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- PDB-7v03: Crystal structure of cytoplasmic triosephosphate isomerase from C... -

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Basic information

Entry
Database: PDB / ID: 7v03
TitleCrystal structure of cytoplasmic 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 / glycolytic process
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
Triosephosphate isomerase
Similarity search - Component
Biological speciesCuscuta australis (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsJones, G. / Vickers, C. / Patrick, W. / Jameson, G.
Funding support New Zealand, 1items
OrganizationGrant numberCountry
Royal Society of New Zealand New Zealand
CitationJournal: To Be Published
Title: Crystal structure of cytoplasmic triosephosphate isomerase from Cuscuta australis
Authors: Jones, G. / Vickers, C. / Patrick, W.
History
DepositionMay 9, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 17, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 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
C: triosephosphate isomerase
D: triosephosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,84810
Polymers118,6354
Non-polymers2136
Water20,0151111
1
A: triosephosphate isomerase
D: triosephosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,4245
Polymers59,3182
Non-polymers1063
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3330 Å2
ΔGint-57 kcal/mol
Surface area17970 Å2
MethodPISA
2
B: triosephosphate isomerase
C: triosephosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,4245
Polymers59,3182
Non-polymers1063
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3400 Å2
ΔGint-61 kcal/mol
Surface area17850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.102, 130.132, 74.998
Angle α, β, γ (deg.)90.000, 90.011, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein
triosephosphate isomerase


Mass: 29658.768 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cuscuta australis (plant) / Gene: DM860_000111 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A328CVN3
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1111 / 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: 2.09 Å3/Da / Density % sol: 39.1 %
Description: Large coffin shaped crystal, condition also contained an unidentified microbial contaminant.
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 0.2 M sodium chloride 0.1 M MES pH 6.0, 20 % w/v PEG 6000

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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: 1.78→45.94 Å / Num. obs: 89461 / % possible obs: 99.57 % / Redundancy: 7 % / Biso Wilson estimate: 13.2 Å2 / CC1/2: 0.999 / Net I/σ(I): 6.31
Reflection shellResolution: 1.78→1.84 Å / Num. unique obs: 8804 / CC1/2: 0.979 / % possible all: 98.38

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
MOSFLMdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4OBT

4obt


Resolution: 1.78→45.94 Å / SU ML: 0.226 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.582
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2525 4533 5.07 %
Rwork0.2112 84846 -
obs0.2133 89379 99.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 14.07 Å2
Refinement stepCycle: LAST / Resolution: 1.78→45.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7129 0 6 1111 8246
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00697268
X-RAY DIFFRACTIONf_angle_d0.87649913
X-RAY DIFFRACTIONf_chiral_restr0.05831177
X-RAY DIFFRACTIONf_plane_restr0.00841273
X-RAY DIFFRACTIONf_dihedral_angle_d5.99991010
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.78-1.80.25811460.20572711X-RAY DIFFRACTION96.36
1.8-1.820.25381860.19832795X-RAY DIFFRACTION99.37
1.82-1.840.27611360.21242830X-RAY DIFFRACTION99.4
1.84-1.870.25511670.21022803X-RAY DIFFRACTION99.5
1.87-1.890.30111550.2122800X-RAY DIFFRACTION99.43
1.89-1.920.26831700.20812789X-RAY DIFFRACTION99.43
1.92-1.950.2881580.2062849X-RAY DIFFRACTION99.64
1.95-1.970.24831560.19982801X-RAY DIFFRACTION99.33
1.97-2.010.25141390.20422802X-RAY DIFFRACTION99.63
2.01-2.040.26511390.20582888X-RAY DIFFRACTION99.7
2.04-2.070.22541470.2052778X-RAY DIFFRACTION99.63
2.07-2.110.26291320.20562842X-RAY DIFFRACTION99.66
2.11-2.150.28771390.20742858X-RAY DIFFRACTION99.73
2.15-2.20.24331130.19982830X-RAY DIFFRACTION99.7
2.2-2.240.25181370.19912898X-RAY DIFFRACTION99.8
2.24-2.30.27531680.20862780X-RAY DIFFRACTION99.86
2.3-2.350.29911530.21642891X-RAY DIFFRACTION99.93
2.35-2.420.25581710.21592783X-RAY DIFFRACTION99.83
2.42-2.490.26491450.21392812X-RAY DIFFRACTION99.9
2.49-2.570.27581700.21192826X-RAY DIFFRACTION99.83
2.57-2.660.27771260.21722825X-RAY DIFFRACTION99.9
2.66-2.770.23661600.22242876X-RAY DIFFRACTION99.8
2.77-2.890.2631360.21552865X-RAY DIFFRACTION99.73
2.89-3.040.24951570.21632776X-RAY DIFFRACTION99.63
3.05-3.240.26441500.21922878X-RAY DIFFRACTION99.84
3.24-3.490.25541650.21482818X-RAY DIFFRACTION99.87
3.49-3.840.23131360.20472867X-RAY DIFFRACTION99.8
3.84-4.390.20671580.20222824X-RAY DIFFRACTION99.7
4.39-5.530.22881540.20562873X-RAY DIFFRACTION99.77
5.53-45.940.23431640.23522878X-RAY DIFFRACTION99.74

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