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- PDB-1dkw: CRYSTAL STRUCTURE OF TRIOSE-PHOSPHATE ISOMERASE WITH MODIFIED SUB... -

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Basic information

Entry
Database: PDB / ID: 1dkw
TitleCRYSTAL STRUCTURE OF TRIOSE-PHOSPHATE ISOMERASE WITH MODIFIED SUBSTRATE BINDING SITE
ComponentsTRIOSEPHOSPHATE ISOMERASE
KeywordsISOMERASE / TIM BARREL / MODIFIED LOOP-8
Function / homology
Function and homology information


glycosome / triose-phosphate isomerase / triose-phosphate isomerase activity / glyceraldehyde-3-phosphate biosynthetic process / glycerol catabolic process / glycolytic process / gluconeogenesis / cytoplasm / 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
TERTIARY-BUTYL ALCOHOL / Triosephosphate isomerase, glycosomal
Similarity search - Component
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodX-RAY DIFFRACTION / Resolution: 2.65 Å
AuthorsNorledge, B.V. / Lambeir, A.M. / Abagyan, R.A. / Rottman, A. / Fernandez, A.M. / Filimonov, V.V. / Peter, M.G. / Wierenga, R.K.
Citation
Journal: Proteins / Year: 2001
Title: Modeling, mutagenesis, and structural studies on the fully conserved phosphate-binding loop (loop 8) of triosephosphate isomerase: toward a new substrate specificity.
Authors: Norledge, B.V. / Lambeir, A.M. / Abagyan, R.A. / Rottmann, A. / Fernandez, A.M. / Filimonov, V.V. / Peter, M.G. / Wierenga, R.K.
#1: Journal: Structure / Year: 1993
Title: The Crystal Structure of an Engineered Monomeric Triosephosphate Isomerase, monoTIM: The Correct Modelling of an Eight-Residue Loop.
Authors: Borchert, T.V. / Abagyan, R. / Radha Kishan, K.V. / Zeelen, J.P. / Wierenga, R.K.
#2: Journal: Protein Eng. / Year: 1997
Title: Protein Engineering with Monomeric Triosephosphate Isomerase (monoTIM): The Modelling and Structure Verification of a Seven Residue Loop
Authors: Thanki, N. / Zeelen, J.P. / Mathieu, M. / Jaenicke, R. / Abagyan, R.A. / Wierenga, R.K. / Schliebs, W.
History
DepositionDec 8, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 3, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

Downloads & links

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Assembly

Deposited unit
A: TRIOSEPHOSPHATE ISOMERASE
B: TRIOSEPHOSPHATE ISOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,7234
Polymers51,5752
Non-polymers1482
Water2,612145
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.570, 88.530, 56.220
Angle α, β, γ (deg.)90.00, 97.26, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein TRIOSEPHOSPHATE ISOMERASE


Mass: 25787.414 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Species: Trypanosoma brucei / Strain: brucei / Production host: Escherichia coli (E. coli) / References: UniProt: P04789, triose-phosphate isomerase
#2: Chemical ChemComp-TBU / TERTIARY-BUTYL ALCOHOL / 2-METHYL-2-PROPANOL


Mass: 74.122 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / 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: 2.23 Å3/Da / Density % sol: 44.8 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 1.0 M CITRIC ACID PH 6.5, 20% PEG6000, 2.5% T-BUTANOL, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.1 Msodium citrate1reservoir
25 %tertiary butanol1reservoir

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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: Mar 20, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→22 Å / Num. all: 12311 / Num. obs: 12311 / % possible obs: 92.9 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 40 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 8.7
Reflection shellResolution: 2.65→2.74 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.181 / % possible all: 73.4
Reflection
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 22 Å / Num. obs: 13258 / % possible obs: 92.9 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Rmerge(I) obs: 0.087 / Biso Wilson estimate: 40 Å2
Reflection shell
*PLUS
Highest resolution: 2.65 Å / Lowest resolution: 2.74 Å / % possible obs: 73.4 % / Redundancy: 2.4 % / Rmerge(I) obs: 0.181 / Mean I/σ(I) obs: 3.3

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Processing

Software
NameVersionClassification
AMoREphasing
REFMACrefinement
DENZOdata reduction
CCP4(TRUNCATE)data scaling
RefinementResolution: 2.65→22 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.242 593 -RANDOM
Rwork0.183 ---
all0.186 12114 --
obs0.186 12114 92.9 %-
Refinement stepCycle: LAST / Resolution: 2.65→22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3587 0 0 155 3742
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.65 Å / Lowest resolution: 22 Å / Num. reflection all: 12114 / Num. reflection obs: 12114 / σ(I): 0 / σ(F): 0 / Num. reflection Rfree: 593 / % reflection Rfree: 5 % / Rfactor Rfree: 0.242 / Rfactor Rwork: 0.183
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 49.1 Å2
Refine LS restraints
*PLUS
Type: p_bond_d / Dev ideal: 0.013

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