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- PDB-3cm0: Crystal structure of adenylate kinase from Thermus thermophilus HB8 -

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Basic information

Entry
Database: PDB / ID: 3cm0
TitleCrystal structure of adenylate kinase from Thermus thermophilus HB8
ComponentsAdenylate kinase
KeywordsTRANSFERASE / Adenylate kinase / ATP-binding / Cytoplasm / Nucleotide biosynthesis / Nucleotide-binding / Structural Genomics / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


adenylate kinase / AMP kinase activity / AMP salvage / ATP binding / cytoplasm
Similarity search - Function
Adenylate kinase, conserved site / Adenylate kinase signature. / Adenylate kinase/UMP-CMP kinase / Adenylate 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 speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsNakagawa, N. / Kondo, N. / Masui, R. / Matsuda, Z. / Iwamoto, I. / Yokoyama, S. / Kuramitsu, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of adenylate kinase from Thermus thermophilus HB8.
Authors: Nakagawa, N. / Kondo, N. / Masui, R. / Yokoyama, S. / Kuramitsu, S.
History
DepositionMar 20, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 23, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Aug 14, 2024Group: Database references / Category: citation / Item: _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Adenylate kinase


Theoretical massNumber of molelcules
Total (without water)20,7841
Polymers20,7841
Non-polymers00
Water1,58588
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.446, 51.446, 131.474
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-264-

HOH

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Components

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


Mass: 20783.779 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: adk / Plasmid: pET-3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5SHQ9, adenylate kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / 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: 2.42 Å3/Da / Density % sol: 49.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 4.5
Details: 40% 1,2-propanediol, 0.1M NaAcetate, pH4.5, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45PX / Wavelength: 1 Å
DetectorType: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Mar 10, 2003
RadiationMonochromator: Diamond crystals / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 19365 / % possible obs: 99.5 % / Observed criterion σ(I): 1 / Biso Wilson estimate: 18.8 Å2 / Rmerge(I) obs: 0.068
Reflection shellResolution: 1.8→1.86 Å / Rmerge(I) obs: 0.243 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2AK2

2ak2


Resolution: 1.8→44.55 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1140508.95 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.242 1888 9.9 %RANDOM
Rwork0.205 ---
obs0.205 19109 98.3 %-
all-19365 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 68.002 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 27.6 Å2
Baniso -1Baniso -2Baniso -3
1--0.86 Å20 Å20 Å2
2---0.86 Å20 Å2
3---1.71 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.11 Å
Refinement stepCycle: LAST / Resolution: 1.8→44.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1445 0 0 88 1533
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d20.7
X-RAY DIFFRACTIONc_improper_angle_d0.91
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.299 303 10 %
Rwork0.24 2731 -
obs-2731 95 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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