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- PDB-2y70: CRYSTALLOGRAPHIC STRUCTURE OF GM23, MUTANT G89D, AN EXAMPLE OF CA... -

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Basic information

Entry
Database: PDB / ID: 2y70
TitleCRYSTALLOGRAPHIC STRUCTURE OF GM23, MUTANT G89D, AN EXAMPLE OF CATALYTIC MIGRATION FROM TIM TO THIAMIN PHOSPHATE SYNTHASE.
ComponentsTRIOSE-PHOSPHATE ISOMERASE
KeywordsISOMERASE
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 / cytoplasm
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 / Triosephosphate isomerase, glycosomal
Similarity search - Component
Biological speciesTRYPANOSOMA BRUCEI BRUCEI (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsSaab-Rincon, G. / Olvera, L. / Olvera, M. / Rudino-Pinera, E. / Soberon, X. / Morett, E.
CitationJournal: J.Mol.Biol. / Year: 2012
Title: Evolutionary Walk between (Beta/Alpha)(8) Barrels: Catalytic Migration from Triosephosphate Isomerase to Thiamin Phosphate Synthase.
Authors: Saab-Rincon, G. / Olvera, L. / Olvera, M. / Rudino-Pinera, E. / Benites, E. / Soberon, X. / Morett, E.
History
DepositionJan 27, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 7, 2011Provider: repository / Type: Initial release
Revision 1.1Jan 25, 2012Group: Other
Revision 1.2Feb 8, 2012Group: Other
Revision 1.3Dec 20, 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 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "CA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "DA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TRIOSE-PHOSPHATE ISOMERASE
B: TRIOSE-PHOSPHATE ISOMERASE
C: TRIOSE-PHOSPHATE ISOMERASE
D: TRIOSE-PHOSPHATE ISOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,89225
Polymers105,5044
Non-polymers1,38821
Water10,124562
1
B: TRIOSE-PHOSPHATE ISOMERASE
C: TRIOSE-PHOSPHATE ISOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,35811
Polymers52,7522
Non-polymers6059
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3330 Å2
ΔGint-58.4 kcal/mol
Surface area19040 Å2
MethodPISA
2
A: TRIOSE-PHOSPHATE ISOMERASE
D: TRIOSE-PHOSPHATE ISOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,53514
Polymers52,7522
Non-polymers78312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4200 Å2
ΔGint-58.8 kcal/mol
Surface area19210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.444, 109.444, 95.240
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESSEQ 22:35 OR RESSEQ 37:68 OR RESSEQ 70:265 )
211CHAIN B AND (RESSEQ 22:35 OR RESSEQ 37:68 OR RESSEQ 70:265 )
311CHAIN C AND (RESSEQ 22:35 OR RESSEQ 37:68 OR RESSEQ 70:265 )
411CHAIN D AND (RESSEQ 22:35 OR RESSEQ 37:68 OR RESSEQ 70:265 )

