[English] 日本語
Yorodumi
- PDB-2cnb: Trypanosoma brucei UDP-galactose-4-epimerase in ternary complex w... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2cnb
TitleTrypanosoma brucei UDP-galactose-4-epimerase in ternary complex with NAD and the substrate analogue UDP-4-deoxy-4-fluoro-alpha-D-galactose
ComponentsUDP-GALACTOSE-4-EPIMERASE
KeywordsEPIMERASE / SHORT-CHAIN DEHYDROGENASE/REDUCTASE / UDP-GALACTOSE-4- EPIMERASE / NAD / ISOMERASE / TRYPANOSOMA BRUCEI / UDP-4-DEOXY- 4-FLUORO-ALPHA-D-GALACTOSE
Function / homology
Function and homology information


UDP-glucose 4-epimerase / UDP-glucose 4-epimerase activity / galactose metabolic process / glycosome / nucleotide binding
Similarity search - Function
UDP-glucose 4-epimerase / UDP-galactose 4-epimerase, domain 1 / UDP-galactose 4-epimerase; domain 1 / NAD-dependent epimerase/dehydratase / NAD dependent epimerase/dehydratase family / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Chem-UFG / UDP-glucose 4-epimerase
Similarity search - Component
Biological speciesTRYPANOSOMA BRUCEI (eukaryote)
MethodX-RAY DIFFRACTION / OTHER / Resolution: 2.7 Å
AuthorsAlphey, M.S. / Ferguson, M.A.J. / Hunter, W.N.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2006
Title: Trypanosoma Brucei Udp-Galactose-4-Epimerase in Ternary Complex with Nad+ and the Substrate Analogue Udp-4-Deoxy-4-Fluoro-Alpha-D-Galactose
Authors: Alphey, M.S. / Burton, A. / Urbaniak, M. / Boons, G.J. / Ferguson, M.A.J. / Hunter, W.N.
History
DepositionMay 18, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 12, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: UDP-GALACTOSE-4-EPIMERASE
B: UDP-GALACTOSE-4-EPIMERASE
C: UDP-GALACTOSE-4-EPIMERASE
D: UDP-GALACTOSE-4-EPIMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,15312
Polymers175,2264
Non-polymers4,9278
Water7,494416
1
A: UDP-GALACTOSE-4-EPIMERASE
B: UDP-GALACTOSE-4-EPIMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,0776
Polymers87,6132
Non-polymers2,4634
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
C: UDP-GALACTOSE-4-EPIMERASE
D: UDP-GALACTOSE-4-EPIMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,0776
Polymers87,6132
Non-polymers2,4634
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)101.724, 111.694, 160.873
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.3229, 0.8009, 0.5043), (0.7888, -0.06665, 0.611), (0.523, 0.5951, -0.6102)-7.992, -57.25, 98.81
2given(-0.9985, -0.04752, 0.02796), (0.04747, -0.9989, -0.00274), (0.02806, -0.001409, 0.9996)101.7, 111, 21.84
3given(0.351, -0.7873, 0.5069), (-0.7775, 0.05667, 0.6264), (-0.5219, -0.6139, -0.5922)58.63, 28.39, 204.3

-
Components

#1: Protein
UDP-GALACTOSE-4-EPIMERASE


Mass: 43806.547 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) TRYPANOSOMA BRUCEI (eukaryote) / Plasmid: PET15B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q8T8E9, UDP-glucose 4-epimerase
#2: Chemical
ChemComp-UFG / URIDINE-5'-DIPHOSPHATE-4-DEOXY-4-FLUORO-ALPHA-D-GALACTOSE


Mass: 568.293 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H23FN2O16P2
#3: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 416 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsSER -1 AND HIS 0 IN EACH SUBUNIT CORRESPOND TO A VISIBLE FRAGMENT OF THE 6HIS AFFINITY TAG USED FOR ...SER -1 AND HIS 0 IN EACH SUBUNIT CORRESPOND TO A VISIBLE FRAGMENT OF THE 6HIS AFFINITY TAG USED FOR PURIFICATION

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3 Å3/Da / Density % sol: 58.7 %
Crystal growpH: 8
Details: 8% PEG 8000, 200MM KCL, 50MM NA2B4O7, 5% GLYCEROL, PH 8.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418
DetectorType: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Date: Nov 11, 2005 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→92 Å / Num. obs: 49501 / % possible obs: 96.8 % / Observed criterion σ(I): 2 / Redundancy: 4.5 % / Biso Wilson estimate: 64.7 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 15.2
Reflection shellResolution: 2.7→2.77 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 2.4 / % possible all: 78.9

-
Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: OTHER / Resolution: 2.7→91.67 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.906 / SU B: 15.525 / SU ML: 0.309 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.402 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.281 2454 5.05 %RANDOM
Rwork0.199 ---
obs0.203 48640 95.3 %-
Solvent computationIon probe radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 48.29 Å2
Baniso -1Baniso -2Baniso -3
1-3.481 Å20 Å20 Å2
2--0.428 Å20 Å2
3----3.909 Å2
Refinement stepCycle: LAST / Resolution: 2.7→91.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11348 0 320 416 12084
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02212058
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4641.99216409
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.20651477
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.01223.063542
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.99151936
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6171598
X-RAY DIFFRACTIONr_chiral_restr0.0990.21803
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.029134
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.220.26045
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3140.28051
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1710.2699
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2260.241
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1870.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6241.57444
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.135211752
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.43935159
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.2664.54644
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 11.98→91.67 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.267 21
Rwork0.224 466

+
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