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- PDB-1sq7: Understanding protein lids: Structural analysis of active hinge m... -

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Basic information

Entry
Database: PDB / ID: 1sq7
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 / canonical glycolysis / glycerol catabolic process / gluconeogenesis / glycolytic process / 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
Triosephosphate isomerase
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 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 18, 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 / Category: database_2 / diffrn_source / struct_ref_seq_dif
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
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

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Assembly

Deposited unit
A: Triosephosphate isomerase
B: Triosephosphate isomerase


Theoretical massNumber of molelcules
Total (without water)53,1912
Polymers53,1912
Non-polymers00
Water3,801211
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3310 Å2
ΔGint-22 kcal/mol
Surface area19990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.670, 61.670, 500.886
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11B-329-

HOH

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

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Components

#1: Protein Triosephosphate isomerase / TIM


Mass: 26595.348 Da / Num. of mol.: 2 / Mutation: K174L, T175W
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 211 / 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: 2.58 Å3/Da / Density % sol: 52.4 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.2
Details: PEG 6000, citrate, t-butanol, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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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: Jun 15, 2002 / 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: 2.8→30 Å / Num. all: 16236 / Num. obs: 15311 / % possible obs: 94.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.62 % / Biso Wilson estimate: 20.4 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 10.42
Reflection shellResolution: 2.76→2.93 Å / Redundancy: 5.29 % / Rmerge(I) obs: 0.117 / Mean I/σ(I) obs: 7 / Num. unique all: 2572 / % possible all: 82.4

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Processing

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

8tim


Resolution: 2.85→28.28 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.875 / SU B: 14.334 / SU ML: 0.274 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.399 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25185 698 5 %RANDOM
Rwork0.20214 ---
all0.20468 13977 --
obs0.20468 13279 100 %-
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: 3.209 Å2
Baniso -1Baniso -2Baniso -3
1-1.41 Å20.71 Å20 Å2
2--1.41 Å20 Å2
3----2.12 Å2
Refinement stepCycle: LAST / Resolution: 2.85→28.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3744 0 0 211 3955
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0213822
X-RAY DIFFRACTIONr_bond_other_d0.0030.023486
X-RAY DIFFRACTIONr_angle_refined_deg1.0741.9385168
X-RAY DIFFRACTIONr_angle_other_deg0.83738130
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.1935492
X-RAY DIFFRACTIONr_chiral_restr0.050.2574
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.024288
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02738
X-RAY DIFFRACTIONr_nbd_refined0.1590.2710
X-RAY DIFFRACTIONr_nbd_other0.2120.23831
X-RAY DIFFRACTIONr_nbtor_other0.0780.22207
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1330.2142
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0990.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1710.235
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0820.210
X-RAY DIFFRACTIONr_mcbond_it0.0891.52428
X-RAY DIFFRACTIONr_mcangle_it0.16523868
X-RAY DIFFRACTIONr_scbond_it0.29331394
X-RAY DIFFRACTIONr_scangle_it0.4884.51300
LS refinement shellResolution: 2.85→2.923 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.341 50 -
Rwork0.253 952 -
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)
11.33020.2814-0.22251.2727-0.60251.93520.0127-0.05190.1414-0.0496-0.0310.0123-0.2016-0.03890.01830.03410.02230.01420.08860.00440.08167.088335.39111.0815
22.14380.2759-0.02262.2096-0.11250.7498-0.00580.1356-0.16880.01040.0203-0.06240.1710.0407-0.01450.07460.0337-0.01280.15150.02930.01387.44782.688422.2357
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 2481 - 247
2X-RAY DIFFRACTION2BB2 - 2481 - 247

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