[English] 日本語
Yorodumi
- PDB-3d6e: Crystal structure of the engineered 1,3-1,4-beta-glucanase protei... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3d6e
TitleCrystal structure of the engineered 1,3-1,4-beta-glucanase protein from Bacillus licheniformis
ComponentsBeta-glucanase
KeywordsHYDROLASE / Beta-glucan hydrolysis / Calcium binding motif / Protein engineering / Glycosidase
Function / homology
Function and homology information


licheninase activity / licheninase / carbohydrate metabolic process
Similarity search - Function
Beta-glucanase/XTH / Beta-glucanase / Glycoside hydrolase, family 16, active site / Glycosyl hydrolases family 16 active sites. / Glycosyl hydrolases family 16 / Glycoside hydrolase family 16 / Glycosyl hydrolases family 16 (GH16) domain profile. / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls ...Beta-glucanase/XTH / Beta-glucanase / Glycoside hydrolase, family 16, active site / Glycosyl hydrolases family 16 active sites. / Glycosyl hydrolases family 16 / Glycoside hydrolase family 16 / Glycosyl hydrolases family 16 (GH16) domain profile. / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesBacillus licheniformis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsFita, I. / Planas, A. / Calisto, B.M. / Addington, T.
Citation
Journal: Proteins / Year: 2011
Title: Re-engineering specificity in 1,3-1,4-beta-glucanase to accept branched xyloglucan substrates
Authors: Addington, T. / Calisto, B. / Alfonso-Prieto, M. / Rovira, C. / Fita, I. / Planas, A.
#1: Journal: FEBS Lett. / Year: 1995
Title: Crystal structure of Bacillus licheniformis 1,3-1,4-beta-D-glucan 4-glucanohydrolase at 1.8 A resolution
Authors: Hahn, M. / Pons, J. / Planas, A. / Querol, E. / Heinemann, U.
History
DepositionMay 19, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 19, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_ref_seq_dif / 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.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details / _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-glucanase
B: Beta-glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,5864
Polymers45,5062
Non-polymers802
Water2,468137
1
A: Beta-glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,7932
Polymers22,7531
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,7932
Polymers22,7531
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.551, 54.813, 54.910
Angle α, β, γ (deg.)61.38, 85.72, 86.10
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / End auth comp-ID: THR / End label comp-ID: THR / Refine code: 4 / Auth seq-ID: 1 - 199 / Label seq-ID: 1 - 199

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

-
Components

#1: Protein Beta-glucanase / Endo-beta-1 / 3-1 / 4 glucanase / 1 / 3-1 / 4-beta-D-glucan 4-glucanohydrolase / Lichenase


Mass: 22753.035 Da / Num. of mol.: 2
Mutation: R22A, A23F, N24D, N25H, C48G, E50G, R52Q, S77A, F79Y, Y81S, M167Y, N169S, N172A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus licheniformis (bacteria) / Plasmid: pET16b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Star / References: UniProt: P27051, licheninase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 137 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHERE ARE CONFLICTS BETWEEN THE DATABASE REFERENCE SEQUENCE AND THE COORDINATES. THE DEPOSITOR ...THERE ARE CONFLICTS BETWEEN THE DATABASE REFERENCE SEQUENCE AND THE COORDINATES. THE DEPOSITOR BELIEVE THAT THE SEQRES IS CORRECT AND THE ELECTRON DENSITY SHOWS CLEAR EVIDENCE FOR THESE RESIDUES.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.28 Å3/Da / Density % sol: 46.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 16% PEG MME 2000, 0.1M Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 11, 2008 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. all: 14740 / Num. obs: 14739 / % possible obs: 93.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 1.8 % / Biso Wilson estimate: 15 Å2 / Rmerge(I) obs: 0.043 / Rsym value: 0.037 / Net I/σ(I): 18.7
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.121 / Mean I/σ(I) obs: 6.25 / Num. unique all: 14739 / Rsym value: 0.126 / % possible all: 79.2

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DNAdata collection
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GBG

1gbg


Resolution: 2.4→30 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.894 / SU B: 17.13 / SU ML: 0.204 / Cross valid method: THROUGHOUT / σ(F): 1 / σ(I): 1 / ESU R: 0.721 / ESU R Free: 0.299 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25481 731 5 %RANDOM
Rwork0.21042 ---
obs0.21259 14011 93.43 %-
all-14740 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.538 Å2
Baniso -1Baniso -2Baniso -3
1--1.17 Å2-0.24 Å2-0.16 Å2
2--0.48 Å20.39 Å2
3---0.37 Å2
Refinement stepCycle: LAST / Resolution: 2.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2953 0 2 137 3092
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0223047
X-RAY DIFFRACTIONr_bond_other_d0.0010.021955
X-RAY DIFFRACTIONr_angle_refined_deg1.0931.9044154
X-RAY DIFFRACTIONr_angle_other_deg1.05534740
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2915367
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.25824.533150
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.13515439
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.648156
X-RAY DIFFRACTIONr_chiral_restr0.1820.2422
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.023469
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02667
X-RAY DIFFRACTIONr_nbd_refined0.1480.2574
X-RAY DIFFRACTIONr_nbd_other0.1770.22033
X-RAY DIFFRACTIONr_nbtor_refined0.180.21441
X-RAY DIFFRACTIONr_nbtor_other0.0790.21544
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1330.2137
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0330.22
X-RAY DIFFRACTIONr_metal_ion_refined0.0720.25
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1330.215
X-RAY DIFFRACTIONr_symmetry_vdw_other0.120.251
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0310.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.2441.51881
X-RAY DIFFRACTIONr_mcbond_other0.0231.5763
X-RAY DIFFRACTIONr_mcangle_it0.43622926
X-RAY DIFFRACTIONr_scbond_it0.32531425
X-RAY DIFFRACTIONr_scangle_it0.5084.51228
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 2379 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
medium positional0.30.5
medium thermal0.062
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.434 44 -
Rwork0.27 865 -
obs-826 78.43 %

+
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