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Basic information

Entry
Database: PDB / ID: 1su5
TitleUnderstanding protein lids: Structural analysis of active hinge mutants in triosephosphate isomerase
ComponentsTriosephosphate isomerase
KeywordsISOMERASE / archae / evolution / flexible loop-6 / TIM / N-hinge
Function / homology
Function and homology information


Glycolysis / Glycolysis / Gluconeogenesis / Gluconeogenesis / methylglyoxal biosynthetic process / methylglyoxal synthase / methylglyoxal synthase activity / triose-phosphate isomerase / triose-phosphate isomerase activity / glyceraldehyde-3-phosphate biosynthetic process ...Glycolysis / Glycolysis / Gluconeogenesis / Gluconeogenesis / methylglyoxal biosynthetic process / methylglyoxal synthase / methylglyoxal synthase activity / triose-phosphate isomerase / triose-phosphate isomerase activity / glyceraldehyde-3-phosphate biosynthetic process / glycerol catabolic process / canonical glycolysis / glycolytic process / gluconeogenesis / ubiquitin protein ligase binding / protein homodimerization activity / 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 speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsKursula, I. / Salin, M. / Sun, J. / Norledge, B.V. / Haapalainen, A.M. / Sampson, N.S. / Wierenga, R.K.
CitationJournal: Protein Eng.Des.Sel. / Year: 2004
Title: Understanding protein lids: structural analysis of active hinge mutants in triosephosphate isomerase
Authors: Kursula, I. / Salin, M. / Sun, J. / Norledge, B.V. / Haapalainen, A.M. / Sampson, N.S. / Wierenga, R.K.
History
DepositionMar 26, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 24, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Nov 10, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / diffrn_source ...database_2 / diffrn_source / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 25, 2023Group: 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)54,55316
Polymers53,1002
Non-polymers1,45314
Water3,963220
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5970 Å2
ΔGint-133 kcal/mol
Surface area19650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.756, 86.756, 163.376
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-368-

HOH

Detailsasymmetric unit contains one biological unit, dimer (chains A and B)

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Components

#1: Protein Triosephosphate isomerase / TIM


Mass: 26550.221 Da / Num. of mol.: 2 / Mutation: K174N, T175P, A176N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: TPI1 / Plasmid: pBSX1c / Production host: Escherichia coli (E. coli) / Strain (production host): DF502 / References: UniProt: P00940, triose-phosphate isomerase
#2: Chemical ChemComp-PGA / 2-PHOSPHOGLYCOLIC ACID


Mass: 156.031 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C2H5O6P
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: 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: 2.89 Å3/Da / Density % sol: 57.49 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: Citrate, ammonium sulphate, sodium chloride, 2-phosphoglycolate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.8 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: May 27, 2001 / Details: Bent mirror
RadiationMonochromator: triangular / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 2.6→100 Å / Num. all: 20107 / Num. obs: 19906 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.7 % / Biso Wilson estimate: 19.1 Å2 / Rmerge(I) obs: 0.109 / Rsym value: 0.095 / Net I/σ(I): 16.5
Reflection shellResolution: 2.59→2.69 Å / Rmerge(I) obs: 0.392 / Mean I/σ(I) obs: 5.2 / Num. unique all: 1961 / Rsym value: 0.382 / % possible all: 97.5

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MAR345data collection
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 8TIM

8tim


Resolution: 2.7→17.79 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.887 / SU B: 11.13 / SU ML: 0.223 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 1.307 / ESU R Free: 0.319 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23638 903 5.1 %RANDOM
Rwork0.18465 ---
all0.18726 17698 --
obs0.18726 16795 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 15.207 Å2
Baniso -1Baniso -2Baniso -3
1-2.18 Å20 Å20 Å2
2--2.18 Å20 Å2
3----4.36 Å2
Refinement stepCycle: LAST / Resolution: 2.7→17.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3736 0 81 220 4037
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0213879
X-RAY DIFFRACTIONr_bond_other_d0.0020.023483
X-RAY DIFFRACTIONr_angle_refined_deg1.2351.9585245
X-RAY DIFFRACTIONr_angle_other_deg0.77838139
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4055492
X-RAY DIFFRACTIONr_chiral_restr0.0670.2572
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024294
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02726
X-RAY DIFFRACTIONr_nbd_refined0.2060.2947
X-RAY DIFFRACTIONr_nbd_other0.2510.24225
X-RAY DIFFRACTIONr_nbtor_other0.0870.22237
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2130.2251
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1430.219
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2970.242
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2460.214
X-RAY DIFFRACTIONr_mcbond_it0.2681.52430
X-RAY DIFFRACTIONr_mcangle_it0.48823876
X-RAY DIFFRACTIONr_scbond_it1.08831449
X-RAY DIFFRACTIONr_scangle_it1.4594.51369
LS refinement shellResolution: 2.7→2.769 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 75 -
Rwork0.239 1195 -
obs-1195 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)
11.92510.3274-0.16771.5527-0.29721.5248-0.1019-0.1098-0.25760.04680.0515-0.07490.21720.04240.05040.06390.00830.01180.0146-0.02460.05286.254722.63731.5638
21.64650.08350.13162.2294-0.25262.1841-0.14440.1290.29780.02420.09450.0775-0.2999-0.13490.04990.0404-0.0199-0.01860.0501-0.01210.04831.443253.328117.268
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 2481 - 247
2X-RAY DIFFRACTION1AC3001
3X-RAY DIFFRACTION2BB2 - 2481 - 247
4X-RAY DIFFRACTION2BD13001

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