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

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Basic information

Entry
Database: PDB / ID: 1yum
TitleCrystal Structure of Nicotinic Acid Mononucleotide Adenylyltransferase from Pseudomonas aeruginosa
Components'Probable 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 / NICOTINATE MONONUCLEOTIDE / Probable nicotinate-nucleotide adenylyltransferase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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
Revision 1.3Mar 29, 2017Group: Refinement description
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Remark 300BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 4 CHAINS. ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 4 CHAINS. 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
B: 'Probable nicotinate-nucleotide adenylyltransferase
C: 'Probable nicotinate-nucleotide adenylyltransferase
D: 'Probable nicotinate-nucleotide adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,40812
Polymers108,2994
Non-polymers2,1098
Water14,646813
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.179, 110.655, 65.203
Angle α, β, γ (deg.)90.00, 89.99, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is a dimer generated from the tetramer in the asymmetric unit by the operations: -x, 1/2+y, -z

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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: 27074.783 Da / Num. of mol.: 4
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.: 4 / Source method: obtained synthetically / Formula: C6H8O7
#3: Chemical
ChemComp-NCN / NICOTINATE MONONUCLEOTIDE / NAMN


Mass: 335.204 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H14NO9P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 813 / 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: SPring-8 / Beamline: BL38B1 / Wavelength: 0.85 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 16, 2004 / Details: mirrors
RadiationMonochromator: quasi-monochromatic X-ray / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.85 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. all: 118067 / Num. obs: 118041 / % possible obs: 96.8 % / Observed criterion σ(I): -3 / Redundancy: 3.1 % / Biso Wilson estimate: 21.74 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 23.5
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 3 % / Rmerge(I) obs: 0.266 / Num. unique all: 12046 / % possible all: 98.9

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Processing

Software
NameClassification
SHELXmodel building
SHELXL-97refinement
HKL-2000data reduction
SCALEPACKdata scaling
SHELXLrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: apo NaMN AT

Resolution: 1.7→10 Å / Num. parameters: 31002 / Num. restraintsaints: 29215 / Cross valid method: THROUGHOUT / σ(I): 0
Details: THIS IS A TWINNED STRUCTURE. THE TWINNING OPERATOR IS (H,K,L) -> (H,-K,-L) AND THE TWINNING FRACTION IS 0.49421
RfactorNum. reflection% reflectionSelection details
Rfree0.2506 5252 -RANDOM
Rwork0.1907 ---
all-92096 --
obs-92096 91.3 %-
Refine analyzeNum. disordered residues: 26 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 7590.14
Refinement stepCycle: LAST / Resolution: 1.7→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6636 0 140 813 7589
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.013
X-RAY DIFFRACTIONs_angle_d0.028
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0281
X-RAY DIFFRACTIONs_zero_chiral_vol0.038
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.046
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.038
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.095
X-RAY DIFFRACTIONs_approx_iso_adps0
LS refinement shell
Resolution (Å)Highest resolution (Å)Rfactor RworkRefine-IDNum. reflection obsTotal num. of bins used% reflection obs (%)
1.7-1.80.25X-RAY DIFFRACTION145931091.38
1.8-1.90.224X-RAY DIFFRACTION125591098.89
1.9-20.212X-RAY DIFFRACTION90121087.09
20.196X-RAY DIFFRACTION141101091.41

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