[English] 日本語
Yorodumi
- PDB-4aem: Structural and biochemical characterization of a novel Carbohydra... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4aem
TitleStructural and biochemical characterization of a novel Carbohydrate Binding Module of endoglucanase Cel5A from Eubacterium cellulosolvens
ComponentsENDOGLUCANASE CEL5A
KeywordsHYDROLASE / FAMILY 5 GLYCOSIDE HYDROLASE / CELLULOSOME
Function / homology
Function and homology information


beta-glucosidase activity / cellulose catabolic process / cell surface / extracellular region
Similarity search - Function
Jelly Rolls - #1070 / Carbohydrate binding module 65 domain 1 / Carbohydrate binding module 65 domain 1 / : / Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / Glycoside hydrolase superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesEUBACTERIUM CELLULOSOLVENS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsLuis, A.S. / Venditto, I. / Prates, J.A.M. / Ferreira, L.M.A. / Gilbert, H.J. / Fontes, C.M.G.A. / Najmudin, S.
Citation
Journal: J.Biol.Chem. / Year: 2013
Title: Understanding How Non-Catalytic Carbohydrate Binding Modules Can Display Specificity for Xyloglucan
Authors: Luis, A.S. / Venditto, I. / Prates, J.A.M. / Ferreira, L.M.A. / Temple, M.J. / Rogowski, A. / Basle, A. / Xue, J. / Knox, J.P. / Najmudin, S. / Fontes, C.M.G.A. / Gilbert, H.J.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2011
Title: Overproduction, Purification, Crystallization and Preliminary X-Ray Characterization of a Novel Carbohydrate-Binding Module of Endoglucanase Cel5A from Eubacterium Cellulosolvens.
Authors: Luis, A.S. / Alves, V.D. / Romao, M.J. / Prates, J.A.M. / Fontes, C.M.G.A. / Najmudin, S.
History
DepositionJan 11, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 23, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 30, 2013Group: Database references
Revision 1.2Feb 27, 2013Group: Database references
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ENDOGLUCANASE CEL5A


Theoretical massNumber of molelcules
Total (without water)14,7991
Polymers14,7991
Non-polymers00
Water1,65792
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)79.320, 79.320, 44.440
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

-
Components

#1: Protein ENDOGLUCANASE CEL5A


Mass: 14799.314 Da / Num. of mol.: 1 / Fragment: CARBOHYDRATE BINDING MODULE, RESIDUES 37-170
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) EUBACTERIUM CELLULOSOLVENS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q3LHN3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / 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: 2.32 Å3/Da / Density % sol: 47 % / Description: NONE
Crystal growTemperature: 292 K / pH: 4.76
Details: 100 MG/ML PROTEIN WAS USED AT 292 K WITH 0.2 M AMMONIUM SULFATE, 0.1 M SODIUM ACETATE TRIHYDRATE PH 4.6, 30% W/V PEG 2K MME. 30% GLYCEROL WAS USED AS CRYOPROTECTANT

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9793
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 24, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.1→68.69 Å / Num. obs: 8165 / % possible obs: 83.6 % / Redundancy: 11.2 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 15.3
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 2.4 / % possible all: 53.4

-
Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4AEK

4aek


Resolution: 2.1→68.69 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.931 / SU B: 10.403 / SU ML: 0.132 / Cross valid method: THROUGHOUT / ESU R: 0.223 / ESU R Free: 0.194 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. PHENIX-1.7.2-869 WAS ALSO USED FOR REFINEMENT, TO GENERATE TLS GROUPS AND UPDATE WATERS. ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. PHENIX-1.7.2-869 WAS ALSO USED FOR REFINEMENT, TO GENERATE TLS GROUPS AND UPDATE WATERS. RESIDUES A37-38 AND A165-170 ARE DISORDERERED. GLU 65, ILE 111, AND GLU 126 WERE GIVEN DUAL CONFORMATIONS. DISORDERED SIDE CHAINS WERE MODELED STEREOCHEMICALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.22704 417 5.1 %RANDOM
Rwork0.17053 ---
obs0.17353 7748 84.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.376 Å2
Baniso -1Baniso -2Baniso -3
1--0.65 Å2-0.33 Å20 Å2
2---0.65 Å20 Å2
3---0.98 Å2
Refinement stepCycle: LAST / Resolution: 2.1→68.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms998 0 0 92 1090
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.021050
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.2131.941439
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7415131
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.03625.20848
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.5815160
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.226151
X-RAY DIFFRACTIONr_chiral_restr0.1450.2154
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021818
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_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 22 -
Rwork0.28 318 -
obs--49.49 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.5927-1.6352-3.55136.20971.7222.8454-0.19920.1123-0.08130.40910.2453-0.49880.3153-0.0775-0.04610.31290.0173-0.16910.16580.01320.134258.068714.5234.904
25.27651.8104-2.83352.4212-2.09312.4043-0.0029-0.1619-0.03710.23010.01420.0701-0.08250.0524-0.01130.12560.004100.1169-0.01780.015756.728526.17429.6716
31.36090.2428-0.27492.8605-0.26780.906-0.03610.1115-0.1176-0.1806-0.0216-0.08090.06310.05120.05770.0878-0.0091-0.00810.1367-0.02230.019153.933722.9325-2.0047
42.6021-0.0417-0.13142.47810.31791.8245-0.0832-0.02930.2566-0.06910.0953-0.0467-0.13380.0039-0.01210.0867-0.0147-0.00870.13690.0030.043547.598626.1345-1.2311
51.3795-0.06470.41551.390.37620.6141-0.04370.13370.0154-0.17580.0021-0.08460.08090.06710.04160.1104-0.00260.02560.1540.00070.017252.593623.86870.2826
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A39 - 52
2X-RAY DIFFRACTION2A53 - 71
3X-RAY DIFFRACTION3A72 - 99
4X-RAY DIFFRACTION4A100 - 127
5X-RAY DIFFRACTION5A128 - 164

+
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