[English] 日本語
Yorodumi
- PDB-3r4z: Crystal structure of alpha-neoagarobiose hydrolase (ALPHA-NABH) i... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3r4z
TitleCrystal structure of alpha-neoagarobiose hydrolase (ALPHA-NABH) in complex with alpha-d-galactopyranose from Saccharophagus degradans 2-40
ComponentsGlycosyl hydrolase family 32, N terminal
KeywordsHYDROLASE / AGAR METABOLISM / NEOAGAROBIOSE / 3 / 6-ANHYDRO-L-GALACTOSE / ALPHA-D-GALACTOPYRANOSE / BIOENERGY
Function / homology
Function and homology information


hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process
Similarity search - Function
Glycoside hydrolase, family 43 / Glycosyl hydrolases family 43 / Glycosyl hydrolase domain; family 43 / 5 Propeller / Tachylectin-2; Chain A / Glycosyl hydrolase, five-bladed beta-propellor domain superfamily / Mainly Beta
Similarity search - Domain/homology
alpha-D-galactopyranose / Glycosyl hydrolase family 32, N terminal
Similarity search - Component
Biological speciesSaccharophagus degradans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsLee, S. / Lee, J.Y. / Ha, S.C. / Shin, D.H. / Kim, K.H. / Bang, W.G. / Kim, S.H. / Choi, I.G.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2011
Title: Crystal structure of a key enzyme in the agarolytic pathway, alpha-neoagarobiose hydrolase from Saccharophagus degradans 2-40
Authors: Ha, S.C. / Lee, S. / Lee, J. / Kim, H.T. / Ko, H.J. / Kim, K.H. / Choi, I.G.
History
DepositionMar 18, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 1, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Glycosyl hydrolase family 32, N terminal
B: Glycosyl hydrolase family 32, N terminal
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,2404
Polymers84,8802
Non-polymers3602
Water12,484693
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6260 Å2
ΔGint-32 kcal/mol
Surface area26910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.207, 77.128, 90.971
Angle α, β, γ (deg.)90.00, 101.95, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-485-

HOH

21B-618-

HOH

-
Components

#1: Protein Glycosyl hydrolase family 32, N terminal / ALPHA-NEOAGAROBIOSE HYDROLASE


Mass: 42439.934 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharophagus degradans (bacteria) / Strain: 2-40 / Gene: Sde_2657 / Plasmid: pJL / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3)
References: UniProt: Q21HB2, Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds
#2: Sugar ChemComp-GLA / alpha-D-galactopyranose / alpha-D-galactose / D-galactose / galactose / ALPHA D-GALACTOSE / Galactose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGalpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-galactopyranoseCOMMON NAMEGMML 1.0
a-D-GalpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 693 / 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: 2.63 Å3/Da / Density % sol: 53.28 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 2.4M SODIUM MALONATE, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 30, 2009
RadiationMonochromator: DOUBLE-CRYSTAL, SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.55→50 Å / Num. obs: 125096 / % possible obs: 98.2 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 24
Reflection shellResolution: 1.55→1.61 Å / Rmerge(I) obs: 0.314 / Mean I/σ(I) obs: 2.3 / % possible all: 85.4

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→19.77 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.96 / SU B: 1.202 / SU ML: 0.044 / Cross valid method: THROUGHOUT / ESU R Free: 0.07 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.18481 6060 5 %RANDOM
Rwork0.16353 ---
obs0.1646 114630 96.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 17.147 Å2
Baniso -1Baniso -2Baniso -3
1--0.46 Å20 Å20.48 Å2
2---0.7 Å20 Å2
3---1.36 Å2
Refinement stepCycle: LAST / Resolution: 1.55→19.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5744 0 24 693 6461
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0215956
X-RAY DIFFRACTIONr_angle_refined_deg1.271.9348092
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6945715
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.29824.128298
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.58915927
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5891528
X-RAY DIFFRACTIONr_chiral_restr0.0840.2814
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024686
X-RAY DIFFRACTIONr_nbd_refined0.1920.22655
X-RAY DIFFRACTIONr_nbtor_refined0.310.24000
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.2675
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1330.238
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1520.218
X-RAY DIFFRACTIONr_mcbond_it0.7121.53643
X-RAY DIFFRACTIONr_mcangle_it1.1925724
X-RAY DIFFRACTIONr_scbond_it2.02532714
X-RAY DIFFRACTIONr_scangle_it34.52367
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.233 352 -
Rwork0.218 6522 -
obs--89.94 %

+
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