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- PDB-1yul: Crystal Structure of Nicotinic Acid Mononucleotide Adenylyltransf... -

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Basic information

Entry
Database: PDB / ID: 1yul
TitleCrystal Structure of Nicotinic Acid Mononucleotide Adenylyltransferase from Pseudomonas aeruginosa
ComponentsProbable nicotinate-nucleotide adenylyltransferase
KeywordsTRANSFERASE / alpha/beta domain
Function / homology
Function and homology information


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 / Probable nicotinate-nucleotide adenylyltransferase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsYoon, H.J. / Kim, H.L. / Mikami, B. / Suh, S.W.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: Crystal structure of nicotinic acid mononucleotide adenylyltransferase from Pseudomonas aeruginosa in its Apo and substrate-complexed forms reveals a fully open conformation
Authors: Yoon, H.J. / Kim, H.L. / Mikami, B. / Suh, S.W.
History
DepositionFeb 14, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 8, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Remark 300BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN. ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN. THE BIOLOGICAL UNIT IS NOT ASSIGNED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable nicotinate-nucleotide adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4542
Polymers27,2621
Non-polymers1921
Water3,405189
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.525, 65.525, 110.340
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322
DetailsThe biological assembly is a dimer generated from the monomer in the asymmetric unit by the operations

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Components

#1: Protein Probable nicotinate-nucleotide adenylyltransferase / nicotinic acid mononucleotide adenylyltransferase / NaMN AT / Deamido-NAD+ / pyrophosphorylase / ...nicotinic acid mononucleotide adenylyltransferase / NaMN AT / Deamido-NAD+ / pyrophosphorylase / Deamido-NAD+ / diphosphorylase / Nicotinate mononucleotide adenylyltransferase / NaMN adenylyltransferase


Mass: 27262.365 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: nadD (PA4006) / Plasmid: pET-28b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3)
References: UniProt: Q9HX21, nicotinate-nucleotide adenylyltransferase
#2: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 189 / 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: 2.15 Å3/Da / Density % sol: 42.7 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: bis-tris propane, trisodium citrate, glycerol , pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-18B / Wavelength: 0.9791, 0.9793, 0.9500
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 28, 2003 / Details: mirrors
RadiationMonochromator: Ge(111) crystals / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97911
20.97931
30.951
ReflectionResolution: 2→50 Å / Num. all: 31029 / Num. obs: 31029 / % possible obs: 100 % / Observed criterion σ(F): -3 / Redundancy: 7.6 % / Biso Wilson estimate: 13.5 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 11.5
Reflection shellResolution: 2→2.07 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.325 / Mean I/σ(I) obs: 11.5 / Num. unique all: 3103 / % possible all: 99.9

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2→9.97 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 128706.74 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.248 2917 9.7 %RANDOM
Rwork0.202 ---
obs0.202 30151 97.9 %-
all-30785 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 68.1046 Å2 / ksol: 0.472626 e/Å3
Displacement parametersBiso mean: 28.7 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20 Å20 Å2
2--0.06 Å20 Å2
3----0.12 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 2→9.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1647 0 13 189 1849
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
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_d22.3
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_it3.111.5
X-RAY DIFFRACTIONc_mcangle_it4.942
X-RAY DIFFRACTIONc_scbond_it5.082
X-RAY DIFFRACTIONc_scangle_it7.612.5
LS refinement shellResolution: 2→2.12 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.277 496 10.2 %
Rwork0.228 4368 -
obs--94.8 %
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
X-RAY DIFFRACTION4CIT.PARAMCIT.TOP

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