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- PDB-7r9b: Crystal structure of Triosephosphate isomerase from Candidatus Ro... -

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Basic information

Entry
Database: PDB / ID: 7r9b
TitleCrystal structure of Triosephosphate isomerase from Candidatus Roizmanbacteria
ComponentsTriosephosphate isomerase
KeywordsISOMERASE / TIM / triosephosphate isomerase / glycolysis / gluconeogenesis
Function / homology
Function and homology information


triose-phosphate isomerase / triose-phosphate isomerase activity / glyceraldehyde-3-phosphate biosynthetic process / glycerol catabolic process / glycolytic process / gluconeogenesis / cytosol
Similarity search - Function
Triosephosphate isomerase / Triosephosphate isomerase superfamily / Triosephosphate isomerase / Triosephosphate isomerase (TIM) family profile. / Aldolase-type TIM barrel
Similarity search - Domain/homology
PHOSPHATE ION / Triosephosphate isomerase
Similarity search - Component
Biological speciesCandidatus Roizmanbacteria (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsVickers, C.J. / Patrick, W.M. / Fraga, D.
Funding support New Zealand, 1items
OrganizationGrant numberCountry
Royal Society of New Zealand New Zealand
CitationJournal: To Be Published
Title: Crystal structure of Triosephosphate isomerase from Candidatus Roizmanbacteria
Authors: Vickers, C.J. / Patrick, W.M. / Fraga, D.
History
DepositionJun 28, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 6, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7742
Polymers24,6791
Non-polymers951
Water1,36976
1
A: Triosephosphate isomerase
hetero molecules

A: Triosephosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,5484
Polymers49,3582
Non-polymers1902
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_765-x+2,-x+y+1,-z+1/31
Buried area3760 Å2
ΔGint-41 kcal/mol
Surface area16870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.937, 108.937, 41.015
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11A-445-

HOH

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Components

#1: Protein Triosephosphate isomerase


Mass: 24678.947 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candidatus Roizmanbacteria (bacteria) / Gene: A3B50_02135 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1F7J4N7, triose-phosphate isomerase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.85 Å3/Da / Density % sol: 56.79 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / Details: 0.1 M phosphate/citrate pH 4.2, 40% v/v PEG 300.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.95372 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Sep 30, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 2.2→41.01 Å / Num. obs: 14485 / % possible obs: 99.8 % / Redundancy: 20.5 % / Biso Wilson estimate: 39.87 Å2 / CC1/2: 1 / Net I/σ(I): 35.3
Reflection shellResolution: 2.2→2.26 Å / Num. unique obs: 1205 / CC1/2: 0.953

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YYA

1yya


Resolution: 2.2→37.61 Å / SU ML: 0.2569 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.1243
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2302 714 4.93 %
Rwork0.1872 13758 -
obs0.1892 14472 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.92 Å2
Refinement stepCycle: LAST / Resolution: 2.2→37.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1698 0 5 76 1779
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00731738
X-RAY DIFFRACTIONf_angle_d0.94022365
X-RAY DIFFRACTIONf_chiral_restr0.0555272
X-RAY DIFFRACTIONf_plane_restr0.0063306
X-RAY DIFFRACTIONf_dihedral_angle_d13.2654231
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.370.2891540.21842678X-RAY DIFFRACTION98.92
2.37-2.60.26341520.21072715X-RAY DIFFRACTION100
2.6-2.980.2581020.2192783X-RAY DIFFRACTION100
2.98-3.760.26241450.19182757X-RAY DIFFRACTION99.97
3.76-37.610.19061610.16412825X-RAY DIFFRACTION100

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