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- PDB-6jox: triosephosphate isomerase-scylla paramamosain -

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Basic information

Entry
Database: PDB / ID: 6jox
Titletriosephosphate isomerase-scylla paramamosain
ComponentsTriosephosphate isomerase
KeywordsISOMERASE / triosephosphate isomerase / allergen / blue crab / food allergy
Function / homology
Function and homology information


methylglyoxal biosynthetic process / methylglyoxal synthase / methylglyoxal synthase activity / IgE binding / triose-phosphate isomerase / triose-phosphate isomerase activity / gluconeogenesis / glycolytic process / protein homodimerization activity / cytoplasm
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
Similarity search - Component
Biological speciesScylla paramamosain (green mud crab)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.803 Å
AuthorsXia, F. / Jin, T.
CitationJournal: J.Agric.Food Chem. / Year: 2019
Title: Crystal Structure Analysis and Conformational Epitope Mutation of Triosephosphate Isomerase, a Mud Crab Allergen.
Authors: Xia, F. / Li, M.S. / Liu, Q.M. / Liu, M. / Yang, Y. / Cao, M.J. / Chen, G.X. / Jin, T. / Liu, G.M.
History
DepositionMar 25, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 4, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Triosephosphate isomerase
A: Triosephosphate isomerase


Theoretical massNumber of molelcules
Total (without water)58,6152
Polymers58,6152
Non-polymers00
Water5,909328
1
B: Triosephosphate isomerase


Theoretical massNumber of molelcules
Total (without water)29,3071
Polymers29,3071
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Triosephosphate isomerase


Theoretical massNumber of molelcules
Total (without water)29,3071
Polymers29,3071
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)154.712, 154.712, 52.713
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321

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Components

#1: Protein Triosephosphate isomerase /


Mass: 29307.457 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Scylla paramamosain (green mud crab) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1L5YRA2, triose-phosphate isomerase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 328 / 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: 3.11 Å3/Da / Density % sol: 60.41 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6 / Details: 22% PEG6000, 0.1M Citric Acid pH 4.6 / Temp details: Room temperature

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Data collection

DiffractionMean temperature: 190 K / Ambient temp details: Nitrogen steam / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 22, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 66802 / % possible obs: 100 % / Redundancy: 9.9 % / Rpim(I) all: 0.035 / Rrim(I) all: 0.11 / Net I/σ(I): 20.01
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 8.8 % / Num. unique obs: 3313 / CC1/2: 0.827 / Rpim(I) all: 0.34 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASER5eywphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5EYW

5eyw


Resolution: 1.803→44.662 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 15.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1791 3334 4.99 %
Rwork0.155 --
obs0.1562 66755 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.803→44.662 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3730 0 0 328 4058
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063825
X-RAY DIFFRACTIONf_angle_d0.7735179
X-RAY DIFFRACTIONf_dihedral_angle_d7.5642727
X-RAY DIFFRACTIONf_chiral_restr0.052569
X-RAY DIFFRACTIONf_plane_restr0.005678
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8029-1.82870.21611360.20782604X-RAY DIFFRACTION100
1.8287-1.8560.23351370.19832615X-RAY DIFFRACTION100
1.856-1.8850.23011410.1792656X-RAY DIFFRACTION100
1.885-1.91590.22071400.17692591X-RAY DIFFRACTION100
1.9159-1.94890.18621370.16062651X-RAY DIFFRACTION100
1.9489-1.98440.19031360.15742624X-RAY DIFFRACTION100
1.9844-2.02250.1531410.15292631X-RAY DIFFRACTION100
2.0225-2.06380.1771330.15142598X-RAY DIFFRACTION100
2.0638-2.10870.16461390.14492666X-RAY DIFFRACTION100
2.1087-2.15780.19441340.14462584X-RAY DIFFRACTION100
2.1578-2.21170.17491430.13982678X-RAY DIFFRACTION100
2.2117-2.27150.19191380.14462622X-RAY DIFFRACTION100
2.2715-2.33830.15931350.14182626X-RAY DIFFRACTION100
2.3383-2.41380.1851410.14722625X-RAY DIFFRACTION100
2.4138-2.50010.18921350.15322650X-RAY DIFFRACTION100
2.5001-2.60020.19471400.15182639X-RAY DIFFRACTION100
2.6002-2.71850.18281340.14572647X-RAY DIFFRACTION100
2.7185-2.86180.16391410.14442638X-RAY DIFFRACTION100
2.8618-3.04110.15871380.14432652X-RAY DIFFRACTION100
3.0411-3.27580.18281410.14112678X-RAY DIFFRACTION100
3.2758-3.60530.14851390.13532644X-RAY DIFFRACTION100
3.6053-4.12670.18361450.14432671X-RAY DIFFRACTION100
4.1267-5.1980.16851420.16222695X-RAY DIFFRACTION100
5.198-44.67520.19631480.2052736X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 53.8413 Å / Origin y: 51.7024 Å / Origin z: 32.3125 Å
111213212223313233
T0.1049 Å20.0305 Å20.0126 Å2-0.1748 Å20.0078 Å2--0.1364 Å2
L0.4392 °20.0193 °20.1719 °2-0.5181 °20.3495 °2--0.9259 °2
S0.0258 Å °-0.0269 Å °-0.0037 Å °-0.0208 Å °-0.0276 Å °0.0047 Å °-0.0287 Å °-0.0883 Å °0.0059 Å °
Refinement TLS groupSelection details: all

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