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- PDB-9quu: Triosephosphate isomerase of Rhodococcus sp. JG-3 -

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Basic information

Entry
Database: PDB / ID: 9quu
TitleTriosephosphate isomerase of Rhodococcus sp. JG-3
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 speciesRhodococcus sp. JG-3 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.63 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,6165
Polymers54,4482
Non-polymers1683
Water5,909328
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Elutes as homodimer from Superdex 200 10/300 GL Inc
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3920 Å2
ΔGint-40 kcal/mol
Surface area18830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.102, 86.102, 152.835
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

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


Mass: 27223.996 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodococcus sp. JG-3 (bacteria) / Gene: tpiA, EOP29_15510 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A520EUU7, triose-phosphate isomerase
#2: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 328 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.6 Å3/Da / Density % sol: 52.71 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop
Details: 17% (w/v) PEG 10,000 100 mM Bis-Tris/ Hydrochloric acid pH 5.5 100 mM Ammonium acetat

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Apr 13, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.63→47.62 Å / Num. obs: 69600 / % possible obs: 87.09 % / Redundancy: 20.3 % / Biso Wilson estimate: 38.95 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.0869 / Rrim(I) all: 0.08876 / Net I/σ(I): 22.55
Reflection shellResolution: 1.63→1.68 Å / Mean I/σ(I) obs: 0.09 / Num. unique obs: 9619 / CC1/2: 0.0257 / CC star: 0.224 / Rrim(I) all: 9.223 / % possible all: 2.68

