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- PDB-2v2d: The A178L mutation in the C-terminal hinge of the flexible loop-6... -

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Basic information

Entry
Database: PDB / ID: 2v2d
TitleThe A178L mutation in the C-terminal hinge of the flexible loop-6 of triosephosphate isomerase (TIM) induces a more closed conformation of this hinge region in dimeric and monomeric TIM
ComponentsTRIOSEPHOSPHATE ISOMERASE GLYCOSOMAL
KeywordsISOMERASE / GLUCONEOGENESIS / LIPID SYNTHESIS / ENGINEERING / PENTOSE SHUNT / POINT MUTATION / TIM / A178L / LOOP6 / HINGE / LOOP-6 / ENZYME / FATTY ACID BIOSYNTHESIS / TRIOSEPHOSPHATE ISOMERASE / GLYCOSOME / MONOMERIC / TIM-BARREL / GLYCOLYSIS
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 / cytoplasm / 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
PHOSPHATE ION / Triosephosphate isomerase, glycosomal
Similarity search - Component
Biological speciesTRYPANOSOMA BRUCEI BRUCEI (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsAlahuhta, M. / Casteleijn, M.G. / Neubauer, P. / Wierenga, R.K.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2008
Title: Structural Studies Show that the A178L Mutation in the C-Terminal Hinge of the Catalytic Loop-6 of Triosephosphate Isomerase (Tim) Induces a Closed- Like Conformation in Dimeric and Monomeric Tim.
Authors: Alahuhta, M. / Casteleijn, M.G. / Neubauer, P. / Wierenga, R.K.
History
DepositionJun 5, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 19, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
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 9-STRANDED BARREL THIS IS REPRESENTED BY A 10-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 GLYCOSOMAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1712
Polymers26,0761
Non-polymers951
Water2,396133
1
A: TRIOSEPHOSPHATE ISOMERASE GLYCOSOMAL
hetero molecules

A: TRIOSEPHOSPHATE ISOMERASE GLYCOSOMAL
hetero molecules

A: TRIOSEPHOSPHATE ISOMERASE GLYCOSOMAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,5126
Polymers78,2273
Non-polymers2853
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_445-x+y-1,-x-1,z1
crystal symmetry operation2_455-y-1,x-y,z1
Buried area5380 Å2
ΔGint-38 kcal/mol
Surface area34160 Å2
MethodPQS
Unit cell
Length a, b, c (Å)95.230, 95.230, 48.820
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

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


Mass: 26075.824 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) TRYPANOSOMA BRUCEI BRUCEI (eukaryote) / Plasmid: PET3A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 PLYSS / References: UniProt: P04789, triose-phosphate isomerase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 133 / 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: 2.56 Å3/Da / Density % sol: 52.02 % / Description: NONE
Crystal growpH: 8.2 / Details: 1.75 M (NH4)2PO4, PH 8.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.847
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 26, 2004 / Details: FLAT PRE-MIRROR AND BENT, VERTICALLY FOCUSSING
RadiationMonochromator: SI 111, HORIZONTALLY FOCUSSING / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.847 Å / Relative weight: 1
ReflectionResolution: 2.3→25 Å / Num. obs: 11321 / % possible obs: 99.2 % / Observed criterion σ(I): 3 / Redundancy: 12.1 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 24.45
Reflection shellResolution: 2.3→2.35 Å / Redundancy: 12.44 % / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 13.03 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.3.0028refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ML1

1ml1


Resolution: 2.3→19.22 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.894 / SU B: 14.951 / SU ML: 0.196 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.39 / ESU R Free: 0.271 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.27 565 5 %RANDOM
Rwork0.201 ---
obs0.204 10755 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.92 Å2
Baniso -1Baniso -2Baniso -3
1--1.87 Å2-0.94 Å20 Å2
2---1.87 Å20 Å2
3---2.81 Å2
Refinement stepCycle: LAST / Resolution: 2.3→19.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1829 0 5 133 1967
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221875
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4581.9382546
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1975240
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.39424.47476
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.98915312
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.613159
X-RAY DIFFRACTIONr_chiral_restr0.1020.2294
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021390
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2270.2873
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3010.21268
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1660.2137
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1930.245
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3320.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5981.51227
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.9721913
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.6323748
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.3494.5632
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: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.252 42 -
Rwork0.195 788 -
obs--100 %
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)
113.3735-0.6007-0.84238.1341-0.09275.2148-0.3961-0.50940.68440.20530.42010.05460.2666-0.1835-0.0240.22220.0586-0.01020.1423-0.1370.0994-27.0182-19.11554.7536
211.71381.7008-2.41816.231-0.13984.0888-0.1692-0.7551-0.06880.72050.28030.15930.2538-0.2839-0.11110.48120.1423-0.01140.2617-0.09630.1225-35.9268-15.011315.3207
32.3624-2.4918-0.28033.11641.55633.2885-0.1999-0.37390.28960.23270.2211-0.048-0.207-0.4108-0.02110.24540.07330.04490.1515-0.05660.1102-36.7769-13.33955.6013
43.4556-1.87360.07173.21740.55881.78740.24260.26180.149-0.2613-0.015-0.30360.00960.1479-0.22760.15740.02920.07620.1627-0.03180.0833-25.7867-25.668-7.1307
54.3631-2.5265-0.61965.65931.40054.3394-0.2807-0.81460.3251.03370.5889-0.51990.30010.2291-0.30820.23340.1066-0.07910.2055-0.15110.1263-22.5924-23.6439.8155
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 15
2X-RAY DIFFRACTION2A16 - 35
3X-RAY DIFFRACTION3A36 - 65
4X-RAY DIFFRACTION4A66 - 206
5X-RAY DIFFRACTION5A207 - 250

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