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- PDB-7n8u: Crystal structure of Triosephosphate isomerase from Candidatus Pr... -

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Basic information

Entry
Database: PDB / ID: 7n8u
TitleCrystal structure of Triosephosphate isomerase from Candidatus Prometheoarchaeum syntrophicum
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, 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 speciesCandidatus Prometheoarchaeum syntrophicum (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 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: Structure of PsyTPI - Candidatus Prometheoarchaeum syntrophicum triosephosphate isomerase.
Authors: Vickers, C.J. / Patrick, W.M. / Fraga, D.
History
DepositionJun 15, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 15, 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
B: Triosephosphate isomerase


Theoretical massNumber of molelcules
Total (without water)58,1992
Polymers58,1992
Non-polymers00
Water8,665481
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3320 Å2
ΔGint-21 kcal/mol
Surface area19710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.289, 121.350, 129.263
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Triosephosphate isomerase


Mass: 29099.555 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candidatus Prometheoarchaeum syntrophicum (archaea)
Gene: tpiA, DSAG12_02076 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A5B9DC34, triose-phosphate isomerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 481 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsThe sequence annotated as insertion is actually the actual start site of the gene. It is not ...The sequence annotated as insertion is actually the actual start site of the gene. It is not present in the UniProt sequence used for the sequence reference.

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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: 2.58 Å3/Da / Density % sol: 52.32 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 25 % v/v Polyethylene glycol monomethyl ether 550, 50 mM HEPES; pH 7.0, 10 mM Magnesium chloride

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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: 1.98→44.24 Å / Num. obs: 43128 / % possible obs: 99.8 % / Redundancy: 13.5 % / Biso Wilson estimate: 25.22 Å2 / CC1/2: 0.999 / Net I/σ(I): 20.1
Reflection shellResolution: 1.98→2.1 Å / Num. unique obs: 6790 / CC1/2: 0.921

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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: 1.98→44.24 Å / SU ML: 0.1492 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.0693
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2067 1989 4.61 %
Rwork0.1658 41131 -
obs0.1678 43120 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.31 Å2
Refinement stepCycle: LAST / Resolution: 1.98→44.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3904 0 0 481 4385
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073958
X-RAY DIFFRACTIONf_angle_d0.86175360
X-RAY DIFFRACTIONf_chiral_restr0.0542637
X-RAY DIFFRACTIONf_plane_restr0.0057693
X-RAY DIFFRACTIONf_dihedral_angle_d9.2242551
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.98-2.030.24531450.2052843X-RAY DIFFRACTION97.46
2.03-2.080.22311230.17212890X-RAY DIFFRACTION100
2.08-2.140.19731450.16372902X-RAY DIFFRACTION100
2.14-2.210.2051400.16012883X-RAY DIFFRACTION99.93
2.21-2.290.23391490.16552888X-RAY DIFFRACTION100
2.29-2.380.19711200.1562956X-RAY DIFFRACTION100
2.38-2.490.21231550.16822868X-RAY DIFFRACTION100
2.49-2.620.23941380.17492911X-RAY DIFFRACTION99.93
2.62-2.790.19761410.16752940X-RAY DIFFRACTION99.97
2.79-30.21041420.16772945X-RAY DIFFRACTION99.94
3-3.30.22841460.17012942X-RAY DIFFRACTION100
3.3-3.780.18871470.16142985X-RAY DIFFRACTION100
3.78-4.760.16681410.14663018X-RAY DIFFRACTION99.97
4.76-44.240.22751570.17923160X-RAY DIFFRACTION99.94

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