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- PDB-8uz7: Crystal structure of a novel triose phosphate isomerase identifie... -

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Basic information

Entry
Database: PDB / ID: 8uz7
TitleCrystal structure of a novel triose phosphate isomerase identified on the shrimp transcriptome
ComponentsTriosephosphate isomerase
KeywordsISOMERASE / triose phosphate isomerase / shrimp
Function / homology
Function and homology information


triose-phosphate isomerase / triose-phosphate isomerase activity / glyceraldehyde-3-phosphate biosynthetic process / glycerol catabolic process / glycolytic process / gluconeogenesis / metal ion binding / cytosol
Similarity search - Function
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 speciesPenaeus vannamei (Pacific white shrimp)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsSotelo-Mundo, R.R. / Gomez-Yanes, A.C. / Lopez-Zavala, A.A. / Lopez-Garcia, J.A. / Ochoa-Leyva, A.
Funding support Mexico, 2items
OrganizationGrant numberCountry
Consejo Nacional de Ciencia y Tecnologia (CONACYT)CF-2019-263986 Mexico
Not fundedUNAM PAPIIT IN215520
CitationJournal: To Be Published
Title: Crystal structure of a novel triose phosphate isomerase from shrimp
Authors: Sotelo-Mundo, R.R. / Gomez-Yanes, A.C. / Lopez-Zavala, A.A. / Ochoa-Leyva, A.
History
DepositionNov 14, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 6, 2023Provider: repository / Type: Initial release

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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)109,99911
Polymers109,7624
Non-polymers2377
Water9,908550
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.564, 84.253, 73.739
Angle α, β, γ (deg.)90.000, 92.690, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb

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Components

#1: Protein
Triosephosphate isomerase


Mass: 27440.498 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Penaeus vannamei (Pacific white shrimp)
Gene: C7M84_025338 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A3R7QX74
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 550 / Source method: isolated from a natural source / Formula: H2O
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: 2.08 Å3/Da / Density % sol: 40.86 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Index kit (Hampton Research) No. 83 (0.2 M MgCl2-6H2O, 0.1 M Bis-Tris pH 6.5, 25% W/V PEG-3350, 20% PEG-400 as cryo-protectant)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 1.181 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 25, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.181 Å / Relative weight: 1
ReflectionResolution: 1.7→55.45 Å / Num. obs: 91724 / % possible obs: 93.1 % / Redundancy: 6.1 % / Biso Wilson estimate: 19.93 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.07959 / Rrim(I) all: 0.09037 / Net I/σ(I): 13.73
Reflection shellResolution: 1.702→1.763 Å / Rmerge(I) obs: 0.8205 / Mean I/σ(I) obs: 2.22 / Num. unique obs: 9794 / Rpim(I) all: 0.4462 / Rrim(I) all: 0.9364

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000data reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→55.45 Å / SU ML: 0.164 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.8092
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1909 2025 2.21 %
Rwork0.1889 89684 -
obs0.189 91709 93.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.01 Å2
Refinement stepCycle: LAST / Resolution: 1.7→55.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7548 0 7 550 8105
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00677701
X-RAY DIFFRACTIONf_angle_d0.831110408
X-RAY DIFFRACTIONf_chiral_restr0.05331168
X-RAY DIFFRACTIONf_plane_restr0.00491354
X-RAY DIFFRACTIONf_dihedral_angle_d14.22212851
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.740.28131480.30776854X-RAY DIFFRACTION99.91
1.74-1.790.31071610.28186827X-RAY DIFFRACTION99.81
1.79-1.840.24541610.21686860X-RAY DIFFRACTION99.9
1.84-1.90.23871360.21116836X-RAY DIFFRACTION99.91
1.9-1.970.20011590.20026870X-RAY DIFFRACTION99.93
1.97-2.050.17351580.19516843X-RAY DIFFRACTION99.87
2.05-2.140.2028900.18894101X-RAY DIFFRACTION59.89
2.14-2.230.18911270.18285472X-RAY DIFFRACTION98.04
2.27-2.40.16941480.18556232X-RAY DIFFRACTION96.93
2.4-2.580.21841550.1916822X-RAY DIFFRACTION99.77
2.58-2.840.18311420.1856168X-RAY DIFFRACTION89.25
2.84-3.260.20231530.17836855X-RAY DIFFRACTION99.6
3.26-4.10.16421350.16436049X-RAY DIFFRACTION86.99
4.1-55.450.16311520.18016895X-RAY DIFFRACTION98.31

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