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- PDB-1b9b: TRIOSEPHOSPHATE ISOMERASE OF THERMOTOGA MARITIMA -

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Basic information

Entry
Database: PDB / ID: 1b9b
TitleTRIOSEPHOSPHATE ISOMERASE OF THERMOTOGA MARITIMA
ComponentsPROTEIN (TRIOSEPHOSPHATE ISOMERASE)
KeywordsISOMERASE / THERMOPHILIC / THERMOTOGA MARITIMA
Function / homology
Function and homology information


phosphoglycerate kinase / phosphoglycerate kinase activity / triose-phosphate isomerase / triose-phosphate isomerase activity / glycolytic process / gluconeogenesis / ADP binding / fatty acid biosynthetic process / ATP binding / cytosol
Similarity search - Function
Phosphoglycerate kinase / Phosphoglycerate kinase, N-terminal / Phosphoglycerate kinase, conserved site / Phosphoglycerate kinase superfamily / Phosphoglycerate kinase / Phosphoglycerate kinase signature. / Triosephosphate isomerase, bacterial/eukaryotic / Triosephosphate isomerase, active site / Triosephosphate isomerase active site. / Triosephosphate isomerase ...Phosphoglycerate kinase / Phosphoglycerate kinase, N-terminal / Phosphoglycerate kinase, conserved site / Phosphoglycerate kinase superfamily / Phosphoglycerate kinase / Phosphoglycerate kinase signature. / 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
Bifunctional PGK/TIM
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsMaes, D. / Wierenga, R.K.
CitationJournal: Proteins / Year: 1999
Title: The crystal structure of triosephosphate isomerase (TIM) from Thermotoga maritima: a comparative thermostability structural analysis of ten different TIM structures.
Authors: Maes, D. / Zeelen, J.P. / Thanki, N. / Beaucamp, N. / Alvarez, M. / Thi, M.H. / Backmann, J. / Martial, J.A. / Wyns, L. / Jaenicke, R. / Wierenga, R.K.
History
DepositionFeb 9, 1999Deposition site: PDBE / Processing site: RCSB
Revision 1.0Jan 1, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 9, 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
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)57,3004
Polymers57,1082
Non-polymers1922
Water93752
1
A: PROTEIN (TRIOSEPHOSPHATE ISOMERASE)
B: PROTEIN (TRIOSEPHOSPHATE ISOMERASE)
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)114,6008
Polymers114,2164
Non-polymers3844
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area10190 Å2
ΔGint-140 kcal/mol
Surface area37150 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)125.950, 125.950, 103.720
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Cell settingtrigonal
Space group name H-MP3221
DetailsTHIS TIM FROM A HYPERTHERMOPHILIC ORGANISM EXISTS IN VIVO AS A PGK-TIM FUSION PROTEIN. THE RECOMBINANT SEPARATE TIM-ENZYME IS ALSO HYPERTHERMOPHILIC. IT IS A TETRAMER. THE TETRAMER IS FORMED BY APPLYING THE CRYSTALLOGRAPHIC TWOFOLD AXIS ON THE ASYMETRIC UNIT (A DIMER). THE MAIN INTERDIMERIC CONTACTS ARE 2 DISULFIDE BONDS.

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Components

#1: Protein PROTEIN (TRIOSEPHOSPHATE ISOMERASE) / E.C.5.3.1.1 / TIM


Mass: 28554.045 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: A SULFATE MOLECULE IS OBSERVED IN THE ACTIVE SITE OF BOTH SUBUNITS
Source: (gene. exp.) Thermotoga maritima (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P36204, triose-phosphate isomerase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 4.16 Å3/Da / Density % sol: 70 %
Crystal growpH: 7 / Details: pH 7.0
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
18.5 mg/mlprotein1drop
270 mMTris-HCl1drop
32 mMEDTA1drop
45 mMcysteamine1drop
5400 mM1dropNaCl
6100 mMTris-HCl1reservoir
72.0 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 15, 1996 / Details: DOUBLE FOCUSSING MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.85→20 Å / Num. all: 22000 / Num. obs: 22000 / % possible obs: 97.8 % / Redundancy: 3.1 % / Biso Wilson estimate: 38.7 Å2 / Rmerge(I) obs: 0.086 / Rsym value: 0.07 / Net I/σ(I): 9
Reflection shellResolution: 2.85→2.9 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.299 / Mean I/σ(I) obs: 6.7 / Rsym value: 0.247 / % possible all: 90
Reflection
*PLUS
Num. measured all: 88489
Reflection shell
*PLUS
% possible obs: 90 %

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Processing

Software
NameVersionClassification
AMoREphasing
CNS0.4refinement
DENZOdata reduction
CCP4data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: BACILLUS STEAROTHERMOPHILUS TIM (PDB ENTRY 1BIM)

1bim


Resolution: 2.85→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.249 -5 %RANDOM
Rwork0.2109 ---
all-22000 --
obs-22000 97.5 %-
Solvent computationSolvent model: BULK SOLVENT MODEL / Bsol: 53 Å2 / ksol: 0.289 e/Å3
Refinement stepCycle: LAST / Resolution: 2.85→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3988 0 10 52 4050
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.3
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.85→2.9 Å / Total num. of bins used: 21
RfactorNum. reflection% reflection
Rfree0.33 -5 %
Rwork0.36 910 -
obs--90 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PROTEIN_REP.PARAM
X-RAY DIFFRACTION2WATER_REP.PARAM
X-RAY DIFFRACTION3ION.PARAM
Software
*PLUS
Name: CNS / Version: 0.4 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.211
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDType
X-RAY DIFFRACTIONc_bond_d
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shell
*PLUS
Rfactor Rfree: 0.33 / % reflection Rfree: 5 % / Rfactor Rwork: 0.36

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