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- PDB-4bi6: CRYSTAL STRUCTURE OF A TRIPLE MUTANT (A198V, C202A AND C222N) OF ... -

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Basic information

Entry
Database: PDB / ID: 4bi6
TitleCRYSTAL STRUCTURE OF A TRIPLE MUTANT (A198V, C202A AND C222N) OF TRIOSEPHOSPHATE ISOMERASE FROM GIARDIA LAMBLIA. COMPLEXED WITH 2- PHOSPHOGLYCOLIC ACID
ComponentsTRIOSEPHOSPHATE ISOMERASE
KeywordsISOMERASE
Function / homology
Function and homology information


methylglyoxal synthase / methylglyoxal synthase activity / 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
2-PHOSPHOGLYCOLIC ACID / Triosephosphate isomerase
Similarity search - Component
Biological speciesGIARDIA INTESTINALIS (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsTorres-Larios, A. / Enriquez-Flores, S. / Reyes-Vivas, H. / Oria-Hernandez, J. / Hernandez-Alcantara, G.
CitationJournal: Plos One / Year: 2013
Title: Structural and Functional Perturbation of Giardia Lamblia Triosephosphate Isomerase by Modification of a Non-Catalytic, Non-Conserved Region.
Authors: Hernandez-Alcantara, G. / Torres-Larios, A. / Enriquez-Flores, S. / Garcia-Torres, I. / Castillo-Villanueva, A. / Mendez, S.T. / De La Mora-De La Mora, I. / Gomez-Manzo, S. / Torres-Arroyo, ...Authors: Hernandez-Alcantara, G. / Torres-Larios, A. / Enriquez-Flores, S. / Garcia-Torres, I. / Castillo-Villanueva, A. / Mendez, S.T. / De La Mora-De La Mora, I. / Gomez-Manzo, S. / Torres-Arroyo, A. / Lopez-Velazquez, G. / Reyes-Vivas, H. / Oria-Hernandez, J.
History
DepositionApr 9, 2013Deposition site: PDBE / Processing site: PDBE
SupersessionMay 29, 2013ID: 2YC6
Revision 1.0May 29, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 14, 2013Group: Database references
Revision 1.2Dec 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 2.0May 1, 2024Group: Atomic model / Category: atom_site
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
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.

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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)28,1032
Polymers27,9471
Non-polymers1561
Water3,963220
1
A: TRIOSEPHOSPHATE ISOMERASE
hetero molecules

A: TRIOSEPHOSPHATE ISOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,2064
Polymers55,8942
Non-polymers3122
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area3760 Å2
ΔGint-34.9 kcal/mol
Surface area19620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.578, 100.474, 118.147
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-2022-

HOH

21A-2036-

HOH

31A-2062-

HOH

41A-2116-

HOH

51A-2139-

HOH

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Components

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


Mass: 27947.135 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) GIARDIA INTESTINALIS (eukaryote) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYS / References: UniProt: P36186, triose-phosphate isomerase
#2: Chemical ChemComp-PGA / 2-PHOSPHOGLYCOLIC ACID


Mass: 156.031 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C2H5O6P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 220 / Source method: isolated from a natural source / Formula: H2O

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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: 2.98 Å3/Da / Density % sol: 58.71 % / Description: NONE
Crystal growpH: 5.6
Details: PROTEIN WAS CRYSTALLYZED FROM 0.5 M SODIUM CHLORIDE, 0.1 M SODIUM CITRATE TRIBASIC DIHYDRATE PH 5.6, 2 % V/V ETHYLENE IMINE POLYMER.

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97857
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 5, 2009 / Details: MIRRORS
RadiationMonochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.45→37.55 Å / Num. obs: 58919 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 3.7
Reflection shellResolution: 1.45→1.53 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 2.1 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALEPACKdata scaling
PHASERFOR MRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2DP3

2dp3


Resolution: 1.45→37.55 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.955 / Cross valid method: THROUGHOUT / ESU R: 0.061 / ESU R Free: 0.061 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.20687 2979 5.1 %RANDOM
Rwork0.18982 ---
obs0.19068 55823 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.761 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.45→37.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1941 0 9 220 2170
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0221910
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg11.9482562
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7785238
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.2124.51282
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.21715345
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.671512
X-RAY DIFFRACTIONr_chiral_restr0.0670.2290
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211527
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.5631.51210
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.62821924
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.2763700
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it6.1354.5638
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.45→1.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 236 -
Rwork0.271 4055 -
obs--99.88 %

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