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- PDB-1sw0: Triosephosphate isomerase from Gallus gallus, loop 6 hinge mutant... -

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Basic information

Entry
Database: PDB / ID: 1sw0
TitleTriosephosphate isomerase from Gallus gallus, loop 6 hinge mutant K174L, T175W
ComponentsTriosephosphate isomerase
KeywordsISOMERASE / TIM barrel / flexible loop / 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 / MOLECULAR REPLACEMENT / Resolution: 1.71 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 30, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 24, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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)53,7654
Polymers53,4532
Non-polymers3122
Water6,557364
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4010 Å2
ΔGint-32 kcal/mol
Surface area19400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.744, 73.447, 135.846
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Ens-ID: 1 / Refine code: 6

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALASERSERAA2 - 452 - 45
21ALAALASERSERBB2 - 452 - 45
12TYRTYRLEULEUAA47 - 5547 - 55
22TYRTYRLEULEUBB47 - 5547 - 55
13ALAALAHISHISAA57 - 24857 - 248
23ALAALAHISHISBB57 - 24857 - 248
14PGAPGAPGAPGAAC350
24PGAPGAPGAPGABD1350

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Components

#1: Protein Triosephosphate isomerase / TIM


Mass: 26726.543 Da / Num. of mol.: 2 / Mutation: K174L, T175W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: TPI1 / Production host: Escherichia coli (E. coli) / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 364 / 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: 2.69 Å3/Da / Density % sol: 54.34 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.4M Na-citrate, 0.1M TEA, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 15, 1998 / Details: mirrors
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→13.18 Å / Num. obs: 47599 / % possible obs: 62.6 % / Observed criterion σ(I): -3
Reflection shellResolution: 1.7→1.73 Å / % possible all: 23.4

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
CCP4(TRUNCATE)data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1tph

1tph


Resolution: 1.71→13.18 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.924 / SU B: 2.465 / SU ML: 0.08 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.134 / ESU R Free: 0.126 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2276 2530 5 %RANDOM
Rwork0.1965 ---
obs0.19812 40543 79.25 %-
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: 7.907 Å2
Baniso -1Baniso -2Baniso -3
1-1.07 Å20 Å20 Å2
2---0.58 Å20 Å2
3----0.48 Å2
Refinement stepCycle: LAST / Resolution: 1.71→13.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3744 0 18 364 4126
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0213838
X-RAY DIFFRACTIONr_bond_other_d0.0020.023490
X-RAY DIFFRACTIONr_angle_refined_deg1.4711.9425190
X-RAY DIFFRACTIONr_angle_other_deg0.88938140
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.245492
X-RAY DIFFRACTIONr_chiral_restr0.1010.2574
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024296
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02738
X-RAY DIFFRACTIONr_nbd_refined0.2120.2729
X-RAY DIFFRACTIONr_nbd_other0.2470.23909
X-RAY DIFFRACTIONr_nbtor_other0.0870.22253
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1860.2264
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1540.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2470.237
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2610.214
X-RAY DIFFRACTIONr_mcbond_it0.7181.52428
X-RAY DIFFRACTIONr_mcangle_it1.23523868
X-RAY DIFFRACTIONr_scbond_it2.11631410
X-RAY DIFFRACTIONr_scangle_it3.2574.51322
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDNumberTypeRms dev position (Å)Weight position
A3585loose positional0.275
B11loose positional0.085
A3585loose thermal1.3210
B11loose thermal0.8210
LS refinement shellResolution: 1.708→1.752 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.329 129
Rwork0.263 2521
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)
10.6338-0.03080.10571.26950.27752.08080.01940.03230.0178-0.1141-0.03470.0156-0.0457-0.13260.01530.00060.0020.0050.22320.01160.222627.4288.45212.286
20.8494-0.20050.60311.0781-0.6712.9144-0.00780.02690.03150.0485-0.0439-0.13440.01940.24390.05170.0055-0.0126-0.00490.2349-0.00050.236844.91810.26342.434
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 2482 - 248
2X-RAY DIFFRACTION1AC350
3X-RAY DIFFRACTION2BB2 - 2482 - 248
4X-RAY DIFFRACTION2BD1350

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