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- PDB-4w5h: New structural conformations of adenylate kinase from Streptococc... -

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Basic information

Entry
Database: PDB / ID: 4w5h
TitleNew structural conformations of adenylate kinase from Streptococcus pneumoniae D39
ComponentsAdenylate kinase
KeywordsTRANSFERASE / adenylate kinase / NMP/LID domain / AMP/ATP binding / phosphotransferase
Function / homology
Function and homology information


adenylate kinase / adenylate kinase activity / AMP salvage / phosphorylation / ATP binding / cytoplasm
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 / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesStreptococcus pneumoniae D39 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsThach, T.T. / Lee, S.H.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2014
Title: New crystal structures of adenylate kinase from Streptococcus pneumoniae D39 in two conformations.
Authors: Thach, T.T. / Lee, S.
History
DepositionAug 18, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 26, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 16, 2017Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Source and taxonomy
Category: entity_src_gen / pdbx_database_status ...entity_src_gen / pdbx_database_status / pdbx_related_exp_data_set / pdbx_struct_oper_list
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)24,6384
Polymers24,1551
Non-polymers4833
Water2,648147
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.508, 54.331, 62.711
Angle α, β, γ (deg.)90.00, 118.85, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-411-

HOH

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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 D39 (bacteria)
Gene: adk, SPD_0214 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q04ML5, adenylate kinase
#2: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 147 / 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: 2.37 Å3/Da / Density % sol: 48.02 % / Description: plate-shape
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 1.0 M sodium citrate, 0.1M HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Apr 8, 2012
RadiationMonochromator: Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.96→29.06 Å / Num. obs: 15454 / % possible obs: 98.9 % / Redundancy: 4.5 % / Biso Wilson estimate: 31.4 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 12.3
Reflection shellResolution: 1.96→1.99 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 6.3 / % possible all: 96.1

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.8.4_1496)refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NTZ

4ntz


Resolution: 1.96→29.06 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / Phase error: 22.56
RfactorNum. reflection% reflection
Rfree0.219 1534 10.02 %
Rwork0.177 --
obs0.181 15309 98 %
Solvent computationSolvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.89 Å2
Refinement stepCycle: LAST / Resolution: 1.96→29.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1627 0 31 147 1805
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051679
X-RAY DIFFRACTIONf_angle_d0.8852264
X-RAY DIFFRACTIONf_dihedral_angle_d13.836645
X-RAY DIFFRACTIONf_chiral_restr0.034253
X-RAY DIFFRACTIONf_plane_restr0.005294
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9622-2.02550.26691340.2031197X-RAY DIFFRACTION94
2.0255-2.09780.25121400.18061250X-RAY DIFFRACTION98
2.0978-2.18180.23211390.19011255X-RAY DIFFRACTION98
2.1818-2.28110.23891380.19011258X-RAY DIFFRACTION99
2.2811-2.40130.27011420.18771262X-RAY DIFFRACTION99
2.4013-2.55160.2251380.20131245X-RAY DIFFRACTION99
2.5516-2.74850.23321420.19631271X-RAY DIFFRACTION100
2.7485-3.02490.22871420.20481278X-RAY DIFFRACTION100
3.0249-3.46190.1971420.1771273X-RAY DIFFRACTION100
3.4619-4.35930.18721390.13911253X-RAY DIFFRACTION97
4.3593-29.06010.21911380.17711233X-RAY DIFFRACTION93

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