[English] 日本語
Yorodumi
- PDB-1fob: CRYSTAL STRUCTURE OF BETA-1,4-GALACTANASE FROM ASPERGILLUS ACULEA... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1fob
TitleCRYSTAL STRUCTURE OF BETA-1,4-GALACTANASE FROM ASPERGILLUS ACULEATUS AT 100K
ComponentsBETA-1,4-GALACTANASE
KeywordsHYDROLASE / B/A barrel / glycosyl hydrolase / family 53 / clan GH-A
Function / homology
Function and homology information


arabinogalactan endo-beta-1,4-galactanase / arabinogalactan endo-1,4-beta-galactosidase activity / glucosidase activity / pectin catabolic process
Similarity search - Function
Glycosyl hydrolase family 53 / Glycosyl hydrolase family 53 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Arabinogalactan endo-beta-1,4-galactanase
Similarity search - Component
Biological speciesAspergillus aculeatus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.8 Å
AuthorsRyttersgaard, C. / Larsen, S.
Citation
Journal: Biochemistry / Year: 2002
Title: Aspergillus aculeatus beta-1,4-Galactanase: Substrate Recognition and Relations to Other Glycoside Hydrolases in Clan GH-A
Authors: Ryttersgaard, C. / Leggio, L.L. / Coutinho, P.M. / Henrissat, B. / Larsen, S.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1999
Title: Crystallization and Preliminary X-ray Studies of beta-1,4-galactanase from Aspergillus aculeatus
Authors: Ryttersgaard, C. / Poulsen, J. / Christgau, S. / Sandal, T. / Dalboge, H. / Larsen, S.
History
DepositionAug 27, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 3, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Data collection / Refinement description / Category: diffrn_source / software / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Oct 16, 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _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-GALACTANASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8162
Polymers36,7751
Non-polymers401
Water3,477193
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.700, 87.980, 128.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-408-

HOH

-
Components

#1: Protein BETA-1,4-GALACTANASE


Mass: 36775.438 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Aspergillus aculeatus (mold)
References: UniProt: P48842, arabinogalactan endo-beta-1,4-galactanase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 193 / 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: 2.29 Å3/Da / Density % sol: 46.24 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 400, calcium chloride, sodium hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Details: Ryttersgaard, C., (1999) Acta Crystallogr.,Sect.D, 55, 929.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
130 %(v/v)PEG4001reservoir
20.2 M1reservoirCaCl2
30.1 Msodium HEPES1reservoirpH7.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.0874
DetectorType: MARRESEARCH / Detector: AREA DETECTOR / Date: Jan 27, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0874 Å / Relative weight: 1
ReflectionResolution: 1.8→28.59 Å / Num. all: 31237 / Num. obs: 31237 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 23.5 Å2 / Rmerge(I) obs: 0.041 / Net I/σ(I): 14.5
Reflection shellResolution: 1.8→1.91 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.354 / Num. unique all: 1477 / % possible all: 91.4
Reflection shell
*PLUS
Lowest resolution: 1.83 Å / % possible obs: 97.7 % / Mean I/σ(I) obs: 66.6

-
Processing

Software
NameClassification
MAR345data collection
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementResolution: 1.8→28.59 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 2119317.83 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.251 1576 5 %RANDOM
Rwork0.211 ---
all0.211 31237 --
obs0.211 31237 98.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 51.01 Å2 / ksol: 0.3744 e/Å3
Displacement parametersBiso mean: 28 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å20 Å20 Å2
2---2.82 Å20 Å2
3---2.73 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.18 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 1.8→28.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2607 0 1 193 2801
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.6
X-RAY DIFFRACTIONc_improper_angle_d0.77
X-RAY DIFFRACTIONc_mcbond_it1.31.5
X-RAY DIFFRACTIONc_mcangle_it1.882
X-RAY DIFFRACTIONc_scbond_it1.92
X-RAY DIFFRACTIONc_scangle_it2.682.5
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.296 249 5.2 %
Rwork0.271 4522 -
obs--91.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
Refinement
*PLUS
Rfactor Rfree: 0.252 / Rfactor Rwork: 0.212
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.77

+
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