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

+
Open data


ID or keywords:

Loading...

-
Basic information

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


glucan catabolic process / beta-glucosidase activity / 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
ACETATE ION / Endoglucanase cel5A
Similarity search - Component
Biological speciesEUBACTERIUM CELLULOSOLVENS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 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. / Ferrieira, 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 19, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 19, 2012Provider: 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 / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / pdbx_struct_special_symmetry / struct_conn
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_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: ENDOGLUCANASE CEL5A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,3928
Polymers14,8791
Non-polymers5127
Water2,342130
1
A: ENDOGLUCANASE CEL5A
hetero molecules

A: ENDOGLUCANASE CEL5A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,78316
Polymers29,7582
Non-polymers1,02514
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area4260 Å2
ΔGint-9.6 kcal/mol
Surface area12070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.740, 48.740, 193.720
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-1170-

ACT

21A-2001-

HOH

-
Components

#1: Protein ENDOGLUCANASE CEL5A


Mass: 14879.080 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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsGLYCEROL (GOL): FROM THE CRYOPROTECTANT. ACETATE ION (ACT): FROM THE CRYSTALLISATION BUFFER.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.65 Å3/Da / Density % sol: 66 % / Description: NONE
Crystal growTemperature: 292 K / pH: 4.6
Details: 80 MG/ML OF PROTEIN AT 292 K WERE GROWN IN 0.2 M AMMONIUM SULFATE, 0.1 M SODIUM ACETATE TRIHYDRATE PH 4.6, 26% W/V PEG 2K MME. CRYSTALS WERE SOAKED WITH 10 MM CELLOHEXAOSE FOR A FEW HOURS. ...Details: 80 MG/ML OF PROTEIN AT 292 K WERE GROWN IN 0.2 M AMMONIUM SULFATE, 0.1 M SODIUM ACETATE TRIHYDRATE PH 4.6, 26% W/V PEG 2K MME. CRYSTALS WERE SOAKED WITH 10 MM CELLOHEXAOSE FOR A FEW HOURS. 30% GLYCEROL WAS USED AS A CRYOPROTECTANT.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97934
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 4, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.25→38.74 Å / Num. obs: 35557 / % possible obs: 91.2 % / Redundancy: 21.6 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 28.2
Reflection shellResolution: 1.25→1.32 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 4 / % possible all: 62.4

-
Processing

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

4aek


Resolution: 1.25→38.7 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.963 / SU B: 1.074 / SU ML: 0.023 / Cross valid method: THROUGHOUT / ESU R: 0.043 / ESU R Free: 0.044 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES.PHENIX-1.7.2-869 WAS USED IN THE PENULTIMATE STEP FOR OCCUPANCY REFINEMENT AND ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES.PHENIX-1.7.2-869 WAS USED IN THE PENULTIMATE STEP FOR OCCUPANCY REFINEMENT AND TLS GROUP DETERMINATION. RESIDUES 37-38 AND 166-170 ARE DISORDERED. ASP A118 WAS MODELLED WITH ALTERNATE CONFORMATION. IT MAY ALSO HAVE RADIATION DAMAGE AS IN PDB 4AFD. DISORDERED SIDE CHAINS WERE MODELED STEREOCHEMICALLY. FOLLOWING WERE GIVEN ALTERNATE CONFORMATIONS, SER A45, GLU A51, GLN A67, GLN A71, MSE A73, GLU A82, ILE A83, IL3 A95 GLU A100, SER A103, SER A112, VAL A116, GLN A126, LYS A130, MSE A154, VAL A160 AND SER A162.
RfactorNum. reflection% reflectionSelection details
Rfree0.17306 1788 5 %RANDOM
Rwork0.15798 ---
obs0.15874 33704 91.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.031 Å2
Baniso -1Baniso -2Baniso -3
1-0.15 Å20.08 Å20 Å2
2--0.15 Å20 Å2
3----0.23 Å2
Refinement stepCycle: LAST / Resolution: 1.25→38.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1003 0 34 130 1167
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0310.021175
X-RAY DIFFRACTIONr_bond_other_d0.0010.0212
X-RAY DIFFRACTIONr_angle_refined_deg2.8731.9731623
X-RAY DIFFRACTIONr_angle_other_deg0.178324
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.4285163
X-RAY DIFFRACTIONr_dihedral_angle_2_deg44.20125.6653
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.29715177
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.1151
X-RAY DIFFRACTIONr_chiral_restr0.1680.2177
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.021926
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: 1.25→1.282 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 69 -
Rwork0.284 1377 -
obs--54.4 %
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)
10.55080.5710.49030.87791.00791.3097-0.0493-0.0165-0.022-0.0133-0.00040.01440.02680.01260.04960.05760.01030.00630.00340.00040.0356-1.22674.11493.9345
20.513-0.2693-0.75051.06650.71461.2096-0.0048-0.10330.0251-0.04350.0714-0.0945-0.00940.1556-0.06660.03830.01630.00960.0543-0.00950.026810.589511.323511.125
30.31220.02310.030.10080.04520.0911-0.02870.01940.0261-0.0170.0392-0.0017-0.0217-0.0025-0.01060.054-0.00490.01020.02170.00280.03237.990313.588-2.3683
40.44390.14660.17340.08740.33082.0105-0.05530.0143-0.0071-0.0190.00310.0067-0.062-0.01710.05220.06540.01060.00380.00440.00180.0335-2.40018.4998-0.5192
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A39 - 50
2X-RAY DIFFRACTION2A51 - 66
3X-RAY DIFFRACTION3A67 - 153
4X-RAY DIFFRACTION4A154 - 165

+
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://pdbjlc1.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