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- PDB-7az9: Perdeuterated E65Q-TIM complexed with PHOSPHOGLYCOLOHYDROXAMATE -

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Basic information

Entry
Database: PDB / ID: 7az9
TitlePerdeuterated E65Q-TIM complexed with PHOSPHOGLYCOLOHYDROXAMATE
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
PHOSPHOGLYCOLOHYDROXAMIC ACID / Triosephosphate isomerase
Similarity search - Component
Biological speciesLeishmania mexicana (eukaryote)
MethodX-RAY DIFFRACTION / NEUTRON DIFFRACTION / SYNCHROTRON / NUCLEAR REACTOR / MOLECULAR REPLACEMENT / Resolution: 1.1 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 1.1May 1, 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
Item: _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)27,3792
Polymers27,2081
Non-polymers1711
Water3,621201
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area400 Å2
ΔGint-5 kcal/mol
Surface area10740 Å2
Unit cell
Length a, b, c (Å)98.323, 52.678, 58.665
Angle α, β, γ (deg.)90.000, 117.860, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-465-

HOH

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Components

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


Mass: 27208.236 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania mexicana (eukaryote) / Production host: Escherichia coli (E. coli) / Strain (production host): MDS42-T7 / References: UniProt: P48499, triose-phosphate isomerase
#2: Chemical ChemComp-PGH / PHOSPHOGLYCOLOHYDROXAMIC ACID


Mass: 171.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6NO6P / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 201 / 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: 2.47 Å3/Da / Density % sol: 50.16 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
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)
SYNCHROTRONPETRA III, EMBL c/o DESY P14 (MX2)10.89
NUCLEAR REACTORILL LADI III22.7-3.5
Detector
TypeIDDetectorDate
DECTRIS PILATUS3 6M1PIXELNov 1, 2016
CUSTOM-MADE2IMAGE PLATEMar 28, 2018
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2LAUELneutron2
Radiation wavelength
IDWavelength (Å)Relative weight
10.891
22.71
33.51
Reflection

Entry-ID: 7AZ9

Resolution (Å)Num. obs% possible obs (%)Redundancy (%)CC1/2Rrim(I) allDiffraction-IDNet I/σ(I)
1.1-45.01104600963.20.9990.043114.77
1.8-4019145785.20.9550.19423.8
Reflection shell
Resolution (Å)Mean I/σ(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID% possible all
1.1-1.162.1155490.6630.96188.88
1.8-1.92.57760.6660.5142

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
XDSdata reduction
LAUEGENdata reduction
XSCALEdata scaling
SCALAdata scaling
PHASERphasing
Refinement

SU ML: 0.12 / Cross valid method: THROUGHOUT / Method to determine structure: MOLECULAR REPLACEMENT / Phase error: 17.93 / 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 Rfree (%)% reflection obs (%)Diffraction-IDσ(F)
1.1-45.01X-RAY DIFFRACTION76.2323.47068.30.15760.14370.14445194993811045754.9796.1711.35
1.8-30.5502NEUTRON DIFFRACTION0.25930.22010.222965191445.0477.3720
Refinement stepCycle: final / Resolution: 1.1→45.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1871 0 14 381 2266
Biso mean--18.95 34.38 -
Num. residues----249
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014124
X-RAY DIFFRACTIONf_angle_d1.3937250
X-RAY DIFFRACTIONf_chiral_restr0.099323
X-RAY DIFFRACTIONf_plane_restr0.008634
X-RAY DIFFRACTIONf_dihedral_angle_d19.6261081
LS refinement shell

Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.89490.37891190.3611985NEUTRON DIFFRACTION60
1.8949-2.01360.35951050.31152216NEUTRON DIFFRACTION66
2.0136-2.1690.27351340.2582368NEUTRON DIFFRACTION71
2.169-2.38720.30341400.23372542NEUTRON DIFFRACTION76
2.3872-2.73250.25621480.21682735NEUTRON DIFFRACTION82
2.7325-3.44190.23421580.20723039NEUTRON DIFFRACTION90
3.4419-30.55020.22441610.18863294NEUTRON DIFFRACTION96
1.1-1.10760.3728950.33781793X-RAY DIFFRACTION53
1.1076-1.12060.34891660.31953343X-RAY DIFFRACTION98
1.1206-1.13430.32391770.31733371X-RAY DIFFRACTION98
1.1343-1.14870.31581660.27133388X-RAY DIFFRACTION98
1.1487-1.16380.24971920.26333346X-RAY DIFFRACTION99
1.1638-1.17970.26481750.2523381X-RAY DIFFRACTION99
1.1797-1.19660.24421590.2383416X-RAY DIFFRACTION98
1.1966-1.21440.23361920.2373380X-RAY DIFFRACTION99
1.2144-1.23340.22111740.2273371X-RAY DIFFRACTION99
1.2334-1.25360.22851690.21783367X-RAY DIFFRACTION99
1.2536-1.27530.23551690.21563415X-RAY DIFFRACTION98
1.2753-1.29840.21062030.20233373X-RAY DIFFRACTION99
1.2984-1.32340.20351660.19443397X-RAY DIFFRACTION99
1.3234-1.35040.18951740.18293401X-RAY DIFFRACTION98
1.3504-1.37980.18681760.17863348X-RAY DIFFRACTION99
1.3798-1.41190.1821770.17213412X-RAY DIFFRACTION99
1.4119-1.44720.17791910.16463379X-RAY DIFFRACTION99
1.4472-1.48630.17471790.15583380X-RAY DIFFRACTION99
1.4863-1.53010.16851830.15933381X-RAY DIFFRACTION99
1.5301-1.57950.18051810.15593380X-RAY DIFFRACTION98
1.5795-1.63590.17211630.1463400X-RAY DIFFRACTION98
1.6359-1.70140.17611860.14553336X-RAY DIFFRACTION98
1.7014-1.77890.14071770.13593363X-RAY DIFFRACTION97
1.7789-1.87270.15261710.13263334X-RAY DIFFRACTION97
1.8727-1.990.16271790.12793303X-RAY DIFFRACTION96
1.99-2.14360.12951690.12433318X-RAY DIFFRACTION95
2.1436-2.35930.11881630.12073273X-RAY DIFFRACTION95
2.3593-2.70070.14621810.12613307X-RAY DIFFRACTION95
2.7007-3.40240.14151710.12693310X-RAY DIFFRACTION95
3.4024-45.010.12531700.11613415X-RAY DIFFRACTION95

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