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- PDB-7pej: Crystal structure of Triosephosphate Isomerase from Schizosacchar... -

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Basic information

Entry
Database: PDB / ID: 7pej
TitleCrystal structure of Triosephosphate Isomerase from Schizosaccharomyces pombe (SpTIM wt)
ComponentsTriosephosphate isomerase
KeywordsISOMERASE / TIM / TIM barrel / Glycolytic enzyme
Function / homology
Function and homology information


Glycolysis / Gluconeogenesis / triose-phosphate isomerase / triose-phosphate isomerase activity / glyceraldehyde-3-phosphate biosynthetic process / glycerol catabolic process / canonical glycolysis / 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-type TIM barrel
Similarity search - Domain/homology
ACETATE ION / PHOSPHATE ION / Triosephosphate isomerase
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 Å
AuthorsRomero-Romero, S. / Garza-Ramos, G.
Funding support1items
OrganizationGrant numberCountry
Not funded
Citation
Journal: To Be Published
Title: Crystal structure of Triosephosphate Isomerase from Schizosaccharomyces pombe (SpTIM wt)
Authors: Romero-Romero, S. / Garza-Ramos, G.
#1: Journal: Acta Crystallogr., Sect. D: Biol. Crystallogr. / Year: 2012
Title: Towards automated crystallographic structure refinement with phenix.refine.
Authors: Afonine, P.V.
History
DepositionAug 10, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 24, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: 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
C: Triosephosphate isomerase
D: Triosephosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,33114
Polymers108,5194
Non-polymers81110
Water15,403855
1
A: Triosephosphate isomerase
B: Triosephosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,6667
Polymers54,2602
Non-polymers4065
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4460 Å2
ΔGint-74 kcal/mol
Surface area18060 Å2
MethodPISA
2
C: Triosephosphate isomerase
D: Triosephosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,6657
Polymers54,2602
Non-polymers4055
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4350 Å2
ΔGint-62 kcal/mol
Surface area17970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)149.510, 149.510, 99.910
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4
Space group name HallI4
Symmetry operation#1: x,y,z
#2: -y,x,z
#3: y,-x,z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: -y+1/2,x+1/2,z+1/2
#7: y+1/2,-x+1/2,z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

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


Mass: 27129.814 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Strain: 972 / ATCC 24843 / Gene: tpi1, tpi, SPCC24B10.21 / Plasmid: pET24a(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P07669, triose-phosphate isomerase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 855 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.5 Å3/Da / Density % sol: 50.9 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.6
Details: 2.2 M Ammonium sulphate, 0.2 M Lithium acetate, 9.1 mg/mL protein concentration

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 20, 2021
RadiationMonochromator: DCM Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.79→37.38 Å / Num. obs: 103063 / % possible obs: 99.77 % / Redundancy: 7.6 % / Biso Wilson estimate: 36.36 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.09633 / Rpim(I) all: 0.03754 / Rrim(I) all: 0.1035 / Net I/σ(I): 13.11
Reflection shellResolution: 1.79→1.854 Å / Redundancy: 7.6 % / Rmerge(I) obs: 1.437 / Mean I/σ(I) obs: 0.99 / Num. unique obs: 10149 / CC1/2: 0.307 / CC star: 0.64 / Rpim(I) all: 0.9385 / Rrim(I) all: 0.915 / % possible all: 98.26

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FF7

4ff7


Resolution: 1.79→37.38 Å / SU ML: 0.3221 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.1053
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2179 2100 2.04 %
Rwork0.1817 100929 -
obs0.1825 103029 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.25 Å2
Refinement stepCycle: LAST / Resolution: 1.79→37.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7366 0 46 855 8267
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01517522
X-RAY DIFFRACTIONf_angle_d1.306510196
X-RAY DIFFRACTIONf_chiral_restr0.08351177
X-RAY DIFFRACTIONf_plane_restr0.01051325
X-RAY DIFFRACTIONf_dihedral_angle_d7.10381027
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.79-1.830.61521370.53726567X-RAY DIFFRACTION97.39
1.83-1.880.49711390.41626673X-RAY DIFFRACTION100
1.88-1.930.31621390.30456707X-RAY DIFFRACTION99.94
1.93-1.990.32391400.26096725X-RAY DIFFRACTION99.97
1.99-2.050.27971410.24076753X-RAY DIFFRACTION100
2.05-2.120.27241390.23156704X-RAY DIFFRACTION100
2.12-2.210.27831400.22696731X-RAY DIFFRACTION100
2.21-2.310.23411400.1926706X-RAY DIFFRACTION99.99
2.31-2.430.22791400.18976726X-RAY DIFFRACTION100
2.43-2.580.2371400.1966749X-RAY DIFFRACTION100
2.58-2.780.24781410.1866755X-RAY DIFFRACTION100
2.78-3.060.21071400.17886748X-RAY DIFFRACTION100
3.06-3.50.2251400.16546757X-RAY DIFFRACTION100
3.5-4.410.15761410.13746768X-RAY DIFFRACTION100
4.41-37.380.17531430.1546860X-RAY DIFFRACTION99.52
Refinement TLS params.Method: refined / Origin x: 15.1488993668 Å / Origin y: 32.0074573593 Å / Origin z: -34.1968980036 Å
111213212223313233
T0.256833112697 Å2-0.0267271674031 Å2-0.0292696612469 Å2-0.216928710417 Å20.0638315485604 Å2--0.300135966137 Å2
L0.399278810752 °20.0834259767506 °2-0.354716423525 °2-0.265429798803 °20.0529045158442 °2--1.31482326443 °2
S0.00334399992638 Å °0.015328554019 Å °0.104954355147 Å °-0.0418311627534 Å °-0.00358169788535 Å °-0.031866015838 Å °0.0678284744428 Å °-0.0352106806812 Å °0.00458357344633 Å °
Refinement TLS groupSelection details: all

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