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- PDB-2btm: DOES THE HIS12-LYS13 PAIR PLAY A ROLE IN THE ADAPTATION OF THERMO... -

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Basic information

Entry
Database: PDB / ID: 2btm
TitleDOES THE HIS12-LYS13 PAIR PLAY A ROLE IN THE ADAPTATION OF THERMOPHILIC TIMS TO HIGH TEMPERATURES?
ComponentsPROTEIN (TRIOSEPHOSPHATE ISOMERASE)
KeywordsISOMERASE / THERMOPHILIC TRIOSE-PHOSPHATE / GLYCOLYSIS
Function / homology
Function and homology information


triose-phosphate isomerase / triose-phosphate isomerase activity / glyceraldehyde-3-phosphate biosynthetic process / glycerol catabolic process / gluconeogenesis / glycolytic process / cytosol
Similarity search - Function
Triosephosphate isomerase, bacterial/eukaryotic / Triosephosphate isomerase, active site / Triosephosphate isomerase active site. / Triosephosphate isomerase / Triosephosphate isomerase superfamily / Triosephosphate isomerase / Triosephosphate isomerase (TIM) family profile. / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel ...Triosephosphate isomerase, bacterial/eukaryotic / Triosephosphate isomerase, active site / Triosephosphate isomerase active site. / Triosephosphate isomerase / Triosephosphate isomerase superfamily / Triosephosphate isomerase / Triosephosphate isomerase (TIM) family profile. / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
2-PHOSPHOGLYCOLIC ACID / Triosephosphate isomerase
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsDelboni, L.F. / Mande, S.C. / Hol, W.G.J.
Citation
Journal: J.Biol.Chem. / Year: 1999
Title: Lys13 plays a crucial role in the functional adaptation of the thermophilic triose-phosphate isomerase from Bacillus stearothermophilus to high temperatures.
Authors: Alvarez, M. / Wouters, J. / Maes, D. / Mainfroid, V. / Rentier-Delrue, F. / Wyns, L. / Depiereux, E. / Martial, J.A.
#1: Journal: J.Mol.Biol. / Year: 1993
Title: Cloning and Overexpression of the Triosephosphate Isomerase Genes from Psychrophilic and Thermophilic Bacteria. Structural Comparison of the Predicted Protein Sequences
Authors: Rentier-Delrue, F. / Mande, S.C. / Moyens, S. / Terpstra, P. / Mainfroid, V. / Goraj, K. / Lion, M. / Hol, W.G. / Martial, J.A.
History
DepositionJan 4, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Jan 13, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations / Category: 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 1.4Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (TRIOSEPHOSPHATE ISOMERASE)
B: PROTEIN (TRIOSEPHOSPHATE ISOMERASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,2754
Polymers53,9632
Non-polymers3122
Water2,180121
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4230 Å2
ΔGint-37 kcal/mol
Surface area17120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.132, 107.913, 70.980
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein PROTEIN (TRIOSEPHOSPHATE ISOMERASE) / TIM


Mass: 26981.641 Da / Num. of mol.: 2 / Mutation: H12N, K13G, P230A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Production host: Escherichia coli (E. coli) / References: UniProt: P00943, triose-phosphate isomerase
#2: Chemical ChemComp-PGA / 2-PHOSPHOGLYCOLIC ACID


Mass: 156.031 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H5O6P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 121 / 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: 2.77 Å3/Da / Density % sol: 55.62 %
Crystal growpH: 6.5 / Details: pH 6.5
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
17 mg/mlprotein1drop
25 mMMES1drop
31 mMEDTA1drop
41 mMsodium azide1drop
52 mM2-phosphoglycolate1drop
625 %(w/v)PEG40001reservoir
78 %isopropyl alcohol1reservoir
8100 mMacetate1reservoir
91 mMEDTA1reservoir
101 mMsodium azide1reservoir
112 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 297 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.5 / Wavelength: 1.1
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 15, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. obs: 22732 / % possible obs: 94.3 % / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Rmerge(I) obs: 0.073 / Rsym value: 0.076
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 3 % / Rmerge(I) obs: 0.278 / Rsym value: 0.292 / % possible all: 65
Reflection
*PLUS
Num. measured all: 70035
Reflection shell
*PLUS
% possible obs: 65 %

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Processing

Software
NameVersionClassification
AMoREphasing
CNS0.4Arefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BTM

1btm


Resolution: 2.4→30 Å / Cross valid method: THROUGHOUT / σ(F): 0
Details: THE INITIAL STAGES OF REFINEMENT WERE CARRIED OUT WITH X-PLOR
RfactorNum. reflection% reflectionSelection details
Rfree0.22 -5 %RANDOM
Rwork0.1756 ---
obs0.1756 22732 94.3 %-
Refinement stepCycle: LAST / Resolution: 2.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3672 0 18 121 3811
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.253
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.4→2.44 Å / Total num. of bins used: 22 /
RfactorNum. reflection
Rfree0.2923 -
Rwork0.2474 289
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMWATER.TOP
X-RAY DIFFRACTION2ION.PARAMPROTEIN.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMPGA.TOP
X-RAY DIFFRACTION4PGA.PAR
Software
*PLUS
Name: CNS / Version: 0.4A / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 30 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor Rfree: 0.22
Solvent computation
*PLUS
Displacement parameters
*PLUS

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