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- PDB-7az4: Perdeuterated E65Q-TIM complexed with 2-PHOSPHOGLYCOLIC ACID -

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Basic information

Entry
Database: PDB / ID: 7az4
TitlePerdeuterated E65Q-TIM complexed with 2-PHOSPHOGLYCOLIC ACID
ComponentsTriosephosphate isomerase
KeywordsISOMERASE / GLYCOLYSIS / TIM / TRIOSEPHOSPHATE ISOMERASE / TRANSITION STATE / PERDEUTERATION
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-type TIM barrel
Similarity search - Domain/homology
2-PHOSPHOGLYCOLIC ACID / Triosephosphate isomerase
Similarity search - Component
Biological speciesLeishmania mexicana (eukaryote)
MethodX-RAY DIFFRACTION / NEUTRON DIFFRACTION / SYNCHROTRON / NUCLEAR REACTOR / MOLECULAR REPLACEMENT / Resolution: 1.15 Å
AuthorsKelpsas, V. / Caldararu, O. / von Wachenfeldt, C. / Oksanen, E.
Funding support Sweden, 4items
OrganizationGrant numberCountry
Other private Sweden
Other private Sweden
Other government Sweden
Other government Sweden
CitationJournal: Iucrj / Year: 2021
Title: Neutron structures of Leishmania mexicana triosephosphate isomerase in complex with reaction-intermediate mimics shed light on the proton-shuttling steps.
Authors: Kelpsas, V. / Caldararu, O. / Blakeley, M.P. / Coquelle, N. / Wierenga, R.K. / Ryde, U. / von Wachenfeldt, C. / Oksanen, E.
History
DepositionNov 16, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 28, 2021Provider: repository / Type: Initial release
Revision 2.0May 1, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Triosephosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,3642
Polymers27,2081
Non-polymers1561
Water3,657203
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area370 Å2
ΔGint-6 kcal/mol
Surface area10460 Å2
Unit cell
Length a, b, c (Å)98.341, 52.365, 58.463
Angle α, β, γ (deg.)90.000, 118.030, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-503-

HOH

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Components

#1: Protein Triosephosphate isomerase / TIM / Triose-phosphate isomerase


Mass: 27208.236 Da / Num. of mol.: 1 / Mutation: E65Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania mexicana (eukaryote) / Production host: Escherichia coli (E. coli) / Strain (production host): DA1 / References: UniProt: P48499, triose-phosphate isomerase
#2: Chemical ChemComp-PGA / 2-PHOSPHOGLYCOLIC ACID


Mass: 156.031 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H5O6P / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 203 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

Experiment
MethodNumber of used crystals
X-RAY DIFFRACTION1
NEUTRON DIFFRACTION1

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Sample preparation

CrystalDensity Matthews: 2.44 Å3/Da / Density % sol: 49.63 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion / pH: 5.4
Details: 0.1 M sodium acetate, 1 mM Na EDTA, 1 mM DTT,18% PEG6000

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Data collection

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
12931N
22931N
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONESRF BM30A10.98
NUCLEAR REACTORILL LADI III22.7-3.5
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDApr 23, 2018
CUSTOM-MADE2IMAGE PLATEMar 28, 2018
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2LAUELneutron2
Radiation wavelength
IDWavelength (Å)Relative weight
10.981
22.71
33.51
Reflection

Entry-ID: 7AZ4

Resolution (Å)Num. obs% possible obs (%)Redundancy (%)CC1/2Rrim(I) allDiffraction-IDNet I/σ(I)
1.15-45.6749558499.44.90.9990.049123.49
1.7-402556588.66.60.9970.097213.3
Reflection shell
Resolution (Å)Mean I/σ(I) obsNum. unique obsCC1/2Diffraction-IDRrim(I) all
1.15-1.182.4770080.7671
1.7-1.795.433000.92420.367

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
CNSrefinement
XDSdata reduction
LAUEGENdata reduction
XSCALEdata scaling
SCALAdata scaling
PHASERphasing
Refinement

% reflection Rfree: 2.09 % / SU ML: 0.1 / Cross valid method: THROUGHOUT / Method to determine structure: MOLECULAR REPLACEMENT / Phase error: 17.16 / Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Starting model: 2vxn

2vxn

/ Stereochemistry target values: ML / Solvent model: FLAT BULK SOLVENT MODEL

Resolution (Å)Refine-IDBiso max (Å2)Biso mean (Å2)Biso min (Å2)Rfactor RfreeRfactor RworkRfactor obsNum. reflection RfreeNum. reflection RworkNum. reflection obs% reflection obs (%)Diffraction-IDσ(F)
1.15-25.3325X-RAY DIFFRACTION90.2727.706615.210.15280.14020.14051998935769557499.4811.35
1.7-30.3961NEUTRON DIFFRACTION0.2230.18210.18295332554488.0120
Refinement stepCycle: final / Resolution: 1.15→25.3325 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1858 0 11 434 2303
Biso mean--19.87 39.78 -
Num. residues----248
LS refinement shell

Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.87110.3461180.28255601NEUTRON DIFFRACTION79
1.8711-2.14180.27181260.20295982NEUTRON DIFFRACTION85
2.1418-2.69810.20791400.1816437NEUTRON DIFFRACTION91
2.6981-30.39610.20341490.16586991NEUTRON DIFFRACTION97
1.15-1.16590.25241390.24966507X-RAY DIFFRACTION97
1.1659-1.19740.23171410.22276615X-RAY DIFFRACTION99
1.1974-1.23260.2411420.21726657X-RAY DIFFRACTION100
1.2326-1.27240.231430.20836689X-RAY DIFFRACTION100
1.2724-1.31790.23211420.19876646X-RAY DIFFRACTION100
1.3179-1.37070.21241420.18726665X-RAY DIFFRACTION100
1.3707-1.43310.18651430.17066705X-RAY DIFFRACTION100
1.4331-1.50860.1641430.15846702X-RAY DIFFRACTION100
1.5086-1.60310.18541440.1546710X-RAY DIFFRACTION100
1.6031-1.72680.14121420.14586693X-RAY DIFFRACTION100
1.7268-1.90060.16811440.13246713X-RAY DIFFRACTION100
1.9006-2.17550.13881430.12076739X-RAY DIFFRACTION100
2.1755-2.74030.12781440.12346737X-RAY DIFFRACTION100
2.7403-25.33250.12531460.11896798X-RAY DIFFRACTION99

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