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- PDB-9qus: Triosephosphate isomerase of Rhodonellum psychrophilum -

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Basic information

Entry
Database: PDB / ID: 9qus
TitleTriosephosphate isomerase of Rhodonellum psychrophilum
ComponentsTriosephosphate isomerase
KeywordsISOMERASE / psychrophile / eurypsychrophile / triosephosphate / cold-active
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
Triosephosphate isomerase
Similarity search - Component
Biological speciesRhodonellum psychrophilum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsNowak, J.S. / Olesen, S. / Baerentsen, R.
Funding support Denmark, 1items
OrganizationGrant numberCountry
Independent Research Fund Denmark - Technology and Production Sciences9041-00123B Denmark
CitationJournal: Biochim Biophys Acta Proteins Proteom / Year: 2025
Title: Role of electrostatics in cold adaptation: A comparative study of eury- and stenopsychrophilic triose phosphate isomerase.
Authors: Nowak, J.S. / Olesen, S. / Tian, P. / Baerentsen, R.L. / Brodersen, D.E. / Otzen, D.E.
History
DepositionApr 11, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 14, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Triosephosphate isomerase
B: Triosephosphate isomerase


Theoretical massNumber of molelcules
Total (without water)54,8322
Polymers54,8322
Non-polymers00
Water5,116284
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3350 Å2
ΔGint-29 kcal/mol
Surface area19470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.751, 47.796, 196.022
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 / TIM / TPI / Triose-phosphate isomerase


Mass: 27416.045 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodonellum psychrophilum (bacteria) / Gene: tpiA, P872_01925 / Production host: Escherichia coli (E. coli) / References: UniProt: U5C6G9, triose-phosphate isomerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 284 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.04 Å3/Da / Density % sol: 39.7 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / Details: 0.2M lithium acetate 20% PEG3350 25% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.97623 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Apr 22, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97623 Å / Relative weight: 1
ReflectionResolution: 1.46→49.01 Å / Num. obs: 78225 / % possible obs: 99.06 % / Redundancy: 9.1 % / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.05237 / Rrim(I) all: 0.05549 / Net I/σ(I): 21.63
Reflection shellResolution: 1.46→1.48 Å / Redundancy: 7.2 % / Mean I/σ(I) obs: 0.94 / Num. unique obs: 16319 / CC1/2: 0.615 / CC star: 0.873 / Rrim(I) all: 1.779 / % possible all: 89.12

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→49.01 Å / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 36.5684
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.31 2012 2.77 %
Rwork0.2927 70691 -
obs0.2961 72703 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.09 Å2
Refinement stepCycle: LAST / Resolution: 1.5→49.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3850 0 0 284 4134
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00293918
X-RAY DIFFRACTIONf_angle_d0.49545288
X-RAY DIFFRACTIONf_chiral_restr0.0428594
X-RAY DIFFRACTIONf_plane_restr0.0041686
X-RAY DIFFRACTIONf_dihedral_angle_d15.0741428
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.540.68681470.65434979X-RAY DIFFRACTION96.85
1.54-1.580.58921350.55724932X-RAY DIFFRACTION96.88
1.58-1.630.48941410.48184981X-RAY DIFFRACTION97.02
1.63-1.680.42721400.42984986X-RAY DIFFRACTION96.85
1.68-1.740.40931390.40424991X-RAY DIFFRACTION96.74
1.74-1.810.43251400.37565002X-RAY DIFFRACTION96.94
1.81-1.890.39281420.36085022X-RAY DIFFRACTION96.89
1.89-1.990.35071450.33615053X-RAY DIFFRACTION96.88
1.99-2.110.33281410.32124980X-RAY DIFFRACTION96.83
2.11-2.280.32951480.30315081X-RAY DIFFRACTION96.73
2.28-2.510.28721450.28955059X-RAY DIFFRACTION96.77
2.51-2.870.30371450.27745072X-RAY DIFFRACTION96.9
2.87-3.610.28161500.24355164X-RAY DIFFRACTION96.99
3.61-49.010.22141540.21685389X-RAY DIFFRACTION96.59
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.8439669794430.0866060328163-0.2360542783352.058316029680.1983633544731.43844346225-0.02328643938340.00327338621585-0.05283662905250.0948989933968-0.001108588552650.2044926203590.0843943544989-0.165829360761-6.98859062491E-50.139192638169-0.004027280194820.002431070056040.2494090196330.006008997995960.08198108039449.6334398912-14.9529950115-12.3453676728
20.417590524128-0.0974283067956-0.03522727229480.8173414056740.3577944900990.174543839736-0.00682521819133-0.01324768803050.06938773364340.00272645139067-0.01834653850530.021603237281-0.0419077144555-0.0436417400280.01187403990360.1474374838740.00631695969274-0.008484599706280.2299844643820.008506447175110.10329677712316.60485622320.967029071874-13.5738098734
31.765580927950.4591959019250.0283930696031.676850380130.4109361153591.330152672960.01934834335350.0104162195976-0.2519834624540.00652971281668-0.03298904091980.04805886012320.116651469561-0.04095675205710.006277138206650.127222051123-0.005732575585450.01015720839160.2104367658020.009449042432920.095774280676620.1508378305-26.3045344356-36.752062151
40.7833025493580.00827009258026-0.3298216252490.4658202432170.04067104277530.743891011172-0.0218939026018-0.00743815695904-0.00564993405219-0.0127057435513-0.0219972414495-0.0681208933605-0.007968653151770.1692079976960.02627812829050.1238555022410.003588487262370.002414185431260.2696530466430.02592838079060.11128794709636.5367520037-20.4757720985-35.5504099167
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 21 through 76 )AA21 - 761 - 56
22chain 'A' and (resid 77 through 273 )AA77 - 27357 - 253
33chain 'B' and (resid 21 through 76 )BB21 - 761 - 56
44chain 'B' and (resid 77 through 273 )BB77 - 27357 - 253

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