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- PDB-4ntz: Crystal structure of Adenylate kinase from Streptococcus pneumoniae -

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Basic information

Entry
Database: PDB / ID: 4ntz
TitleCrystal structure of Adenylate kinase from Streptococcus pneumoniae
ComponentsAdenylate kinase
KeywordsTRANSFERASE / adenylate kinase / capsular polysaccharide / growth / CORE / NMP/LID domain / AMP/ATP binding / phosphotransferase
Function / homology
Function and homology information


CDP biosynthetic process / (d)CMP kinase activity / UMP kinase activity / adenylate kinase / adenylate kinase activity / AMP salvage / UDP biosynthetic process / nucleoside diphosphate kinase activity / ATP binding / cytosol
Similarity search - Function
Adenylate kinase subfamily / Adenylate kinase / Adenylate kinase, conserved site / Adenylate kinase signature. / Adenylate kinase/UMP-CMP kinase / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.69 Å
AuthorsThach, T.T. / Luong, T.T. / Lee, S.H. / Rhee, D.K.
CitationJournal: FEBS Open Bio / Year: 2014
Title: Adenylate kinase from Streptococcus pneumoniae is essential for growth through its catalytic activity
Authors: Thach, T.T. / Luong, T.T. / Lee, S.H. / Rhee, D.K.
History
DepositionDec 3, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 23, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 1, 2014Group: Database references
Revision 1.2Mar 20, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Adenylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2512
Polymers24,1551
Non-polymers961
Water6,413356
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.220, 53.700, 50.870
Angle α, β, γ (deg.)90.000, 114.460, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Adenylate kinase / AK / ATP-AMP transphosphorylase / ATP-AMP phosphotransferase / Adenylate monophosphate kinase


Mass: 24155.322 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Strain: D39 / Gene: adk, SPD_0214 / Production host: Escherichia coli (E. coli) / References: UniProt: Q04ML5, adenylate kinase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 356 / 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: 2.31 Å3/Da / Density % sol: 46.67 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 9.5
Details: 2.0M (NH4)2SO4, 0.1M CHES pH 9.5, 0.2M Li2SO4, 0.1M CsCl2, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Nov 10, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.69→25.05 Å / Num. all: 23924 / Num. obs: 23924 / % possible obs: 97.84 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.05
Reflection shellResolution: 1.69→1.73 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.118 / Mean I/σ(I) obs: 6.8 / % possible all: 98.72

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASESphasing
PHENIX1.7.2_869refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.69→25.046 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.46 / σ(F): 1.41 / Phase error: 20.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2222 1223 5.12 %RANDOM
Rwork0.1838 ---
obs0.1857 23897 97.73 %-
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.853 Å2 / ksol: 0.411 e/Å3
Displacement parametersBiso max: 44.22 Å2 / Biso mean: 14.4084 Å2 / Biso min: 4.82 Å2
Baniso -1Baniso -2Baniso -3
1-2.6837 Å2-0 Å2-2.6537 Å2
2---2.6173 Å2-0 Å2
3----0.0664 Å2
Refinement stepCycle: LAST / Resolution: 1.69→25.046 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1674 0 5 356 2035
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_angle_d1.39
X-RAY DIFFRACTIONf_bond_d0.019
LS refinement shellResolution: 1.69→1.73 Å / % reflection obs: 98.72 %

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