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- PDB-7rcq: Crystal structure of triosephosphate isomerase from Ktedonobacter... -

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Basic information

Entry
Database: PDB / ID: 7rcq
TitleCrystal structure of triosephosphate isomerase from Ktedonobacter racemifer
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, 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
NITRATE ION / Triosephosphate isomerase
Similarity search - Component
Biological speciesKtedonobacter racemifer (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 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 Ktedonobacter racemifer
Authors: Vickers, C.J. / Patrick, W.M. / Fraga, D.
History
DepositionJul 7, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 13, 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)29,2634
Polymers29,0771
Non-polymers1863
Water4,864270
1
A: Triosephosphate isomerase
hetero molecules

A: Triosephosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,5268
Polymers58,1542
Non-polymers3726
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area4190 Å2
ΔGint-18 kcal/mol
Surface area18170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.580, 54.741, 74.843
Angle α, β, γ (deg.)90.000, 115.196, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-687-

HOH

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Components

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


Mass: 29076.879 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ktedonobacter racemifer (bacteria) / Gene: tpiA, Krac_9127 / Production host: Escherichia coli (E. coli) / References: UniProt: D6TR79, triose-phosphate isomerase
#2: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: NO3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 270 / 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: 2.06 Å3/Da / Density % sol: 40.25 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / Details: 0.2 M ammonium nitrate, 20 % w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: Agilent SuperNova / Wavelength: 1.5406 Å
DetectorType: AGILENT TITAN CCD / Detector: CCD / Date: Jul 28, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5406 Å / Relative weight: 1
ReflectionResolution: 1.7→13.18 Å / Num. obs: 25558 / % possible obs: 98.2 % / Redundancy: 3 % / Biso Wilson estimate: 10.33 Å2 / CC1/2: 0.998 / Net I/σ(I): 15.6
Reflection shellResolution: 1.7→1.73 Å / Num. unique obs: 1282 / CC1/2: 0.972

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4y8f

4y8f


Resolution: 1.7→13.18 Å / SU ML: 0.1574 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.776
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1892 1314 5.14 %
Rwork0.1578 24238 -
obs0.1594 25552 98.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 12.88 Å2
Refinement stepCycle: LAST / Resolution: 1.7→13.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1841 0 12 270 2123
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00621882
X-RAY DIFFRACTIONf_angle_d0.84712563
X-RAY DIFFRACTIONf_chiral_restr0.0548304
X-RAY DIFFRACTIONf_plane_restr0.0058336
X-RAY DIFFRACTIONf_dihedral_angle_d12.3331267
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.770.20011480.16752612X-RAY DIFFRACTION96.37
1.77-1.850.21971220.16562667X-RAY DIFFRACTION97.45
1.85-1.950.21461460.15972663X-RAY DIFFRACTION97.57
1.95-2.070.19731510.16142677X-RAY DIFFRACTION98.23
2.07-2.230.19841510.15632713X-RAY DIFFRACTION98.76
2.23-2.450.17141330.16492713X-RAY DIFFRACTION98.68
2.45-2.80.19021550.16372716X-RAY DIFFRACTION99.17
2.8-3.520.2061680.15562728X-RAY DIFFRACTION99.52
3.52-13.180.15611400.1472749X-RAY DIFFRACTION97.6

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