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- PDB-7skj: Crystal structure of chloroplast triosephosphate isomerase from C... -

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Basic information

Entry
Database: PDB / ID: 7skj
TitleCrystal structure of chloroplast triosephosphate isomerase from Cuscuta australis
ComponentsTriosephosphate isomerase
KeywordsISOMERASE / TIM / triosephosphate isomerase / glycolysis / gluconeogenesis / Calvin-Benson-Bassham Cycle
Function / homology
Function and homology information


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-type TIM barrel
Similarity search - Domain/homology
ACETATE ION / Triosephosphate isomerase
Similarity search - Component
Biological speciesCuscuta australis (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsJones, G. / Vickers, C. / Patrick, W.
Funding support New Zealand, 1items
OrganizationGrant numberCountry
Royal Society of New Zealand New Zealand
CitationJournal: To Be Published
Title: Crystal structure of chloroplast triosephosphate isomerase from Cuscuta australis
Authors: Jones, G. / Vickers, C. / Patrick, W.
History
DepositionOct 20, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 26, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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

Downloads & links

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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)118,3926
Polymers118,2744
Non-polymers1182
Water16,069892
1
A: Triosephosphate isomerase
B: Triosephosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,1963
Polymers59,1372
Non-polymers591
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3380 Å2
ΔGint-22 kcal/mol
Surface area18530 Å2
MethodPISA
2
C: Triosephosphate isomerase
D: Triosephosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,1963
Polymers59,1372
Non-polymers591
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3290 Å2
ΔGint-22 kcal/mol
Surface area17970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.949, 82.118, 154.246
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein
Triosephosphate isomerase


Mass: 29568.379 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cuscuta australis (plant) / Gene: DM860_005218 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A328DYS8
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 892 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.01 Å3/Da / Density % sol: 38.7 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Ammonium acetate, 0.1 M HEPES pH 7.5, 25% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9464 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 5, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9464 Å / Relative weight: 1
ReflectionResolution: 1.9→44.97 Å / Num. obs: 75939 / % possible obs: 99.8 % / Redundancy: 13.6 % / Biso Wilson estimate: 24.25 Å2 / CC1/2: 0.999 / Net I/σ(I): 16.3
Reflection shellResolution: 1.9→1.94 Å / Num. unique obs: 4271 / CC1/2: 0.928

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
MOSFLMdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4OHQ

4ohq


Resolution: 1.9→44.97 Å / SU ML: 0.2141 / Cross valid method: FREE R-VALUE / Phase error: 22.4965
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2352 1999 2.64 %
Rwork0.1852 73854 -
obs0.1866 75853 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.53 Å2
Refinement stepCycle: LAST / Resolution: 1.9→44.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7063 0 8 892 7963
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00787198
X-RAY DIFFRACTIONf_angle_d0.85949774
X-RAY DIFFRACTIONf_chiral_restr0.05721113
X-RAY DIFFRACTIONf_plane_restr0.00591272
X-RAY DIFFRACTIONf_dihedral_angle_d5.7461001
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.940.28181370.21295035X-RAY DIFFRACTION96.64
1.94-20.28291410.20885223X-RAY DIFFRACTION100
2-2.060.3281410.21355242X-RAY DIFFRACTION99.98
2.06-2.120.25381410.19745203X-RAY DIFFRACTION100
2.12-2.20.2131430.18845252X-RAY DIFFRACTION100
2.2-2.290.25151420.18545241X-RAY DIFFRACTION100
2.29-2.390.24021410.1885224X-RAY DIFFRACTION99.98
2.39-2.520.23641430.19165270X-RAY DIFFRACTION100
2.52-2.670.25621430.19535278X-RAY DIFFRACTION100
2.67-2.880.25031430.20355283X-RAY DIFFRACTION99.98
2.88-3.170.23531440.19455308X-RAY DIFFRACTION100
3.17-3.630.20731430.17865306X-RAY DIFFRACTION100
3.63-4.570.21131460.15655391X-RAY DIFFRACTION100
4.57-44.970.22961510.18215598X-RAY DIFFRACTION99.91

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