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- PDB-2vxn: E65Q-TIM complexed with phosphoglycolohydroxamate at 0.82 A resolution -

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Basic information

Entry
Database: PDB / ID: 2vxn
TitleE65Q-TIM complexed with phosphoglycolohydroxamate at 0.82 A resolution
ComponentsTRIOSEPHOSPHATE ISOMERASE
KeywordsISOMERASE / FATTY ACID BIOSYNTHESIS / TRANSITION STATE ANALOGUE / GLYCOLYSIS / PENTOSE SHUNT / GLUCONEOGENESIS / TIM / GLYCOSOME / TRIOSEPHOSPHATE ISOMERASE / ENZYME-LIGAND COMPLEX / LIPID SYNTHESIS / TRANSITION STATE / PROTONATION STATE
Function / homology
Function and homology information


glycosome / 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
ACETATE ION / 2-PHOSPHOGLYCOLIC ACID / PHOSPHOGLYCOLOHYDROXAMIC ACID / Triosephosphate isomerase
Similarity search - Component
Biological speciesLEISHMANIA MEXICANA (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.82 Å
AuthorsAlahuhta, M. / Wierenga, R.K.
CitationJournal: Proteins / Year: 2010
Title: Atomic Resolution Crystallography of a Complex of Triosephosphate Isomerase with a Reaction-Intermediate Analog: New Insight in the Proton Transfer Reaction Mechanism
Authors: Alahuhta, M. / Wierenga, R.K.
History
DepositionJul 8, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 14, 2009Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5May 1, 2024Group: Database references / Category: citation / Item: _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TRIOSEPHOSPHATE ISOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0559
Polymers27,2081
Non-polymers8478
Water7,548419
1
A: TRIOSEPHOSPHATE ISOMERASE
hetero molecules

A: TRIOSEPHOSPHATE ISOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,11018
Polymers54,4162
Non-polymers1,69316
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area6670 Å2
ΔGint-52.1 kcal/mol
Surface area19150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.360, 50.650, 58.660
Angle α, β, γ (deg.)90.00, 117.56, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1253-

GOL

21A-2024-

HOH

31A-2234-

HOH

41A-2407-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein TRIOSEPHOSPHATE ISOMERASE / TIM / TRIOSE-PHOSPHATE ISOMERASE


Mass: 27208.236 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) LEISHMANIA MEXICANA (eukaryote) / Plasmid: PET3A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 PLYSS / References: UniProt: P48499, triose-phosphate isomerase

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Non-polymers , 5 types, 427 molecules

#2: Chemical ChemComp-PGH / PHOSPHOGLYCOLOHYDROXAMIC ACID


Mass: 171.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6NO6P
#3: Chemical ChemComp-PGA / 2-PHOSPHOGLYCOLIC ACID


Mass: 156.031 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C2H5O6P
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 419 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsENGINEERED RESIDUE IN CHAIN A, GLU 66 TO GLN

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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: 2.59 Å3/Da / Density % sol: 52.55 % / Description: NONE
Crystal growpH: 5
Details: 24.1 % PEG6000, 0.1 M ACETIC ACID PH 4.5, 1 MM DTT, 1 MM EDTA, 1 MM NAN3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8426
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 1, 2005 / Details: BENT
RadiationMonochromator: SI, HORIZONTALLY FOCUSSING / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8426 Å / Relative weight: 1
ReflectionResolution: 0.82→10 Å / Num. obs: 223330 / % possible obs: 89.6 % / Observed criterion σ(I): 3 / Redundancy: 5 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 22.96
Reflection shellResolution: 0.82→0.83 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 6.12 / % possible all: 84.8

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Processing

Software
NameClassification
SHELXL-97refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1N55

1n55


Resolution: 0.82→10 Å / Num. parameters: 22625 / Num. restraintsaints: 28759 / Cross valid method: THROUGHOUT / σ(F): 3 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.103 11174 5 %RANDOM
all0.092 223329 --
obs0.092 -89.6 %-
Refinement stepCycle: LAST / Resolution: 0.82→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1900 0 53 419 2372
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.026
X-RAY DIFFRACTIONs_angle_d0.031
X-RAY DIFFRACTIONs_similar_dist0.037
X-RAY DIFFRACTIONs_from_restr_planes0.032
X-RAY DIFFRACTIONs_zero_chiral_vol0.109
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.118
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.051
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt
X-RAY DIFFRACTIONs_approx_iso_adps

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