[English] 日本語
Yorodumi
- PDB-9quu: Triosephosphate isomerase of Rhodococcus sp. JG-3 -

+
Open data


ID or keywords:

Loading...

-
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 / gluconeogenesis / glycolytic process / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more