[English] 日本語
Yorodumi
- PDB-7r1n: Crystal structure of the Tetrameric C-terminal Big_2-CBM56 domain... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7r1n
TitleCrystal structure of the Tetrameric C-terminal Big_2-CBM56 domains from Paenibacillus illinoisensis (Bacillus circulans IAM1165) beta-1,3-glucanase H
ComponentsBeta-1,3-glucanase bglH
KeywordsHYDROLASE / laminarinase / GH16 sub-family 8 / Big_2 / CBM56
Function / homology
Function and homology information


hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate binding / carbohydrate metabolic process / metal ion binding
Similarity search - Function
: / CBM56 (carbohydrate binding type-56) domain profile. / Glycoside hydrolase, family 16, active site / Glycosyl hydrolases family 16 active sites. / Invasin/intimin cell-adhesion fragments / Glycosyl hydrolases family 16 / Bacterial Ig-like domain (group 2) / Glycoside hydrolase family 16 / Glycosyl hydrolases family 16 (GH16) domain profile. / Bacterial Ig-like domain 2 ...: / CBM56 (carbohydrate binding type-56) domain profile. / Glycoside hydrolase, family 16, active site / Glycosyl hydrolases family 16 active sites. / Invasin/intimin cell-adhesion fragments / Glycosyl hydrolases family 16 / Bacterial Ig-like domain (group 2) / Glycoside hydrolase family 16 / Glycosyl hydrolases family 16 (GH16) domain profile. / Bacterial Ig-like domain 2 / Bacterial Ig-like domain, group 2 / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Beta-1,3-glucanase
Similarity search - Component
Biological speciesPaenibacillus illinoisensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.072 Å
AuthorsNajmudin, S. / Venditto, I. / Fontes, C.M.G.A. / Bule, P.
Funding supportEuropean Union, 2items
OrganizationGrant numberCountry
Fundacao para a Ciencia e a TecnologiaPTDC/BIA-PRO/103980/2008European Union
European Communitys Seventh Framework Programme263916European Union
CitationJournal: To be published
Title: Structural and biochemical characterization of C-terminal Big_2-CBM56 domains of Paenibacillus illinoisensis IAM1165 beta-1,3-glucanase H and Paenibacillus sp CBM56
Authors: Najmudin, S. / Venditto, I. / Pires, V.R. / Caseiro, C. / Correia, M.A.S. / Romao, M.J. / Carvalho, A.L. / Fontes, C.M.G.A. / Bule, P.
History
DepositionFeb 3, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 15, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
AAA: Beta-1,3-glucanase bglH
BBB: Beta-1,3-glucanase bglH
CCC: Beta-1,3-glucanase bglH
DDD: Beta-1,3-glucanase bglH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,18420
Polymers85,6304
Non-polymers1,55416
Water5,873326
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: Also seen in pdb 7quz
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13060 Å2
ΔGint-61 kcal/mol
Surface area30260 Å2
Unit cell
Length a, b, c (Å)76.650, 101.140, 107.000
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 1 types, 4 molecules AAABBBCCCDDD

#1: Protein
Beta-1,3-glucanase bglH


Mass: 21407.545 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: C-terminal Big_2-CBM56 domains / Source: (gene. exp.) Paenibacillus illinoisensis (bacteria) / Gene: bglH, beta-1,3-glucanase / Plasmid: pET28A / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q45095

-
Non-polymers , 6 types, 342 molecules

#2: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 326 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.78 Å3/Da / Density % sol: 56 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 20/30/50 mg/ml Protein concentration in 0.2 Magnesium chloride hexahydrate, 0.1 M HEPES sodium salt pH 7.5. 30% v/v PEG400

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 4, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.07→53.5 Å / Num. obs: 50525 / % possible obs: 98.7 % / Redundancy: 3.5 % / CC1/2: 0.989 / Rmerge(I) obs: 0.116 / Rpim(I) all: 0.097 / Rrim(I) all: 0.152 / Net I/σ(I): 6.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
9-53.53.60.037070.9990.0250.039
2.07-2.132.90.76237010.5270.6330.997

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
REFMAC5.8.0267refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7quz