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Components

#1: Protein
TRIOSE-PHOSPHATE ISOMERASE / GM23 / TIM


Mass: 26376.072 Da / Num. of mol.: 4 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) TRYPANOSOMA BRUCEI BRUCEI (eukaryote) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): CM1061 THIE- / References: UniProt: P04789, triose-phosphate isomerase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 562 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, SER 43 TO PRO ENGINEERED RESIDUE IN CHAIN A, THR 44 TO SER ...ENGINEERED RESIDUE IN CHAIN A, SER 43 TO PRO ENGINEERED RESIDUE IN CHAIN A, THR 44 TO SER ENGINEERED RESIDUE IN CHAIN A, PHE 45 TO TRP ENGINEERED RESIDUE IN CHAIN A, VAL 46 TO TYR ENGINEERED RESIDUE IN CHAIN A, HIS 47 TO MET ENGINEERED RESIDUE IN CHAIN A, LEU 48 TO GLN ENGINEERED RESIDUE IN CHAIN A, ILE 68 TO GLY ENGINEERED RESIDUE IN CHAIN A, ALA 69 TO ASN ENGINEERED RESIDUE IN CHAIN A, LYS 70 TO ALA ENGINEERED RESIDUE IN CHAIN A, SER 71 TO ASP ENGINEERED RESIDUE IN CHAIN A, SER 79 TO ALA ENGINEERED RESIDUE IN CHAIN A, PRO 81 TO ALA ENGINEERED RESIDUE IN CHAIN A, ILE 82 TO SER ENGINEERED RESIDUE IN CHAIN A, VAL 88 TO ILE ENGINEERED RESIDUE IN CHAIN A, ASN 89 TO SER ENGINEERED RESIDUE IN CHAIN A, GLY 94 TO ASP ENGINEERED RESIDUE IN CHAIN A, GLU 135 TO SER ENGINEERED RESIDUE IN CHAIN A, ALA 148 TO THR ENGINEERED RESIDUE IN CHAIN A, ILE 198 TO VAL ENGINEERED RESIDUE IN CHAIN A, LYS 217 TO ARG ENGINEERED RESIDUE IN CHAIN A, GLN 250 TO GLU ENGINEERED RESIDUE IN CHAIN B, SER 43 TO PRO ENGINEERED RESIDUE IN CHAIN B, THR 44 TO SER ENGINEERED RESIDUE IN CHAIN B, PHE 45 TO TRP ENGINEERED RESIDUE IN CHAIN B, VAL 46 TO TYR ENGINEERED RESIDUE IN CHAIN B, HIS 47 TO MET ENGINEERED RESIDUE IN CHAIN B, LEU 48 TO GLN ENGINEERED RESIDUE IN CHAIN B, ILE 68 TO GLY ENGINEERED RESIDUE IN CHAIN B, ALA 69 TO ASN ENGINEERED RESIDUE IN CHAIN B, LYS 70 TO ALA ENGINEERED RESIDUE IN CHAIN B, SER 71 TO ASP ENGINEERED RESIDUE IN CHAIN B, SER 79 TO ALA ENGINEERED RESIDUE IN CHAIN B, PRO 81 TO ALA ENGINEERED RESIDUE IN CHAIN B, ILE 82 TO SER ENGINEERED RESIDUE IN CHAIN B, VAL 88 TO ILE ENGINEERED RESIDUE IN CHAIN B, ASN 89 TO SER ENGINEERED RESIDUE IN CHAIN B, GLY 94 TO ASP ENGINEERED RESIDUE IN CHAIN B, GLU 135 TO SER ENGINEERED RESIDUE IN CHAIN B, ALA 148 TO THR ENGINEERED RESIDUE IN CHAIN B, ILE 198 TO VAL ENGINEERED RESIDUE IN CHAIN B, LYS 217 TO ARG ENGINEERED RESIDUE IN CHAIN B, GLN 250 TO GLU ENGINEERED RESIDUE IN CHAIN C, SER 43 TO PRO ENGINEERED RESIDUE IN CHAIN C, THR 44 TO SER ENGINEERED RESIDUE IN CHAIN C, PHE 45 TO TRP ENGINEERED RESIDUE IN CHAIN C, VAL 46 TO TYR ENGINEERED RESIDUE IN CHAIN C, HIS 47 TO MET ENGINEERED RESIDUE IN CHAIN C, LEU 48 TO GLN ENGINEERED RESIDUE IN CHAIN C, ILE 68 TO GLY ENGINEERED RESIDUE IN CHAIN C, ALA 69 TO ASN ENGINEERED RESIDUE IN CHAIN C, LYS 70 TO ALA ENGINEERED RESIDUE IN CHAIN C, SER 71 TO ASP ENGINEERED RESIDUE IN CHAIN C, SER 79 TO ALA ENGINEERED RESIDUE IN CHAIN C, PRO 81 TO ALA ENGINEERED RESIDUE IN CHAIN C, ILE 82 TO SER ENGINEERED RESIDUE IN CHAIN C, VAL 88 TO ILE ENGINEERED RESIDUE IN CHAIN C, ASN 89 TO SER ENGINEERED RESIDUE IN CHAIN C, GLY 94 TO ASP ENGINEERED RESIDUE IN CHAIN C, GLU 135 TO SER ENGINEERED RESIDUE IN CHAIN C, ALA 148 TO THR ENGINEERED RESIDUE IN CHAIN C, ILE 198 TO VAL ENGINEERED RESIDUE IN CHAIN C, LYS 217 TO ARG ENGINEERED RESIDUE IN CHAIN C, GLN 250 TO GLU ENGINEERED RESIDUE IN CHAIN D, SER 43 TO PRO ENGINEERED RESIDUE IN CHAIN D, THR 44 TO SER ENGINEERED RESIDUE IN CHAIN D, PHE 45 TO TRP ENGINEERED RESIDUE IN CHAIN D, VAL 46 TO TYR ENGINEERED RESIDUE IN CHAIN D, HIS 47 TO MET ENGINEERED RESIDUE IN CHAIN D, LEU 48 TO GLN ENGINEERED RESIDUE IN CHAIN D, ILE 68 TO GLY ENGINEERED RESIDUE IN CHAIN D, ALA 69 TO ASN ENGINEERED RESIDUE IN CHAIN D, LYS 70 TO ALA ENGINEERED RESIDUE IN CHAIN D, SER 71 TO ASP ENGINEERED RESIDUE IN CHAIN D, SER 79 TO ALA ENGINEERED RESIDUE IN CHAIN D, PRO 81 TO ALA ENGINEERED RESIDUE IN CHAIN D, ILE 82 TO SER ENGINEERED RESIDUE IN CHAIN D, VAL 88 TO ILE ENGINEERED RESIDUE IN CHAIN D, ASN 89 TO SER ENGINEERED RESIDUE IN CHAIN D, GLY 94 TO ASP ENGINEERED RESIDUE IN CHAIN D, GLU 135 TO SER ENGINEERED RESIDUE IN CHAIN D, ALA 148 TO THR ENGINEERED RESIDUE IN CHAIN D, ILE 198 TO VAL ENGINEERED RESIDUE IN CHAIN D, LYS 217 TO ARG ENGINEERED RESIDUE IN CHAIN D, GLN 250 TO GLU
Has protein modificationY
Sequence detailsTHE SEQUENCE DEPOSITED IN THIS ENTRY IS 87.9 PER CENT IDENTICAL TO UNIPROT P04789

