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- PDB-6nxx: Crystal structure of Arabidopsis thaliana cytosolic triosephospha... -

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Basic information

Entry
Database: PDB / ID: 6nxx
TitleCrystal structure of Arabidopsis thaliana cytosolic triosephosphate isomerase C218K mutant
ComponentsTriosephosphate isomerase, cytosolic
KeywordsISOMERASE / Triosephosphate isomerase Crystal structure mutant dimer redox regulation
Function / homology
Function and homology information


plant-type cell wall / apoplast / plasmodesma / triose-phosphate isomerase / plant-type vacuole / triose-phosphate isomerase activity / chloroplast stroma / response to zinc ion / glycolytic process / gluconeogenesis ...plant-type cell wall / apoplast / plasmodesma / triose-phosphate isomerase / plant-type vacuole / triose-phosphate isomerase activity / chloroplast stroma / response to zinc ion / glycolytic process / gluconeogenesis / chloroplast / copper ion binding / mitochondrion / plasma membrane / 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, cytosolic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 Å
AuthorsJimenez-Sandoval, P. / Fuentes-Pascacio, A. / Diaz-Quezada, C. / Torres-Larios, A. / Brieba, L.G.
CitationJournal: Plant J. / Year: 2019
Title: Structural basis for the modulation of plant cytosolic triosephosphate isomerase activity by mimicry of redox-based modifications.
Authors: Castro-Torres, E. / Jimenez-Sandoval, P. / Romero-Romero, S. / Fuentes-Pascacio, A. / Lopez-Castillo, L.M. / Diaz-Quezada, C. / Fernandez-Velasco, D.A. / Torres-Larios, A. / Brieba, L.G.
History
DepositionFeb 10, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 19, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 2, 2020Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_struct_conn_angle / struct_conn
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_radiation_wavelength.wavelength

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Triosephosphate isomerase, cytosolic
B: Triosephosphate isomerase, cytosolic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,0774
Polymers55,0312
Non-polymers462
Water7,891438
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3170 Å2
ΔGint-45 kcal/mol
Surface area19380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.410, 92.560, 97.170
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, cytosolic / Triose-phosphate isomerase


Mass: 27515.355 Da / Num. of mol.: 2 / Mutation: C218K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: CTIMC, At3g55440, T22E16.100 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P48491, triose-phosphate isomerase
#2: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 438 / Source method: isolated from a natural source / Formula: H2O

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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: 2.83 Å3/Da / Density % sol: 56.49 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop
Details: 0.03 M Diethylene glycol; 0.03 M Triethylene glycol; 0.03 M Tetraethylene glycol; 0.03 M Pentaethyleneglycol, 0.1 M HEPES/MOPS pH 7.5, 12.5 % v/v MPD; 12.5 % PEG 1000; 12.5 % w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9787 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 26, 2017
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 1.64→67.41 Å / Num. obs: 75395 / % possible obs: 99.7 % / Redundancy: 9.5 % / Biso Wilson estimate: 17.31 Å2 / Net I/σ(I): 17.2
Reflection shellResolution: 1.64→1.66 Å

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Processing

Software
NameClassification
PHENIXrefinement
HKL-2000data reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4OBT

4obt


Resolution: 1.64→67.02 Å / SU ML: 0.1477 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.9051
RfactorNum. reflection% reflectionSelection details
Rfree0.2055 3764 4.99 %0.05
Rwork0.1807 ---
obs0.1819 75395 99.65 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 21.91 Å2
Refinement stepCycle: LAST / Resolution: 1.64→67.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3708 0 2 438 4148
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00533852
X-RAY DIFFRACTIONf_angle_d0.725255
X-RAY DIFFRACTIONf_chiral_restr0.0515606
X-RAY DIFFRACTIONf_plane_restr0.0052690
X-RAY DIFFRACTIONf_dihedral_angle_d2.37973043
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.64-1.660.29611260.23142579X-RAY DIFFRACTION97.79
1.66-1.680.27531290.22322607X-RAY DIFFRACTION98.88
1.68-1.70.21891320.21172607X-RAY DIFFRACTION99.42
1.7-1.730.23411530.20012610X-RAY DIFFRACTION99.42
1.73-1.750.24371330.20352608X-RAY DIFFRACTION99.31
1.75-1.780.26021330.20332625X-RAY DIFFRACTION99.35
1.78-1.810.2341520.20342609X-RAY DIFFRACTION99.35
1.81-1.840.20931290.19892618X-RAY DIFFRACTION99.53
1.84-1.870.21771390.19192637X-RAY DIFFRACTION99.53
1.87-1.910.2011400.18592624X-RAY DIFFRACTION99.68
1.91-1.950.26631370.18432617X-RAY DIFFRACTION99.67
1.95-1.990.20461460.18162623X-RAY DIFFRACTION99.78
1.99-2.040.22921240.1812669X-RAY DIFFRACTION99.82
2.04-2.090.2441430.18962620X-RAY DIFFRACTION99.86
2.09-2.140.2121380.18452663X-RAY DIFFRACTION99.89
2.14-2.210.21561460.18272636X-RAY DIFFRACTION99.93
2.21-2.280.21131330.17672651X-RAY DIFFRACTION99.93
2.28-2.360.19691480.17442637X-RAY DIFFRACTION99.96
2.36-2.450.19211320.17782660X-RAY DIFFRACTION100
2.45-2.570.2311470.17922677X-RAY DIFFRACTION100
2.57-2.70.20461370.18252681X-RAY DIFFRACTION100
2.7-2.870.21251410.18292670X-RAY DIFFRACTION100
2.87-3.090.19071400.18682694X-RAY DIFFRACTION99.96
3.09-3.40.19511450.18162687X-RAY DIFFRACTION100
3.4-3.90.19921400.17532713X-RAY DIFFRACTION100
3.9-4.910.15831440.1512748X-RAY DIFFRACTION100
4.91-67.080.19141570.17742861X-RAY DIFFRACTION99.47

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