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- PDB-1sw7: Triosephosphate isomerase from Gallus gallus, loop 6 mutant K174N... -

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Basic information

Entry
Database: PDB / ID: 1sw7
TitleTriosephosphate isomerase from Gallus gallus, loop 6 mutant K174N, T175S, A176S
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 / canonical glycolysis ...Glycolysis / Glycolysis / Gluconeogenesis / Gluconeogenesis / methylglyoxal biosynthetic process / methylglyoxal synthase / methylglyoxal synthase activity / triose-phosphate isomerase / triose-phosphate isomerase activity / canonical glycolysis / glyceraldehyde-3-phosphate biosynthetic process / 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
2-PHOSPHOGLYCOLIC ACID / Triosephosphate isomerase
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.22 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 / 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,6014
Polymers53,2892
Non-polymers3122
Water5,170287
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4000 Å2
ΔGint-32 kcal/mol
Surface area19150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.218, 87.218, 162.942
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Triosephosphate isomerase / TIM


Mass: 26644.355 Da / Num. of mol.: 2 / Mutation: K174N, T175S, A176S
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.: 287 / 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: 2.91 Å3/Da / Density % sol: 57.68 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 2.6M ammonium sulfate, 0.1M Na-citrate, 0.2M NaCl, pH 5.5, 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 / 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: 2.22→20 Å / Num. obs: 31858 / % possible obs: 100 % / Observed criterion σ(I): -3
Reflection shellResolution: 2.22→2.3 Å / % possible all: 100

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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: 1sw3

1sw3


Resolution: 2.22→20 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.9 / SU B: 4.81 / SU ML: 0.123 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.235 / ESU R Free: 0.194 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23589 1603 5 %RANDOM
Rwork0.19503 ---
obs0.1971 30185 99.99 %-
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: 12.972 Å2
Baniso -1Baniso -2Baniso -3
1--0.42 Å20 Å20 Å2
2---0.42 Å20 Å2
3---0.85 Å2
Refinement stepCycle: LAST / Resolution: 2.22→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3708 0 18 287 4013
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0213799
X-RAY DIFFRACTIONr_bond_other_d0.0020.023438
X-RAY DIFFRACTIONr_angle_refined_deg1.3091.9445129
X-RAY DIFFRACTIONr_angle_other_deg0.81438029
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3195488
X-RAY DIFFRACTIONr_chiral_restr0.0720.2567
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024266
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02726
X-RAY DIFFRACTIONr_nbd_refined0.210.2790
X-RAY DIFFRACTIONr_nbd_other0.2460.23930
X-RAY DIFFRACTIONr_nbtor_other0.0840.22129
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1930.2244
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3870.248
X-RAY DIFFRACTIONr_symmetry_vdw_other0.350.268
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4990.217
X-RAY DIFFRACTIONr_mcbond_it0.4371.52409
X-RAY DIFFRACTIONr_mcangle_it0.82823837
X-RAY DIFFRACTIONr_scbond_it1.52831390
X-RAY DIFFRACTIONr_scangle_it2.5184.51292
LS refinement shellResolution: 2.22→2.277 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.243 123
Rwork0.186 2152
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)
11.29740.0822-0.37940.9442-0.23561.652-0.1247-0.0373-0.2168-0.0260.0684-0.07030.30540.04080.05630.0870.01870.0130.0182-0.02820.06975.881723.063931.2005
20.99930.06760.44341.4206-0.38211.3044-0.10240.07690.2020.02540.09280.0741-0.1906-0.05610.00960.0571-0.0256-0.00670.0489-0.00680.06381.617853.761216.8365
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA4 - 2484 - 248
2X-RAY DIFFRACTION2BB4 - 2484 - 248

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