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- PDB-7qh0: Apo structure of the Leishmania mexicana triose-phosphate isomera... -

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Basic information

Entry
Database: PDB / ID: 7qh0
TitleApo structure of the Leishmania mexicana triose-phosphate isomerase (LmTIM), N11A-E65Q variant, open conformation
ComponentsTriosephosphate isomerase
KeywordsISOMERASE / triose-phosphate isomerase / TIM / structural enzymology
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 / 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
Triosephosphate isomerase
Similarity search - Component
Biological speciesLeishmania mexicana mexicana (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsCordara, G. / Wierenga, R.K.
Funding support Finland, 1items
OrganizationGrant numberCountry
Academy of Finland Finland
CitationJournal: Biochemistry / Year: 2023
Title: The Role of Asn11 in Catalysis by Triosephosphate Isomerase.
Authors: Hegazy, R. / Cordara, G. / Wierenga, R.K. / Richard, J.P.
History
DepositionDec 10, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 19, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 21, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Triosephosphate isomerase
B: Triosephosphate isomerase
C: Triosephosphate isomerase
D: Triosephosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,7557
Polymers108,6614
Non-polymers943
Water5,909328
1
A: Triosephosphate isomerase
B: Triosephosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,3663
Polymers54,3302
Non-polymers351
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3050 Å2
ΔGint-31 kcal/mol
Surface area19510 Å2
MethodPISA
2
C: Triosephosphate isomerase
D: Triosephosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,3894
Polymers54,3302
Non-polymers582
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3260 Å2
ΔGint-43 kcal/mol
Surface area19200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.815, 73.898, 81.080
Angle α, β, γ (deg.)83.117, 89.327, 77.111
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

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


Mass: 27165.213 Da / Num. of mol.: 4 / Mutation: N11A, E65Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania mexicana mexicana (eukaryote)
Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: P48499, triose-phosphate isomerase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 328 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.1 Å3/Da / Density % sol: 41.4 % / Description: irregular prism
Crystal growTemperature: 293.15 K / Method: vapor diffusion / pH: 8
Details: 50 mM Tris-HCl pH 8.0, 22.5% PEG 6000, 0.275 M CaCl2 and 3% v/v tert-butanol

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: cryostream / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Feb 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.15→50.53 Å / Num. obs: 46268 / % possible obs: 97.6 % / Redundancy: 2.6 % / Biso Wilson estimate: 15.11 Å2 / CC1/2: 0.954 / Rmerge(I) obs: 0.2 / Rpim(I) all: 0.154 / Rrim(I) all: 0.268 / Χ2: 0.93 / Net I/σ(I): 2.6
Reflection shellResolution: 2.15→2.21 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.632 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 3712 / CC1/2: 0.678 / Rpim(I) all: 0.455 / Rrim(I) all: 0.783 / Χ2: 0.94 / % possible all: 96.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PHENIX1.17.1_3660refinement
DIALS1.10.4-gc14d9720b-releasedata reduction
STARANISO2.3.52data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1N55

1n55


Resolution: 2.15→50.53 Å / SU ML: 0.3318 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 31.5217
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2775 1856 4.84 %
Rwork0.2347 36488 -
obs0.2367 38344 80.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.66 Å2
Refinement stepCycle: LAST / Resolution: 2.15→50.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7578 0 3 328 7909
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00277983
X-RAY DIFFRACTIONf_angle_d0.515910908
X-RAY DIFFRACTIONf_chiral_restr0.0441271
X-RAY DIFFRACTIONf_plane_restr0.00371414
X-RAY DIFFRACTIONf_dihedral_angle_d7.60141107
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.210.3673730.29511542X-RAY DIFFRACTION44.61
2.21-2.270.4356860.2911799X-RAY DIFFRACTION51.01
2.27-2.350.33991000.27461922X-RAY DIFFRACTION56.39
2.35-2.430.37741110.2762204X-RAY DIFFRACTION62.74
2.43-2.530.34041060.27012457X-RAY DIFFRACTION70.59
2.53-2.640.33331620.27712892X-RAY DIFFRACTION83.79
2.64-2.780.32871900.27433290X-RAY DIFFRACTION94.85
2.78-2.960.31291850.26773373X-RAY DIFFRACTION97.59
2.96-3.180.27771890.26123343X-RAY DIFFRACTION97.57
3.18-3.50.28041560.233447X-RAY DIFFRACTION97.93
3.5-4.010.24571800.21163364X-RAY DIFFRACTION97.93
4.01-5.050.20141610.18283444X-RAY DIFFRACTION98.36
5.05-50.530.1971570.18763411X-RAY DIFFRACTION97.83

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