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- PDB-1m6j: CRYSTAL STRUCTURE OF TRIOSEPHOSPHATE ISOMERASE FROM ENTAMOEBA HIS... -

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Basic information

Entry
Database: PDB / ID: 1m6j
TitleCRYSTAL STRUCTURE OF TRIOSEPHOSPHATE ISOMERASE FROM ENTAMOEBA HISTOLYTICA
ComponentsTriosephosphate Isomerase
KeywordsISOMERASE / Asymmetry / Entamoeba histolytica / monomer stability / triosephosphate isomerase
Function / homology
Function and homology information


triose-phosphate isomerase / triose-phosphate isomerase activity / glyceraldehyde-3-phosphate biosynthetic process / glycerol catabolic process / glycolytic process / gluconeogenesis / 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
Triosephosphate isomerase
Similarity search - Component
Biological speciesEntamoeba histolytica (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsRodriguez-Romero, A. / Hernandez-Santoyo, A. / Fernandez-Velasco, D.A.
Citation
Journal: J.Mol.Biol. / Year: 2002
Title: Structure and Inactivation of Triosephosphate Isomerase from Entamoeba histolytica
Authors: Rodriguez-Romero, A. / Hernandez-Santoyo, A. / Del Pozo-Yauner, L. / Kornhauser, A. / Fernandez-Velasco, D.A.
#1: Journal: Eur.J.Biochem. / Year: 1997
Title: Sequencing, Expression and Properties of Triosephosphate Isomerase from Entamoeba histolytica
Authors: Landa, A. / Rojo-Dominguez, A. / Jimenez, A. / Fernandez-Velasco, D.A.
History
DepositionJul 16, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Triosephosphate Isomerase
B: Triosephosphate Isomerase


Theoretical massNumber of molelcules
Total (without water)55,9302
Polymers55,9302
Non-polymers00
Water14,106783
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3160 Å2
ΔGint-30 kcal/mol
Surface area19740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.729, 119.947, 50.392
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Cell settingorthorhombic
Space group name H-MP21212

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Components

#1: Protein Triosephosphate Isomerase / E.C.5.3.1.1 / TIM / TPI


Mass: 27964.918 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Entamoeba histolytica (eukaryote) / Plasmid: pRSET / Production host: Escherichia coli (E. coli) / Strain (production host): TGI / References: UniProt: O02611, triose-phosphate isomerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 783 / 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: 2.3 Å3/Da / Density % sol: 46.5 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 28% PEG 1500, 30% 1,6-hexanediol, pH 7.0, VAPOR DIFFUSION, HANGING DROP at 291K, temperature 291.0K
Crystal grow
*PLUS
Temperature: 18 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15 mg/mlprotein1drop
228 %(w/v)PEG15001reservoir
330 %(v/v)1,6-hexanediol1reservoir

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Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.782 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 19, 1999
RadiationMonochromator: NULL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.782 Å / Relative weight: 1
ReflectionResolution: 1.5→69.75 Å / Num. all: 80900 / Num. obs: 80009 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 16.8 Å2 / Rsym value: 0.05 / Net I/σ(I): 15.7
Reflection shellResolution: 1.5→1.59 Å / % possible all: 76.1
Reflection
*PLUS
Highest resolution: 1.5 Å / Num. obs: 80420 / % possible obs: 99.4 % / Num. measured all: 360647 / Rmerge(I) obs: 0.04

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Processing

Software
NameVersionClassification
CNSrefinement
MOSFLMdata reduction
CCP4(TRUNCATE)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 5TIM

5tim


Resolution: 1.5→69.75 Å / Rfactor Rfree error: 0.002 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
Details: DISCRETELY DISORDERED RESIDUES: GLN 56, THR 76, GLN 107, GLN 115, GLU 118, GLN 145, GLU 148, LYS 167, GLU 192, GLN 195, GLU 203, SER 220, LYS 251 FROM MONOMER A AND GLU 35, GLN 56, LYS 77, ...Details: DISCRETELY DISORDERED RESIDUES: GLN 56, THR 76, GLN 107, GLN 115, GLU 118, GLN 145, GLU 148, LYS 167, GLU 192, GLN 195, GLU 203, SER 220, LYS 251 FROM MONOMER A AND GLU 35, GLN 56, LYS 77, ASP 125, ARG 141, GLN 145, LYS 167, ASN 168, ILE 179, ASP 188, GLN 195, GLU 211, SER 220 FROM MONOMER B.
RfactorNum. reflection% reflectionSelection details
Rfree0.206 8025 10 %RANDOM
Rwork0.184 ---
obs0.184 80009 98.9 %-
all-80900 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 49.7888 Å2 / ksol: 0.359535 e/Å3
Displacement parametersBiso mean: 15 Å2
Baniso -1Baniso -2Baniso -3
1-0.27 Å20 Å20 Å2
2--0.27 Å20 Å2
3----0.54 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.18 Å0.16 Å
Luzzati d res low-5 Å
Luzzati sigma a0.13 Å0.1 Å
Refinement stepCycle: LAST / Resolution: 1.5→69.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4023 0 0 783 4806
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d21.5
X-RAY DIFFRACTIONc_improper_angle_d0.78
X-RAY DIFFRACTIONc_mcbond_it0.941.5
X-RAY DIFFRACTIONc_mcangle_it1.412
X-RAY DIFFRACTIONc_scbond_it1.722
X-RAY DIFFRACTIONc_scangle_it2.462.5
LS refinement shellResolution: 1.5→1.59 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.278 1049 10 %
Rwork0.253 9466 -
obs--76.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Refinement
*PLUS
Highest resolution: 1.5 Å / Lowest resolution: 10 Å / Rfactor obs: 0.184 / Rfactor Rfree: 0.207 / Rfactor Rwork: 0.184
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.78
LS refinement shell
*PLUS
Rfactor Rfree: 0.278 / Rfactor Rwork: 0.253

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