[English] 日本語
Yorodumi
- PDB-5b7z: Crystal Structure of Hyperthermophilic Thermotoga maritima L-Keto... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5b7z
TitleCrystal Structure of Hyperthermophilic Thermotoga maritima L-Ketose-3-Epimerase with Ni2+
ComponentsUncharacterized protein TM_0416
KeywordsISOMERASE / epimerase / Ni2+ / hyperthermophilic / eubacterium
Function / homology
Function and homology information


Isomerases; Intramolecular oxidoreductases; Interconverting aldoses and ketoses, and related compounds / Isomerases; Racemases and epimerases; Acting on carbohydrates and derivatives / racemase and epimerase activity, acting on carbohydrates and derivatives / inositol metabolic process / manganese ion binding / carbohydrate metabolic process
Similarity search - Function
Divalent-metal-dependent TIM barrel enzymes / Xylose isomerase-like, TIM barrel domain / Xylose isomerase-like TIM barrel / Xylose isomerase-like superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Chem-1PG / NICKEL (II) ION / 5-keto-L-gluconate epimerase
Similarity search - Component
Biological speciesThermotoga maritima MSB8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsCao, T.P. / Shin, S.M. / Lee, D.W. / Lee, S.H.
Funding support Korea, Republic Of, 2items
OrganizationGrant numberCountry
National Research Foundation2013R1A1A2057465 Korea, Republic Of
National Research Foundation2014R1A2A2A01006765 Korea, Republic Of
CitationJournal: Appl. Environ. Microbiol. / Year: 2017
Title: TM0416, a Hyperthermophilic Promiscuous Nonphosphorylated Sugar Isomerase, Catalyzes Various C5and C6Epimerization Reactions
Authors: Shin, S.M. / Cao, T.P. / Choi, J.M. / Kim, S.B. / Lee, S.J. / Lee, S.H. / Lee, D.W.
History
DepositionJun 10, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 15, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.2May 2, 2018Group: Data collection / Database references / Category: citation / Item: _citation.title
Revision 1.3Nov 8, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Uncharacterized protein TM_0416
B: Uncharacterized protein TM_0416
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,07213
Polymers65,3552
Non-polymers1,71711
Water12,070670
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4870 Å2
ΔGint-32 kcal/mol
Surface area22460 Å2
Unit cell
Length a, b, c (Å)50.225, 55.220, 58.693
Angle α, β, γ (deg.)107.16, 102.23, 92.35
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein Uncharacterized protein TM_0416 / L-Ketose-3-Epimerase


Mass: 32677.482 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima MSB8 (bacteria) / Strain: MSB8 / Gene: TM_0416 / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q9WYP7
#2: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#4: Chemical
ChemComp-1PG / 2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL / Polyethylene glycol


Mass: 252.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H24O6
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 670 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.31 Å3/Da / Density % sol: 46.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 100mM MES, 5%(w/w) PEG1000, 20%(v/v) PEG200

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9796 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 3, 2016
RadiationMonochromator: DCM Si (111) Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 90302 / % possible obs: 96 % / Redundancy: 3.5 % / Net I/σ(I): 13.27
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 3.13 / % possible all: 92.8

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data processing
MOLREPphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5B7Y

5b7y


Resolution: 1.5→41.513 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 20.32
RfactorNum. reflection% reflection
Rfree0.1972 4399 5.07 %
Rwork0.1722 --
obs0.1735 86681 91.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.5→41.513 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4264 0 105 670 5039
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074449
X-RAY DIFFRACTIONf_angle_d1.1125968
X-RAY DIFFRACTIONf_dihedral_angle_d14.1571687
X-RAY DIFFRACTIONf_chiral_restr0.046668
X-RAY DIFFRACTIONf_plane_restr0.005756
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4973-1.51430.2817880.21931635X-RAY DIFFRACTION56
1.5143-1.53210.2373900.22091999X-RAY DIFFRACTION66
1.5321-1.55080.29241150.21232153X-RAY DIFFRACTION72
1.5508-1.57040.24921520.20872399X-RAY DIFFRACTION80
1.5704-1.59110.23841230.21152552X-RAY DIFFRACTION85
1.5911-1.61290.27041610.2072655X-RAY DIFFRACTION91
1.6129-1.63590.26741520.20192803X-RAY DIFFRACTION93
1.6359-1.66030.24971520.19662834X-RAY DIFFRACTION95
1.6603-1.68630.19761380.18812820X-RAY DIFFRACTION95
1.6863-1.71390.18721440.18432876X-RAY DIFFRACTION96
1.7139-1.74350.23041590.17542843X-RAY DIFFRACTION96
1.7435-1.77520.22861620.18262873X-RAY DIFFRACTION96
1.7752-1.80930.19621280.17792883X-RAY DIFFRACTION96
1.8093-1.84630.22551590.17772851X-RAY DIFFRACTION96
1.8463-1.88640.221560.17462884X-RAY DIFFRACTION96
1.8864-1.93030.17681560.17392862X-RAY DIFFRACTION96
1.9303-1.97860.20481320.17192881X-RAY DIFFRACTION96
1.9786-2.0320.2041560.17222877X-RAY DIFFRACTION97
2.032-2.09180.20581530.16832880X-RAY DIFFRACTION97
2.0918-2.15940.18821580.16712867X-RAY DIFFRACTION97
2.1594-2.23650.19011570.16442896X-RAY DIFFRACTION97
2.2365-2.32610.19231670.16552903X-RAY DIFFRACTION98
2.3261-2.43190.22191470.1682932X-RAY DIFFRACTION97
2.4319-2.56010.18531500.17212896X-RAY DIFFRACTION98
2.5601-2.72050.19051530.16952924X-RAY DIFFRACTION98
2.7205-2.93050.19521660.16742939X-RAY DIFFRACTION98
2.9305-3.22530.18461590.16962876X-RAY DIFFRACTION97
3.2253-3.69170.17821660.15712854X-RAY DIFFRACTION96
3.6917-4.65020.15871470.15332737X-RAY DIFFRACTION92
4.6502-41.52860.18191530.17462898X-RAY DIFFRACTION97

+
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