7quz


Resolution: 2.072→53.108 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.899 / SU B: 13.266 / SU ML: 0.171 / Cross valid method: FREE R-VALUE / ESU R: 0.214 / ESU R Free: 0.199
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2706 2472 4.897 %
Rwork0.2099 48005 -
all0.213 --
obs-50477 98.482 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 28.204 Å2
Baniso -1Baniso -2Baniso -3
1--0.185 Å2-0 Å20 Å2
2--0.611 Å2-0 Å2
3----0.426 Å2
Refinement stepCycle: LAST / Resolution: 2.072→53.108 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5348 0 98 326 5772
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0135546
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175132
X-RAY DIFFRACTIONr_angle_refined_deg1.9711.6487598
X-RAY DIFFRACTIONr_angle_other_deg1.361.5711820
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.1665732
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.9626.731208
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.87215744
X-RAY DIFFRACTIONr_chiral_restr0.0830.2776
X-RAY DIFFRACTIONr_gen_planes_refined0.010.026464
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021152
X-RAY DIFFRACTIONr_nbd_refined0.2040.2890
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1990.24813
X-RAY DIFFRACTIONr_nbtor_refined0.1670.22652
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0860.22832
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1810.2358
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.2160.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2530.248
X-RAY DIFFRACTIONr_nbd_other0.3090.2158
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2250.212
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.020.21
X-RAY DIFFRACTIONr_mcbond_it1.7292.2542940
X-RAY DIFFRACTIONr_mcbond_other1.7292.2532939
X-RAY DIFFRACTIONr_mcangle_it2.8843.3653668
X-RAY DIFFRACTIONr_mcangle_other2.8843.3673669
X-RAY DIFFRACTIONr_scbond_it1.9812.4922606
X-RAY DIFFRACTIONr_scbond_other1.982.4932607
X-RAY DIFFRACTIONr_scangle_it3.1953.6563930
X-RAY DIFFRACTIONr_scangle_other3.1943.6573931
X-RAY DIFFRACTIONr_lrange_it5.39427.7745719
X-RAY DIFFRACTIONr_lrange_other5.32427.5715648
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.072-2.1260.3331710.3333344X-RAY DIFFRACTION93.7333
2.126-2.1840.3621760.3183386X-RAY DIFFRACTION97.8303
2.184-2.2470.3281640.2933273X-RAY DIFFRACTION98.0879
2.247-2.3160.3091700.283251X-RAY DIFFRACTION98.7302
2.316-2.3920.2951800.2573150X-RAY DIFFRACTION98.9305
2.392-2.4760.311470.2493049X-RAY DIFFRACTION98.9474
2.476-2.570.2611460.2282945X-RAY DIFFRACTION99.3252
2.57-2.6750.3161590.2212847X-RAY DIFFRACTION99.3391
2.675-2.7930.2721600.1982715X-RAY DIFFRACTION99.4466
2.793-2.930.2521140.1832653X-RAY DIFFRACTION99.604
2.93-3.0880.261100.1692522X-RAY DIFFRACTION99.697
3.088-3.2750.2241220.172388X-RAY DIFFRACTION99.6823
3.275-3.5010.2351270.1782223X-RAY DIFFRACTION99.7453
3.501-3.7810.2151240.1672073X-RAY DIFFRACTION99.5469
3.781-4.1420.248830.1731934X-RAY DIFFRACTION98.7757
4.142-4.630.221770.1641755X-RAY DIFFRACTION98.6006
4.63-5.3440.2221000.1611523X-RAY DIFFRACTION98.0072
5.344-6.5410.345760.1981264X-RAY DIFFRACTION95.1705
6.541-9.2330.331440.2071080X-RAY DIFFRACTION99.8224
9.233-53.10.3220.231630X-RAY DIFFRACTION98.1928
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)
10.2767-0.01570.09980.0648-0.25471.2069-0.0327-0.0190.02810.0105-0.01110.0036-0.0427-0.04970.04380.09520.0114-0.01140.045-0.02730.0194-9.4764-18.28430.0794
20.2002-0.04150.39160.2149-0.14580.90080.03820.05010.02080.1108-0.0690.0790.04140.02960.03080.088-0.02490.05050.0942-0.0310.0386-9.038-39.642825.7206
30.21540.12730.21760.1190.33661.27280.019-0.0274-0.0527-0.0031-0.0151-0.02360.0134-0.0329-0.0040.09450.0172-0.00720.043-0.00040.02019.8669-38.705827.6193
40.14370.0278-0.08180.26730.46461.6751-0.00930.0608-0.0080.0442-0.0243-0.061-0.06410.04060.03360.0698-0.0149-0.04160.07370.0280.04028.5405-17.393523.4952
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLAAA24 - 207
2X-RAY DIFFRACTION1ALLAaA301
3X-RAY DIFFRACTION1ALLAbA302
4X-RAY DIFFRACTION1ALLAcA303
5X-RAY DIFFRACTION2ALLBBB24 - 207
6X-RAY DIFFRACTION2ALLBaB301
7X-RAY DIFFRACTION3ALLCCC24 - 207
8X-RAY DIFFRACTION4ALLDDD24 - 207
9X-RAY DIFFRACTION4ALLDaD301
10X-RAY DIFFRACTION4ALLDbD302

+
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://pdbjlvh1.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