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- PDB-7pek: Crystal structure of Triosephosphate Isomerase C216A mutant from ... -

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Basic information

Entry
Database: PDB / ID: 7pek
TitleCrystal structure of Triosephosphate Isomerase C216A mutant from Schizosaccharomyces pombe (SpTIM C216A)
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 / canonical glycolysis / glycerol catabolic process / gluconeogenesis / glycolytic process / nucleus / 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
PHOSPHATE ION / Triosephosphate isomerase
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 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 C216A)
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)109,57718
Polymers108,3914
Non-polymers1,18614
Water15,853880
1
A: Triosephosphate isomerase
B: Triosephosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,8569
Polymers54,1962
Non-polymers6617
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4760 Å2
ΔGint-71 kcal/mol
Surface area18210 Å2
MethodPISA
2
C: Triosephosphate isomerase
D: Triosephosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,7219
Polymers54,1962
Non-polymers5257
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4550 Å2
ΔGint-99 kcal/mol
Surface area18220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)149.010, 149.010, 99.510
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

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Protein , 1 types, 4 molecules ABCD

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


Mass: 27097.750 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: C216A mutation
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

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Non-polymers , 5 types, 894 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 880 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.47 Å3/Da / Density % sol: 50.3 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 2.4 M Ammonium sulphate, 0.1 M Bicine pH:9.0, 11.1 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: 1.74→47.12 Å / Num. obs: 110326 / % possible obs: 99.69 % / Redundancy: 7.6 % / Biso Wilson estimate: 33.62 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.09564 / Rpim(I) all: 0.03707 / Rrim(I) all: 0.1027 / Net I/σ(I): 13.49
Reflection shellResolution: 1.74→1.806 Å / Redundancy: 7.3 % / Rmerge(I) obs: 1.241 / Mean I/σ(I) obs: 1.01 / Num. unique obs: 10711 / CC1/2: 0.312 / CC star: 0.654 / Rpim(I) all: 0.8809 / Rrim(I) all: 0.912 / % possible all: 97.55

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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: 1.74→47.12 Å / SU ML: 0.2408 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.7494
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2065 2100 1.9 %
Rwork0.1767 108191 -
obs0.1772 110291 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.65 Å2
Refinement stepCycle: LAST / Resolution: 1.74→47.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7412 0 65 880 8357
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00727584
X-RAY DIFFRACTIONf_angle_d1.071110280
X-RAY DIFFRACTIONf_chiral_restr0.05611185
X-RAY DIFFRACTIONf_plane_restr0.00761328
X-RAY DIFFRACTIONf_dihedral_angle_d6.82881037
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.74-1.780.34531350.34686939X-RAY DIFFRACTION96.36
1.78-1.830.35951400.31297215X-RAY DIFFRACTION99.95
1.83-1.880.3051390.29497177X-RAY DIFFRACTION99.97
1.88-1.930.34211400.28427207X-RAY DIFFRACTION100
1.93-20.29751400.25227212X-RAY DIFFRACTION99.99
2-2.070.25971390.22137199X-RAY DIFFRACTION99.97
2.07-2.150.29491410.2017260X-RAY DIFFRACTION100
2.15-2.250.20781400.18427195X-RAY DIFFRACTION99.97
2.25-2.370.21251410.18527265X-RAY DIFFRACTION99.96
2.37-2.510.25071390.18767174X-RAY DIFFRACTION99.96
2.51-2.710.22911410.18237264X-RAY DIFFRACTION99.95
2.71-2.980.2071400.17877228X-RAY DIFFRACTION99.99
2.98-3.410.19391410.16627245X-RAY DIFFRACTION99.99
3.41-4.30.16571410.13917282X-RAY DIFFRACTION99.91
4.3-47.120.16431430.15287329X-RAY DIFFRACTION99.45
Refinement TLS params.Method: refined / Origin x: -31.9728917254 Å / Origin y: -15.0552597992 Å / Origin z: 34.9495210898 Å
111213212223313233
T0.20402472322 Å2-0.0233762802224 Å20.0529894450584 Å2-0.228946902268 Å2-0.0246976976159 Å2--0.276132251443 Å2
L0.195127283761 °20.0392991894676 °20.0204158651514 °2-0.327045665621 °2-0.347747226719 °2--1.21217755602 °2
S0.008682894733 Å °-0.0528485138002 Å °-0.0173099134501 Å °0.00223639050805 Å °0.00785088952127 Å °0.0728309441927 Å °-0.0230605401505 Å °0.0553302818685 Å °-0.0112153856907 Å °
Refinement TLS groupSelection details: all

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