-3.790.29851540.25132910X-RAY DIFFRACTION99.9
3.79-3.990.26651290.24142922X-RAY DIFFRACTION99.8
3.99-4.240.28361480.2312906X-RAY DIFFRACTION99.74
4.24-4.560.25191510.20782925X-RAY DIFFRACTION99.77
4.56-5.020.23691510.21552907X-RAY DIFFRACTION99.77
5.02-5.750.23561490.21612932X-RAY DIFFRACTION99.77
5.75-7.240.24421640.23852934X-RAY DIFFRACTION99.94
7.24-45.470.21861750.22662946X-RAY DIFFRACTION99.05

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