[English] 日本語
Yorodumi
- PDB-3vup: Beta-1,4-mannanase from the common sea hare Aplysia kurodai -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3vup
TitleBeta-1,4-mannanase from the common sea hare Aplysia kurodai
ComponentsBeta-1,4-mannanase
KeywordsHYDROLASE / Tim Barrel / Beta-1 / 4-mannanase / mannan / digestive fluid
Function / homologyCellulase (glycosyl hydrolase family 5) / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta / Beta-1,4-mannanase
Function and homology information
Biological speciesAplysia kurodai (Kuroda's sea hare)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.05 Å
AuthorsMizutani, K. / Tsuchiya, S. / Toyoda, M. / Nanbu, Y. / Tominaga, K. / Yuasa, K. / Takahashi, N. / Tsuji, A. / Mikami, B.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2012
Title: Structure of beta-1,4-mannanase from the common sea hare Aplysia kurodai at 1.05 A resolution.
Authors: Mizutani, K. / Tsuchiya, S. / Toyoda, M. / Nanbu, Y. / Tominaga, K. / Yuasa, K. / Takahashi, N. / Tsuji, A. / Mikami, B.
History
DepositionJul 4, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 17, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Beta-1,4-mannanase
B: Beta-1,4-mannanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,61918
Polymers80,0302
Non-polymers1,58916
Water21,2401179
1
A: Beta-1,4-mannanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,8099
Polymers40,0151
Non-polymers7958
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-1,4-mannanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,8099
Polymers40,0151
Non-polymers7958
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)110.092, 114.098, 51.138
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein Beta-1,4-mannanase


Mass: 40014.895 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 19-369 / Source method: isolated from a natural source / Source: (natural) Aplysia kurodai (Kuroda's sea hare) / References: UniProt: E5RSM0
#2: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1179 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.01 Å3/Da / Density % sol: 38.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 20% PEG 3350, 0.1M sodium sulfate, 100mM Tris-HCl, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 0.8 Å
DetectorType: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Oct 31, 2010
RadiationMonochromator: Si double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 1.05→50 Å / Num. all: 296609 / Num. obs: 292160 / % possible obs: 98.5 % / Observed criterion σ(I): 25.8
Reflection shellResolution: 1.05→1.07 Å / % possible all: 93.7

-
Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.05→24.95 Å / SU ML: 0.09 / σ(F): 1.35 / Phase error: 12.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1565 14693 5.04 %Random
Rwork0.1367 ---
obs0.1377 291356 97.43 %-
all-299041 --
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.791 Å2 / ksol: 0.353 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.2889 Å20 Å2-0 Å2
2--0.9499 Å2-0 Å2
3----1.2387 Å2
Refinement stepCycle: LAST / Resolution: 1.05→24.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5648 0 86 1179 6913
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066248
X-RAY DIFFRACTIONf_angle_d1.2528487
X-RAY DIFFRACTIONf_dihedral_angle_d13.2542320
X-RAY DIFFRACTIONf_chiral_restr0.094830
X-RAY DIFFRACTIONf_plane_restr0.0061096
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.05-1.06190.20244370.1711882094
1.0619-1.07440.18914820.1622880694
1.0744-1.08750.18144920.1539883394
1.0875-1.10130.17154600.1462878294
1.1013-1.11580.16924580.1391898295
1.1158-1.13110.15794730.1302889395
1.1311-1.14720.1464750.1263899596
1.1472-1.16440.15064960.1264893195
1.1644-1.18250.14514830.1227899096
1.1825-1.20190.16014920.1264916197
1.2019-1.22270.14284920.1188898396
1.2227-1.24490.14624700.1219914897
1.2449-1.26880.15034960.1211921498
1.2688-1.29470.14464810.1207918898
1.2947-1.32290.1624960.1212920898
1.3229-1.35370.15235050.1206924398
1.3537-1.38750.14194880.1182927698
1.3875-1.4250.14364870.1174925198
1.425-1.46690.14434840.1188931698
1.4669-1.51430.14264720.1146933199
1.5143-1.56840.13435080.1144933499
1.5684-1.63120.14114830.117940399
1.6312-1.70540.13725240.1197940199
1.7054-1.79530.14485230.12859411100
1.7953-1.90770.14385000.13169504100
1.9077-2.0550.15215400.13599503100
2.055-2.26170.15834990.14379526100
2.2617-2.58860.17025100.15189598100
2.5886-3.26020.16294910.15249677100
3.2602-24.95720.17464960.1592995599

+
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