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- PDB-7rgc: Crystal structure of triosephosphate isomerase from Candidatus Ab... -

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Basic information

Entry
Database: PDB / ID: 7rgc
TitleCrystal structure of triosephosphate isomerase from Candidatus Absconditabacteria (Sr1) bacterium
ComponentsTriosephosphate isomerase
KeywordsISOMERASE / TIM / triosephosphate isomerase / glycolysis / gluconeogenesis
Function / homology
Function and homology information


triose-phosphate isomerase / triose-phosphate isomerase activity / glycerol catabolic process / glyceraldehyde-3-phosphate biosynthetic process / gluconeogenesis / glycolytic process / cytosol
Similarity search - Function
Triosephosphate isomerase, bacterial/eukaryotic / 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 speciescandidate division SR1 bacterium RAAC1_SR1_1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å
AuthorsVickers, C.J. / Compton, 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 Sr1TPI - Candidatus Absconditabacteria bacterium triosephoshate isomerase
Authors: Vickers, C.J. / Fraga, D. / Compton, J. / Patrick, W.M.
History
DepositionJul 15, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 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
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Triosephosphate isomerase
B: Triosephosphate isomerase


Theoretical massNumber of molelcules
Total (without water)55,2132
Polymers55,2132
Non-polymers00
Water2,018112
1
A: Triosephosphate isomerase

A: Triosephosphate isomerase

B: Triosephosphate isomerase

B: Triosephosphate isomerase


Theoretical massNumber of molelcules
Total (without water)110,4264
Polymers110,4264
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_445x-y-1/3,-y-2/3,-z+1/31
crystal symmetry operation6_555-x,-x+y,-z1
crystal symmetry operation8_445-y-1/3,x-y-2/3,z+1/31
Buried area8550 Å2
ΔGint-69 kcal/mol
Surface area34160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)151.797, 151.797, 118.439
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Space group name HallR32"
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x-y,-y,-z
#5: -x,-x+y,-z
#6: y,x,-z
#7: x+1/3,y+2/3,z+2/3
#8: -y+1/3,x-y+2/3,z+2/3
#9: -x+y+1/3,-x+2/3,z+2/3
#10: x-y+1/3,-y+2/3,-z+2/3
#11: -x+1/3,-x+y+2/3,-z+2/3
#12: y+1/3,x+2/3,-z+2/3
#13: x+2/3,y+1/3,z+1/3
#14: -y+2/3,x-y+1/3,z+1/3
#15: -x+y+2/3,-x+1/3,z+1/3
#16: x-y+2/3,-y+1/3,-z+1/3
#17: -x+2/3,-x+y+1/3,-z+1/3
#18: y+2/3,x+1/3,-z+1/3

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Components

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


Mass: 27606.562 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) candidate division SR1 bacterium RAAC1_SR1_1 (bacteria)
Gene: tpiA, P148_SR1C00001G0257 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A288DKP7, triose-phosphate isomerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.39 Å3/Da / Density % sol: 48.49 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / Details: 2.3 M DL-Malic acid pH 7.0

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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 Å
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: 2.09→45.82 Å / Num. obs: 30881 / % possible obs: 99.2 % / Redundancy: 20.3 % / Biso Wilson estimate: 31.73 Å2 / CC1/2: 0.999 / Net I/σ(I): 12.74
Reflection shellResolution: 2.09→2.22 Å / Num. unique obs: 4732 / CC1/2: 0.83

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1b9b

1b9b


Resolution: 2.09→44 Å / SU ML: 0.2863 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 39.405
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2891 1984 6.47 %
Rwork0.2363 28697 -
obs0.2397 30681 99.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.73 Å2
Refinement stepCycle: LAST / Resolution: 2.09→44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3582 0 0 112 3694
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00693642
X-RAY DIFFRACTIONf_angle_d0.8944947
X-RAY DIFFRACTIONf_chiral_restr0.0531580
X-RAY DIFFRACTIONf_plane_restr0.0061643
X-RAY DIFFRACTIONf_dihedral_angle_d5.7841513
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.09-2.150.53941350.4051923X-RAY DIFFRACTION93.55
2.15-2.210.40551390.38112022X-RAY DIFFRACTION99.91
2.21-2.270.41241420.36572048X-RAY DIFFRACTION99.73
2.27-2.340.43981430.33962054X-RAY DIFFRACTION99.86
2.34-2.430.37061390.31872018X-RAY DIFFRACTION99.91
2.43-2.520.35771430.29642065X-RAY DIFFRACTION99.86
2.52-2.640.36251400.29082027X-RAY DIFFRACTION99.77
2.64-2.780.33811430.27672059X-RAY DIFFRACTION99.86
2.78-2.950.31961410.24472063X-RAY DIFFRACTION99.68
2.95-3.180.28431410.23022052X-RAY DIFFRACTION99.95
3.18-3.50.2921420.20632055X-RAY DIFFRACTION99.59
3.5-4.010.23081430.17562082X-RAY DIFFRACTION99.82
4.01-5.050.19211450.16752076X-RAY DIFFRACTION100
5.05-440.23031480.20822153X-RAY DIFFRACTION99.91

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