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- PDB-7rpn: Crystal structure of triosephosphate isomerase from Bacteroides t... -

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Basic information

Entry
Database: PDB / ID: 7rpn
TitleCrystal structure of triosephosphate isomerase from Bacteroides thetaiotaomicron
ComponentsTriosephosphate isomerase
KeywordsISOMERASE / TIM / triosephosphate isomerase / glycolysis / gluconeogenesis
Function / homology
Function and homology information


triose-phosphate isomerase / triose-phosphate isomerase activity / gluconeogenesis / glycolytic process / 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-type TIM barrel
Similarity search - Domain/homology
Triosephosphate isomerase
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.37 Å
AuthorsVickers, C.J. / Fraga, D. / Patrick, W.M.
Funding support New Zealand, 1items
OrganizationGrant numberCountry
Royal Society of New Zealand New Zealand
CitationJournal: To be published
Title: Structure of BthTPI - Bacteroides thetaiotaomicron triosephoshate isomerase
Authors: Vickers, C.J. / Fraga, D. / Patrick, W.M.
History
DepositionAug 3, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 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

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Assembly

Deposited unit
A: Triosephosphate isomerase


Theoretical massNumber of molelcules
Total (without water)26,8291
Polymers26,8291
Non-polymers00
Water7,188399
1
A: Triosephosphate isomerase

A: Triosephosphate isomerase


Theoretical massNumber of molelcules
Total (without water)53,6572
Polymers53,6572
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-1/31
Buried area3170 Å2
ΔGint-25 kcal/mol
Surface area19060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.650, 51.650, 207.172
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z

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Components

#1: Protein Triosephosphate isomerase / TIM / TPI / Triose-phosphate isomerase


Mass: 26828.510 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria)
Gene: tpiA, BatF92_04170, BSIG_2740, Btheta7330_00522, DW011_22160, DW780_28020, DWY18_05535, DXA83_01600, ERS852511_01061, ERS852557_00096, FE838_09570, GA053_13175, GAN59_07295, GAN75_16360, GAN91_ ...Gene: tpiA, BatF92_04170, BSIG_2740, Btheta7330_00522, DW011_22160, DW780_28020, DWY18_05535, DXA83_01600, ERS852511_01061, ERS852557_00096, FE838_09570, GA053_13175, GAN59_07295, GAN75_16360, GAN91_01280, GAO00_10320, GAO51_28160, HMPREF2534_01356
Production host: Escherichia coli (E. coli) / References: UniProt: A0A0P0FGJ1, triose-phosphate isomerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 399 / 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: 2.97 Å3/Da / Density % sol: 58.63 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / Details: 0.1 M citrate, pH 5.0, 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: 0.95372 A
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 12, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 1.37→44.73 Å / Num. obs: 68732 / % possible obs: 99.9 % / Redundancy: 20 % / Biso Wilson estimate: 10.61 Å2 / CC1/2: 1 / Net I/σ(I): 43.91
Reflection shellResolution: 1.37→1.45 Å / Num. unique obs: 10909 / CC1/2: 0.995

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
MOSFLMdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6NEE

6nee


Resolution: 1.37→44.73 Å / SU ML: 0.0874 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 15.6154
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.174 1963 2.87 %
Rwork0.1572 66407 -
obs0.1577 68370 99.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 13.69 Å2
Refinement stepCycle: LAST / Resolution: 1.37→44.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1850 0 0 399 2249
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00481879
X-RAY DIFFRACTIONf_angle_d0.8512550
X-RAY DIFFRACTIONf_chiral_restr0.0798298
X-RAY DIFFRACTIONf_plane_restr0.0055333
X-RAY DIFFRACTIONf_dihedral_angle_d5.9299263
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.37-1.40.16641400.15274603X-RAY DIFFRACTION97.91
1.4-1.440.17671390.14664627X-RAY DIFFRACTION98.29
1.44-1.490.14991390.14554620X-RAY DIFFRACTION98.71
1.49-1.530.15821350.14154640X-RAY DIFFRACTION99.07
1.53-1.590.1441410.1494659X-RAY DIFFRACTION99.28
1.59-1.650.17341350.14094687X-RAY DIFFRACTION99.57
1.65-1.730.18221390.15634748X-RAY DIFFRACTION99.63
1.73-1.820.17641360.15544699X-RAY DIFFRACTION99.88
1.82-1.930.17191380.15854729X-RAY DIFFRACTION99.88
1.93-2.080.1831470.15354779X-RAY DIFFRACTION99.9
2.08-2.290.18281390.15734770X-RAY DIFFRACTION99.96
2.29-2.620.17971420.16654840X-RAY DIFFRACTION99.98
2.62-3.30.1751460.16654863X-RAY DIFFRACTION100
3.3-44.730.17411470.15815143X-RAY DIFFRACTION99.92

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