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- PDB-1f9a: CRYSTAL STRUCTURE ANALYSIS OF NMN ADENYLYLTRANSFERASE FROM METHAN... -

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Basic information

Entry
Database: PDB / ID: 1f9a
TitleCRYSTAL STRUCTURE ANALYSIS OF NMN ADENYLYLTRANSFERASE FROM METHANOCOCCUS JANNASCHII
ComponentsHYPOTHETICAL PROTEIN MJ0541Hypothesis
KeywordsTRANSFERASE / alpha/beta / transferase / HYPOTHETICAL PROTEIN / STRUCTURAL GENOMICS
Function / homologyNicotinamide-nucleotide adenylyltransferase, archaeal type / Cytidyltransferase-like domain / Rossmann-like alpha/beta/alpha sandwich fold / Cytidylyltransferase-like / nicotinamide-nucleotide adenylyltransferase / nicotinamide-nucleotide adenylyltransferase activity / NAD biosynthetic process / ATP binding / cytoplasm / Nicotinamide-nucleotide adenylyltransferase
Function and homology information
Specimen sourceMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIR / 2 Å resolution
AuthorsD'Angelo, I. / Raffaelli, N. / Dabusti, V. / Lorenzi, T. / Magni, G. / Rizzi, M.
Citation
Journal: Structure Fold.Des. / Year: 2000
Title: Structure of nicotinamide mononucleotide adenylyltransferase: a key enzyme in NAD(+) biosynthesis.
Authors: D'Angelo, I. / Raffaelli, N. / Dabusti, V. / Lorenzi, T. / Magni, G. / Rizzi, M.
#1: Journal: J.Bacteriol. / Year: 1997
Title: Characterization of nicotinamide mononucleotide adenylyltransferase from Thermophilic archaea
Authors: Raffaelli, N. / Pisani, F.M. / Lorenzi, T. / Emanuelli, M. / Amici, A. / Ruggieri, S. / Magni, G.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jul 9, 2000 / Release: Jan 10, 2001
RevisionDateData content typeGroupProviderType
1.0Jan 10, 2001Structure modelrepositoryInitial release
1.1Apr 27, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HYPOTHETICAL PROTEIN MJ0541
B: HYPOTHETICAL PROTEIN MJ0541
C: HYPOTHETICAL PROTEIN MJ0541
D: HYPOTHETICAL PROTEIN MJ0541
E: HYPOTHETICAL PROTEIN MJ0541
F: HYPOTHETICAL PROTEIN MJ0541
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,91918
Polyers117,7306
Non-polymers3,18912
Water11,962664
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)17280
ΔGint (kcal/M)-120
Surface area (Å2)39290
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)78.768, 112.642, 79.869
Angle α, β, γ (deg.)90.00, 116.94, 90.00
Int Tables number4
Space group name H-MP 1 21 1
DetailsThe asymmetric unit contains and homohexamer having 32 point group symmetry

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Components

#1: Protein/peptide
HYPOTHETICAL PROTEIN MJ0541 / Hypothesis


Mass: 19621.697 Da / Num. of mol.: 6 / Fragment: NMN ADENYLYLTRANSFERASE
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Genus: Methanocaldococcus / Plasmid name: PT7-7 / Genus (production host): Escherichia / Production host: Escherichia coli (E. coli) / References: UniProt: Q57961
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Formula: Mg / Magnesium
#3: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 6 / Formula: C10H16N5O13P3 / Adenosine triphosphate / Comment: ATP (energy-carrying molecule) *YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 664 / Formula: H2O / Water

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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: 2.54 / Density percent sol: 53 %
Crystal growTemp: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Jeffamine M600, Hepes, cesium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temp: 4 ℃
components of the solutions
*PLUS

Crystal ID: 1

IDConcCommon nameSol IDDetailsChemical formula
120 mg/mlproteindrop
230 %(v/v)Jeffamine M600reservoirpH7.0
30.05 MreservoirCsCl
40.1 MHEPESreservoirpH7.5

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Data collection

DiffractionMean temperature: 100 kelvins
SourceSource: SYNCHROTRON / Type: EMBL/DESY, HAMBURG BEAMLINE BW7B / Synchrotron site: EMBL/DESY, Hamburg / Beamline: BW7B / Wavelength: 0.8139
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Collection date: Mar 20, 1999
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8139 Å / Relative weight: 1
ReflectionB iso Wilson estimate: 25.5 Å2 / D resolution high: 2 Å / D resolution low: 2 Å / Number all: 200580 / Number obs: 80232 / Observed criterion sigma F: 0 / Observed criterion sigma I: 2 / Rmerge I obs: 0.054 / NetI over sigmaI: 8 / Redundancy: 2.5 % / Percent possible obs: 96
Reflection shellRmerge I obs: 0.178 / Highest resolution: 2 Å / Lowest resolution: 2 Å / Number unique all: 11668 / Redundancy: 2.2 % / Percent possible all: 95.6
Reflection
*PLUS
Number measured all: 200580 / Percent possible obs: 96

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Processing

Software
NameVersionClassification
SHELXSphasing
REFMACrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefineMethod to determine structure: SIR / Details: Used maximum likelihood procedure / R Free selection details: RANDOM / Sigma F: 0 / Sigma I: 0 / Stereochemistry target values: Engh and Huber
Displacement parametersB iso mean: 36.5 Å2
Least-squares processR factor R free: 0.264 / R factor R work: 0.215 / R factor all: 0.215 / R factor obs: 0.215 / Highest resolution: 2 Å / Lowest resolution: 2 Å / Number reflection R free: 1006 / Number reflection all: 83575 / Number reflection obs: 80232 / Percent reflection obs: 96
Refine hist #LASTHighest resolution: 2 Å / Lowest resolution: 2 Å
Number of atoms included #LASTProtein: 8067 / Nucleic acid: 0 / Ligand: 192 / Solvent: 664 / Total: 8923
Refine LS restraints
Refine IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.016
X-RAY DIFFRACTIONp_angle_d0.040
X-RAY DIFFRACTIONp_planar_d0.039
Software
*PLUS
Name: REFMAC / Classification: refinement
Refine
*PLUS
Sigma F: 0
Displacement parameters
*PLUS
B iso mean: 36.5 Å2
Least-squares process
*PLUS
Highest resolution: 2 Å

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