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- PDB-4y9a: Crystal structure of Triosephosphate Isomerase from Streptomyces ... -

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Basic information

Entry
Database: PDB / ID: 4y9a
TitleCrystal structure of Triosephosphate Isomerase from Streptomyces coelicolor
ComponentsTriosephosphate isomerase
KeywordsISOMERASE / TIM Barrel / TPI
Function / homology
Function and homology information


triose-phosphate isomerase / triose-phosphate isomerase activity / glyceraldehyde-3-phosphate biosynthetic process / glycerol catabolic process / glycolytic process / gluconeogenesis / 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 speciesStreptomyces coelicolor (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.294 Å
AuthorsRomero-Romero, S. / Rodriguez-Romero, A. / Fernandez-Velasco, D.A.
Funding support Mexico, 2items
OrganizationGrant numberCountry
Consejo Nacional de Ciencia y Tecnologia de Mexico166472 Mexico
Consejo Nacional de Ciencia y Tecnologia de Mexico99857 Mexico
CitationJournal: Phys Chem Chem Phys / Year: 2015
Title: Reversibility and two state behaviour in the thermal unfolding of oligomeric TIM barrel proteins.
Authors: Romero-Romero, S. / Costas, M. / Rodriguez-Romero, A. / Alejandro Fernandez-Velasco, D.
History
DepositionFeb 17, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 5, 2015Group: Data collection
Revision 1.2Aug 12, 2015Group: Database references
Revision 1.3Nov 1, 2017Group: Author supporting evidence / Derived calculations
Category: pdbx_struct_assembly_auth_evidence / pdbx_struct_oper_list
Item: _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Triosephosphate isomerase
B: Triosephosphate isomerase
C: Triosephosphate isomerase
D: Triosephosphate isomerase


Theoretical massNumber of molelcules
Total (without water)112,2154
Polymers112,2154
Non-polymers00
Water4,504250
1
A: Triosephosphate isomerase
B: Triosephosphate isomerase


Theoretical massNumber of molelcules
Total (without water)56,1082
Polymers56,1082
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3330 Å2
ΔGint-24 kcal/mol
Surface area19630 Å2
MethodPISA
2
C: Triosephosphate isomerase
D: Triosephosphate isomerase


Theoretical massNumber of molelcules
Total (without water)56,1082
Polymers56,1082
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3270 Å2
ΔGint-23 kcal/mol
Surface area19990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.069, 86.069, 133.949
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43
DetailsDimer by Gel Filtration

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Components

#1: Protein
Triosephosphate isomerase / TIM / Triose-phosphate isomerase


Mass: 28053.775 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Expression tag: GSH / Source: (gene. exp.) Streptomyces coelicolor (bacteria) / Strain: A3(2) / M145 / Gene: tpiA, tpi, SCO1945, SCC54.05c / Plasmid: pET-28b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q9Z520, triose-phosphate isomerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 250 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.21 Å3/Da / Density % sol: 44.36 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M TRIS hydrochloride pH 8.5, 2.0 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 13, 2014
RadiationMonochromator: VariMax HF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.29→43.03 Å / Num. obs: 43475 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3 % / Biso Wilson estimate: 32.68 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 10
Reflection shellResolution: 2.29→2.37 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.371 / Mean I/σ(I) obs: 3 / % possible all: 98.1

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
CrystalCleardata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TA6

3ta6


Resolution: 2.294→39.634 Å / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 29.5 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2818 2189 5.13 %
Rwork0.2287 --
obs0.2315 42635 97.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.8 Å2
Refinement stepCycle: LAST / Resolution: 2.294→39.634 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7678 0 0 250 7928
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0097812
X-RAY DIFFRACTIONf_angle_d1.33410574
X-RAY DIFFRACTIONf_dihedral_angle_d13.2412842
X-RAY DIFFRACTIONf_chiral_restr0.0581206
X-RAY DIFFRACTIONf_plane_restr0.0071382
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.294-2.34940.40431220.35442658X-RAY DIFFRACTION92
2.3494-2.40810.45991140.33432715X-RAY DIFFRACTION94
2.4081-2.47320.38521490.34552687X-RAY DIFFRACTION93
2.4732-2.5460.35031530.31552688X-RAY DIFFRACTION93
2.546-2.62810.36111370.32462698X-RAY DIFFRACTION93
2.6281-2.72190.34551630.29072651X-RAY DIFFRACTION92
2.7219-2.83080.37371350.30012709X-RAY DIFFRACTION93
2.8308-2.95950.34841530.27342664X-RAY DIFFRACTION92
2.9595-3.11540.32481410.25732687X-RAY DIFFRACTION93
3.1154-3.31030.32891490.23572729X-RAY DIFFRACTION94
3.3103-3.56540.26341400.21492679X-RAY DIFFRACTION93
3.5654-3.92330.25371470.20312639X-RAY DIFFRACTION91
3.9233-4.4890.22321290.16252697X-RAY DIFFRACTION94
4.489-5.64810.21041560.16352736X-RAY DIFFRACTION94
5.6481-28.05550.18831690.16252764X-RAY DIFFRACTION94

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