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.63→47.62 Å / SU ML: 0.2816 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.5337
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2127 1803 2.88 %
Rwork0.1942 60757 -
obs0.1947 62560 87.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.96 Å2
Refinement stepCycle: LAST / Resolution: 1.63→47.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3765 0 10 328 4103
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063823
X-RAY DIFFRACTIONf_angle_d0.73275186
X-RAY DIFFRACTIONf_chiral_restr0.0499619
X-RAY DIFFRACTIONf_plane_restr0.0055673
X-RAY DIFFRACTIONf_dihedral_angle_d18.76631368
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.63-1.680.978230.9791143X-RAY DIFFRACTION2.69
1.68-1.730.6816680.67062091X-RAY DIFFRACTION39.91
1.73-1.780.52311380.52414630X-RAY DIFFRACTION87.45
1.78-1.850.42431560.40035286X-RAY DIFFRACTION99.76
1.85-1.920.33641560.29615298X-RAY DIFFRACTION99.87
1.92-2.010.30161580.22975293X-RAY DIFFRACTION100
2.01-2.110.23951570.20875333X-RAY DIFFRACTION100
2.11-2.250.20841580.20285342X-RAY DIFFRACTION100
2.25-2.420.21191580.19345339X-RAY DIFFRACTION100
2.42-2.660.2171590.18875370X-RAY DIFFRACTION99.98
2.66-3.050.20651600.20095420X-RAY DIFFRACTION100
3.05-3.840.19821630.17885482X-RAY DIFFRACTION100
3.84-47.620.16891690.14085730X-RAY DIFFRACTION99.98
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)
13.869674301270.8468094367991.562123281933.035644749630.9822397000111.30031425124-0.0713286164540.007469269721570.02877003166110.135675295640.0720403464898-0.194389454535-0.0912468587210.228992711609-0.003067638617770.3385329710270.0399013636005-0.04418458136910.3133370685410.006461091973140.1951580576183.37147268799-28.0827107576-4.98895773985
28.077796682192.597607417173.248747030772.691072441331.366811632983.40020577275-0.1653115083740.3726484144090.077177752101-0.07448280754460.218450236752-0.24689618471-0.1663175327770.446418303521-0.04638239536190.2610380713530.01852399979330.02391602540810.2662747294810.0181055844050.2098934618321.05709603101-26.3344358117-13.3894875703
33.40946786524-0.953872933652-0.1219339490692.805220765370.01575303066291.67659642663-0.01653757475150.290728069068-0.5438681134460.004817330918090.141728342469-0.376662716520.4668955234980.5107324959-0.09470526672990.3552131385870.0983649428612-0.04082669424820.431140024842-0.1447403380810.3928506456046.81878617534-42.4745605371-18.9373357756
44.27991954035-1.038511143863.65383285183.88094852455-4.241031574436.98894227424-0.2539120673110.181468410218-0.42653769731-0.327629865868-0.190667170221-1.08549913380.751089224770.986988339040.4550098691230.4496444761350.1789308708490.05062843081810.737710902694-0.1778706578240.90961117426120.7626225826-44.1105660489-20.2937029715
54.2394124374-0.432881782701-1.653182688982.654887843230.9342864647415.68496825494-0.0660944538867-0.0573710280465-0.1009850138390.2589225353970.172858254329-0.7242070993590.02172892034630.894774724444-0.09025210998050.3264926112420.090244306189-0.1206416983640.522492709137-0.06053668461850.49313733697315.9769310227-34.7585641596-8.008542416
64.705227277634.313849371110.02758757505414.87470521056-0.9782824095321.183934178820.1417459124430.0939534321130.5374314033290.1992675540740.05701844619970.632176896721-0.113598894201-0.0638330696934-0.1975397479130.3157376032870.023227347556-0.01474055775910.186703580363-0.0003472676559930.260409692375-25.3578150999-31.6567755094-19.2724897207
71.75051448173-2.522072954430.8126152054823.84891408071-0.668873411815.448911225670.08650828277670.6762100575240.842647530078-0.0548882101454-0.1359288445520.321907767149-0.5600466370480.0427101351485-0.008842884889490.409619193809-0.00327783819422-0.05247311194320.2843449971620.01771167691770.328958953774-20.9368725588-18.8052874643-21.0747040442
89.089176416550.6677610762441.675568754412.300540077210.7156512624252.75322571111-0.176634157666-0.6240597292970.4646696669640.127209969014-0.06633121970270.571727055402-0.189230718717-0.2471441589230.2550088160890.3678947504370.042831964103-0.003480889776680.212574470219-0.02310052875530.318397816892-25.1331300637-23.9206535142-14.0070525592
97.98124704174-1.499384953311.917383365912.650757683130.1881345427092.7411166631-0.18557063384-0.379485870548-0.1423954691180.5199363855370.193201847207-0.00956460409628-0.006195314901610.000938044612534-0.01798948702980.330000480216-0.0200395354760.03118815058470.2220702763610.0002662603819650.150664982363-15.3589342436-33.7576355143-9.47769948118
102.076772693310.7431614889411.185523369382.661869926261.197632574951.890826804740.115235867608-0.0273442008906-0.2547275229690.303142407811-0.03569198291720.2243907286580.416541172288-0.00352652004452-0.07064122266720.3345533834130.0008632792869480.02650711908730.2293728798540.01297020001560.322225585708-24.157411936-45.4843349907-16.1305711263
115.82002500156-0.7948478221612.985929678510.729710328331-1.111316776532.42423880866-0.172373267567-0.15880656009-0.365431925596-0.0473192357941-0.3746435143080.4808795175210.955433091531-0.5256310686680.5257498231630.442786741742-0.03585133170470.1035540482830.293077729164-0.07345673135220.653403658844-37.8746868483-49.3584212796-16.972550594
124.131856339281.05917800533-0.2374167449677.83258080765-4.920272344186.299667200290.763134245683-0.6550478767450.2449097636011.141306529760.1745199373391.22236053494-0.5976153508640.186825682983-0.9472978192810.364187672723-0.04172844879340.135749333570.272489928166-0.01418143217030.446223671983-36.3369748551-43.3099377491-11.2940639406
135.373010166393.70834644844-3.644319954056.13258356182-4.772114365796.221007768420.09563567793680.2617964069980.287271706751-0.6250262389990.3583043420570.827506045914-0.00615241372046-0.460808786586-0.433773118340.4240850643080.0433361090059-0.04663455415590.281908729172-0.02962392228740.537280312516-37.4695583777-36.7685598256-25.4543325487
145.168552729943.49801881432-2.82370883838.573452739870.4806617045815.42064081553-0.1695312641810.4529207754530.498841236366-0.6575586588610.03124697680530.556664476582-0.239526173574-0.2468655925430.164370325040.3377443361370.0467131496879-0.06975990873640.270325494624-0.005770589531870.364088972735-30.665157931-28.1261716885-24.7285393178
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 2 through 30 )AA2 - 301 - 29
22chain 'A' and (resid 31 through 84 )AA31 - 8430 - 83
33chain 'A' and (resid 85 through 184 )AA85 - 18484 - 183
44chain 'A' and (resid 185 through 203 )AA185 - 203184 - 202
55chain 'A' and (resid 204 through 259 )AA204 - 259203 - 258
66chain 'B' and (resid 2 through 16 )BC2 - 161 - 15
77chain 'B' and (resid 17 through 30 )BC17 - 3016 - 29
88chain 'B' and (resid 31 through 59 )BC31 - 5930 - 58
99chain 'B' and (resid 60 through 84 )BC60 - 8459 - 83
1010chain 'B' and (resid 85 through 184 )BC85 - 18484 - 183
1111chain 'B' and (resid 185 through 202 )BC185 - 202184 - 201
1212chain 'B' and (resid 203 through 216 )BC203 - 216202 - 215
1313chain 'B' and (resid 217 through 234 )BC217 - 234216 - 233
1414chain 'B' and (resid 235 through 257 )BC235 - 257234 - 256

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