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- PDB-1k4m: Crystal structure of E.coli nicotinic acid mononucleotide adenyly... -

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Basic information

Entry
Database: PDB / ID: 1k4m
TitleCrystal structure of E.coli nicotinic acid mononucleotide adenylyltransferase complexed to deamido-NAD
ComponentsNaMN adenylyltransferase
KeywordsTRANSFERASE / Nucleotidyltransferase
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
CITRIC ACID / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinate-nucleotide adenylyltransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsZhang, H. / Zhou, T. / Kurnasov, O. / Cheek, S. / Grishin, N.V. / Osterman, A.
CitationJournal: Structure / Year: 2002
Title: Crystal structures of E. coli nicotinate mononucleotide adenylyltransferase and its complex with deamido-NAD.
Authors: Zhang, H. / Zhou, T. / Kurnasov, O. / Cheek, S. / Grishin, N.V. / Osterman, A.
History
DepositionOct 8, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 8, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 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_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

Downloads & links

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Assembly

Deposited unit
A: NaMN adenylyltransferase
B: NaMN adenylyltransferase
C: NaMN adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,2289
Polymers73,6623
Non-polymers2,5676
Water9,206511
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)114.830, 113.930, 115.670
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
DetailsThe biological unit of the protein is monomer

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Components

#1: Protein NaMN adenylyltransferase


Mass: 24553.871 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: NADD / Production host: Escherichia coli (E. coli)
References: UniProt: P0A752, nicotinate-nucleotide adenylyltransferase
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H8O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 511 / 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: 2.57 Å3/Da / Density % sol: 52.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: Na citrate, NaCl, Tris, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120 mg/mlprotein1drop
250 mMHEPES1droppH7.2
3150 mM1dropNaCl
41 mMdithiothreitol1drop
55 mMNaAD1drop
60.1 MTris1reservoirpH7.0
70.2 M1reservoirNaCl
80.8 Msodium citrate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 5, 2001 / Details: Osmic mirrors
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→40 Å / Num. all: 59943 / Num. obs: 57802 / % possible obs: 95.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection
*PLUS
Highest resolution: 1.9 Å / Num. measured all: 180068 / Rmerge(I) obs: 0.056
Reflection shell
*PLUS
% possible obs: 67.5 % / Rmerge(I) obs: 0.355 / Mean I/σ(I) obs: 1.8

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1k4k

1k4k


Resolution: 1.9→40 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.255 2703 random
Rwork0.206 --
all0.206 59943 -
obs0.206 53217 -
Refinement stepCycle: LAST / Resolution: 1.9→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5202 0 171 511 5884
Refinement
*PLUS
Lowest resolution: 40 Å / % reflection Rfree: 5 % / Rfactor obs: 0.206 / Rfactor Rfree: 0.255 / Rfactor Rwork: 0.206
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.011
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_deg1.61

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