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- PDB-2ekm: Structure of ST1219 protein from Sulfolobus tokodaii -

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Basic information

Entry
Database: PDB / ID: 2ekm
TitleStructure of ST1219 protein from Sulfolobus tokodaii
ComponentsHypothetical protein ST1511
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / hypothetical protein / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homologyTa1353-like / Adenosine specific kinase / Ta1353-like superfamily / Adenosine specific kinase / hypothetical protein tt1634 / 3-Layer(aba) Sandwich / Alpha Beta / Adenosine monophosphate-protein transferase
Function and homology information
Biological speciesSulfolobus tokodaii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.06 Å
AuthorsLokanath, N.K. / Pampa, K.J. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Structure of ST1219 protein from Sulfolobus tokodaii
Authors: Lokanath, N.K. / Pampa, K.J. / Kamiya, T. / Kunishima, N.
History
DepositionMar 23, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 25, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Hypothetical protein ST1511
B: Hypothetical protein ST1511
C: Hypothetical protein ST1511
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,3255
Polymers54,1403
Non-polymers1842
Water7,476415
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11950 Å2
ΔGint-38.1 kcal/mol
Surface area18150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.200, 63.200, 229.460
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Hypothetical protein ST1511


Mass: 18046.809 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus tokodaii (archaea) / Plasmid: pET-21a / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21-Codon(DE3)-RIL / References: UniProt: Q970U0
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 415 / 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: 2.12 Å3/Da / Density % sol: 41.86 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.4
Details: 28% PEG 5k, 0.2M MgSO4, pH 5.4, VAPOR DIFFUSION, SITTING 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 / Detector: IMAGE PLATE / Date: Dec 15, 2006 / Details: GRAPHITE
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.06→50 Å / Num. all: 29765 / Num. obs: 29795 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Biso Wilson estimate: 23 Å2 / Rmerge(I) obs: 0.096 / Net I/σ(I): 6.8
Reflection shellResolution: 2.06→2.13 Å / % possible all: 100

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Processing

Software
NameClassification
HKL-2000data collection
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GLO

2glo


Resolution: 2.06→40 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.228 1471 -random
Rwork0.18 ---
obs0.18 29795 99.9 %-
all-29765 --
Displacement parametersBiso mean: 23.1 Å2
Refinement stepCycle: LAST / Resolution: 2.06→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3774 0 12 415 4201
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d0.0049
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d22.5
X-RAY DIFFRACTIONc_improper_angle_d0.71
LS refinement shellResolution: 2.06→2.13 Å / % reflection obs: 100 %

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