[English] 日本語
Yorodumi
- PDB-3we7: Crystal Structure of Diacetylchitobiose Deacetylase from Pyrococc... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3we7
TitleCrystal Structure of Diacetylchitobiose Deacetylase from Pyrococcus horikoshii
ComponentsPutative uncharacterized protein PH0499
KeywordsHYDROLASE / Rossmann Fold / Zinc Binding / Deacetylation
Function / homology
Function and homology information


N-acetylglucosaminylphosphatidylinositol deacetylase activity / GPI anchor biosynthetic process / metal ion binding
Similarity search - Function
LmbE-like / N-acetylglucosaminyl phosphatidylinositol deacetylase-related / Putative deacetylase LmbE-like domain superfamily / GlcNAc-PI de-N-acetylase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETIC ACID / HEXANE-1,6-DIOL / Diacetylchitobiose deacetylase
Similarity search - Component
Biological speciesPyrococcus horikoshii OT3 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.55 Å
AuthorsMine, S. / Nakamura, T. / Fukuda, Y. / Inoue, T. / Uegaki, K. / Sato, T.
CitationJournal: Febs J. / Year: 2014
Title: Expression from engineered Escherichia coli chromosome and crystallographic study of archaeal N,N'-diacetylchitobiose deacetylase
Authors: Mine, S. / Niiyama, M. / Hashimoto, W. / Ikegami, T. / Koma, D. / Ohmoto, T. / Fukuda, Y. / Inoue, T. / Abe, Y. / Ueda, T. / Morita, J. / Uegaki, K. / Nakamura, T.
History
DepositionJul 1, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 7, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 20, 2014Group: Database references

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Putative uncharacterized protein PH0499
B: Putative uncharacterized protein PH0499
C: Putative uncharacterized protein PH0499
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,16619
Polymers94,9033
Non-polymers1,26316
Water9,854547
1
A: Putative uncharacterized protein PH0499
B: Putative uncharacterized protein PH0499
C: Putative uncharacterized protein PH0499
hetero molecules

A: Putative uncharacterized protein PH0499
B: Putative uncharacterized protein PH0499
C: Putative uncharacterized protein PH0499
hetero molecules


Theoretical massNumber of molelcules
Total (without water)192,33238
Polymers189,8056
Non-polymers2,52732
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_765-x+2,-x+y+1,-z+2/31
Buried area35430 Å2
ΔGint-201 kcal/mol
Surface area52590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.372, 77.372, 230.223
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

-
Components

-
Protein , 1 types, 3 molecules ABC

#1: Protein Putative uncharacterized protein PH0499


Mass: 31634.182 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii OT3 (archaea)
Strain: ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3
Gene: PH0499 / Production host: Escherichia coli (E. coli) / References: UniProt: O58235

-
Non-polymers , 6 types, 563 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H4O2
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Chemical
ChemComp-HEZ / HEXANE-1,6-DIOL


Mass: 118.174 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 547 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.1 Å3/Da / Density % sol: 41.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.01M cobaltous chloride hexahydrate, 0.1M sodium acetate trihydrate, 1.0M 1,6 hexanediol, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

-
Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 0.97895, 0.97926, 0.99498
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.978951
20.979261
30.994981
ReflectionResolution: 1.55→50 Å / Num. obs: 115813

-
Processing

SoftwareName: REFMAC / Version: 5.6.0117 / Classification: refinement
RefinementMethod to determine structure: MAD / Resolution: 1.55→29.62 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.962 / SU B: 1.686 / SU ML: 0.06 / Cross valid method: THROUGHOUT / ESU R: 0.083 / ESU R Free: 0.085 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.20733 5792 5 %RANDOM
Rwork0.17328 ---
obs0.17501 109668 98.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.253 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.55→29.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6570 0 73 547 7190
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.026917
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.3461.9769363
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4235822
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.18923.824340
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.469151187
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0331545
X-RAY DIFFRACTIONr_chiral_restr0.1790.2987
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.0215327
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded8.30253
LS refinement shellResolution: 1.55→1.588 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.338 383 -
Rwork0.31 7495 -
obs--96.98 %

+
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://pdbjlvh1.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