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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: 2.85 Å3/Da / Density % sol: 56.91 % / Description: NONE
Crystal growpH: 6.5
Details: PROTEIN WAS CRYSTALLIZED FROM 2M LI2SO4, 100 MM MES, PH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.9795
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 27, 2006
Details: DOUBLE CRYSTAL CHANNEL CUT, SI(111), 1M LONG RH COATED TOROIDAL MIRROR FOR VERTICAL AND HORIZONTAL FOCUSING.
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. obs: 55952 / % possible obs: 98.7 % / Observed criterion σ(I): 0 / Redundancy: 2.1 % / Biso Wilson estimate: 39.92 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 12.9
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 2 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 2.4 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2Y6Z

2y6z


Resolution: 2.3→47.448 Å / SU ML: 0.35 / σ(F): 1.97 / Phase error: 25.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2304 2831 5.1 %
Rwork0.1992 --
obs0.2014 55899 98.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.987 Å2 / ksol: 0.371 e/Å3
Displacement parametersBiso mean: 51 Å2
Baniso -1Baniso -2Baniso -3
1--0.8293 Å20 Å20 Å2
2---0.8293 Å20 Å2
3---1.6586 Å2
Refinement stepCycle: LAST / Resolution: 2.3→47.448 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7398 0 87 562 8047
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087621
X-RAY DIFFRACTIONf_angle_d1.16210330
X-RAY DIFFRACTIONf_dihedral_angle_d18.5572665
X-RAY DIFFRACTIONf_chiral_restr0.0751176
X-RAY DIFFRACTIONf_plane_restr0.0041318
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1819X-RAY DIFFRACTIONPOSITIONAL
12B1819X-RAY DIFFRACTIONPOSITIONAL0.048
13C1802X-RAY DIFFRACTIONPOSITIONAL0.076
14D1836X-RAY DIFFRACTIONPOSITIONAL0.081
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3001-2.33970.29651640.24652682X-RAY DIFFRACTION100
2.3397-2.38230.25841320.23942722X-RAY DIFFRACTION100
2.3823-2.42810.31921500.26022647X-RAY DIFFRACTION100
2.4281-2.47760.30611240.25232689X-RAY DIFFRACTION100
2.4776-2.53150.26771440.22332718X-RAY DIFFRACTION100
2.5315-2.59040.26981320.24072723X-RAY DIFFRACTION100
2.5904-2.65520.3131310.26292634X-RAY DIFFRACTION99
2.6552-2.7270.28221250.24922680X-RAY DIFFRACTION99
2.727-2.80720.27521700.2152690X-RAY DIFFRACTION100
2.8072-2.89780.25611470.222684X-RAY DIFFRACTION100
2.8978-3.00130.25661420.21962622X-RAY DIFFRACTION99
3.0013-3.12150.28711590.20882695X-RAY DIFFRACTION99
3.1215-3.26350.24461460.19332630X-RAY DIFFRACTION99
3.2635-3.43550.23721500.19592657X-RAY DIFFRACTION99
3.4355-3.65070.21731510.17812668X-RAY DIFFRACTION99
3.6507-3.93250.22291180.17082640X-RAY DIFFRACTION98
3.9325-4.32790.17541470.15172632X-RAY DIFFRACTION98
4.3279-4.95360.17491430.14172601X-RAY DIFFRACTION97
4.9536-6.23880.23991390.17112570X-RAY DIFFRACTION95
6.2388-47.45770.17161170.17272484X-RAY DIFFRACTION92
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.5883-0.9698-1.31391.57250.84591.5639-0.1577-0.0055-0.2040.0461-0.09820.13710.1664-0.09940.22050.1885-0.03620.09370.1377-0.05170.195735.09330.56846.6745
22.482-0.836-1.35541.50140.75181.4657-0.14380.0369-0.20430.0297-0.12550.10880.1728-0.09480.22260.2003-0.04250.08750.1713-0.0640.20837.5498-0.9492-34.5496
32.5135-0.56810.59311.4521-0.7221.125-0.2293-0.03010.40550.3449-0.0872-0.2854-0.39620.04510.29060.298-0.0233-0.18270.13090.0160.266220.1585-28.8338-38.2577
42.4403-0.61260.89272.1625-0.13971.6813-0.25180.28160.4279-0.0343-0.0469-0.2307-0.22360.38730.28040.1797-0.0891-0.09620.23070.14520.255819.6916-28.601410.3223
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN C
4X-RAY DIFFRACTION4CHAIN D

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