[English] 日本語
Yorodumi
- PDB-5wu7: Crystal structure of GH57-type branching enzyme from hyperthermop... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5wu7
TitleCrystal structure of GH57-type branching enzyme from hyperthermophilic archaeon Pyrococcus horikoshii
ComponentsUncharacterized protein
KeywordsHYDROLASE / enzyme / amylase / glycogen branching enzyme
Function / homology
Function and homology information


alpha-glucan biosynthetic process / 1,4-alpha-glucan branching enzyme activity
Similarity search - Function
1,4-alpha-glucan branching enzyme, C-terminal / Glycoside hydrolase families 57, central domain / 1,4-alpha-glucan branching enzyme MT3115-like / 1,4-alpha-glucan branching enzyme, C-terminal / immunoglobulin/albumin-binding domain-like / Families 57/38 glycoside transferase, middle domain / Glycoside hydrolase family 57, N-terminal domain / Glycosyl hydrolase family 57 / Glycoside hydrolase 38, N terminal domain / 7-stranded beta/alpha barrel ...1,4-alpha-glucan branching enzyme, C-terminal / Glycoside hydrolase families 57, central domain / 1,4-alpha-glucan branching enzyme MT3115-like / 1,4-alpha-glucan branching enzyme, C-terminal / immunoglobulin/albumin-binding domain-like / Families 57/38 glycoside transferase, middle domain / Glycoside hydrolase family 57, N-terminal domain / Glycosyl hydrolase family 57 / Glycoside hydrolase 38, N terminal domain / 7-stranded beta/alpha barrel / Glycoside hydrolase 38, N-terminal domain superfamily / Glycoside hydrolase families 57/38, central domain superfamily / Glycoside hydrolase/deacetylase, beta/alpha-barrel / Alpha-Beta Barrel / Up-down Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Uncharacterized protein
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.31 Å
AuthorsNa, S. / Jo, I. / Ha, N.-C.
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2017
Title: Structural basis for the transglycosylase activity of a GH57-type glycogen branching enzyme from Pyrococcus horikoshii.
Authors: Na, S. / Park, M. / Jo, I. / Cha, J. / Ha, N.C.
History
DepositionDec 16, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 8, 2017Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)134,0614
Polymers133,8772
Non-polymers1842
Water1,72996
1
A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,0312
Polymers66,9391
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,0312
Polymers66,9391
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)120.857, 42.326, 122.227
Angle α, β, γ (deg.)90.00, 90.96, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Uncharacterized protein / 1 / 4-alpha-glucan-branching protein


Mass: 66938.508 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: GOL
Source: (gene. exp.) Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3) (archaea)
Strain: ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3
Gene: PH1386 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: O50094
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 96 / 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: 2.33 Å3/Da / Density % sol: 47.32 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 9.3
Details: 20 mM citric acid, 10% (w/v) PEG 3350, 80 mM Bis-Tris propane pH 9.3, 2 mM tris (2-carboxyethyl) phosphine

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9796 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 2, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2.3→33.521 Å / Num. obs: 44048 / % possible obs: 95 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 10.2
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.383 / Mean I/σ(I) obs: 2.08 / % possible all: 72.1

-
Processing

Software
NameVersionClassification
PHENIX(1.11_2567)refinement
DENZOdata reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3N8T
Resolution: 2.31→33.521 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.45 / Phase error: 26.84
RfactorNum. reflection% reflection
Rfree0.2597 2249 5.11 %
Rwork0.1998 --
obs0.2028 44048 79.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.31→33.521 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8901 0 12 96 9009
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0039182
X-RAY DIFFRACTIONf_angle_d0.55412401
X-RAY DIFFRACTIONf_dihedral_angle_d4.4325375
X-RAY DIFFRACTIONf_chiral_restr0.0411246
X-RAY DIFFRACTIONf_plane_restr0.0051574
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3098-2.36010.37640.24631269X-RAY DIFFRACTION39
2.3601-2.41490.3432840.2481572X-RAY DIFFRACTION49
2.4149-2.47530.3424820.23611720X-RAY DIFFRACTION52
2.4753-2.54220.3172950.23451884X-RAY DIFFRACTION58
2.5422-2.6170.31971130.24332042X-RAY DIFFRACTION63
2.617-2.70140.31851250.24562212X-RAY DIFFRACTION68
2.7014-2.79790.30631610.24472399X-RAY DIFFRACTION74
2.7979-2.90990.31841370.23542665X-RAY DIFFRACTION82
2.9099-3.04230.28981680.22792939X-RAY DIFFRACTION90
3.0423-3.20250.28771960.22023223X-RAY DIFFRACTION99
3.2025-3.4030.26791920.22223207X-RAY DIFFRACTION100
3.403-3.66550.25581230.20133324X-RAY DIFFRACTION100
3.6655-4.03380.25882120.18173254X-RAY DIFFRACTION100
4.0338-4.61620.20871690.16793328X-RAY DIFFRACTION100
4.6162-5.8110.23181570.16943324X-RAY DIFFRACTION99
5.811-33.52410.19651710.17273437X-RAY DIFFRACTION99

+
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