[English] 日本語
Yorodumi
- PDB-4txw: Crystal structure of CBM32-4 from the Clostridium perfringens NagH -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4txw
TitleCrystal structure of CBM32-4 from the Clostridium perfringens NagH
ComponentsHyaluronoglucosaminidaseHyaluronidase
Keywordscarbohydrate-binding module / B-sandwich
Function / homology
Function and homology information


hyaluronoglucosaminidase / hyalurononglucosaminidase activity / organonitrogen compound metabolic process / carbohydrate derivative metabolic process / protein modification process => GO:0036211 / polysaccharide catabolic process / beta-N-acetylglucosaminidase activity / metal ion binding
Similarity search - Function
FIVAR domain / : / Hyaluronidase post-catalytic domain-like / Beta-N-acetylglucosaminidase / beta-N-acetylglucosaminidase / Beta-hexosaminidase, bacterial type, N-terminal / Glycosyl hydrolase family 20, domain 2 / Beta-hexosaminidase-like, domain 2 / Dockerin domain / Dockerin domain profile. ...FIVAR domain / : / Hyaluronidase post-catalytic domain-like / Beta-N-acetylglucosaminidase / beta-N-acetylglucosaminidase / Beta-hexosaminidase, bacterial type, N-terminal / Glycosyl hydrolase family 20, domain 2 / Beta-hexosaminidase-like, domain 2 / Dockerin domain / Dockerin domain profile. / Dockerin type I domain / Dockerin type I repeat / Coagulation factor 5/8 C-terminal domain, discoidin domain / Dockerin domain superfamily / Coagulation factors 5/8 type C domain (FA58C) profile. / F5/8 type C domain / Coagulation factor 5/8 C-terminal domain / Galactose-binding domain-like / Glycosyl hydrolase, all-beta / Galactose-binding-like domain superfamily / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / Glycoside hydrolase superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Hyaluronoglucosaminidase / Hyaluronoglucosaminidase
Similarity search - Component
Biological speciesClostridium perfringens (bacteria)
MethodX-RAY DIFFRACTION / SIRAS / Resolution: 1.4 Å
AuthorsGrondin, J.M. / Ficko-Blean, E. / Boraston, A.B. / Smith, S.P.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)MOP 68913 Canada
CitationJournal: To Be Published
Title: Solution Structure and Dynamics of Full-length GH84A, a multimodular B-N-acetylglucosaminidase from Clostridium perfringens
Authors: Grondin, J.M. / Chitayat, S. / Ficko-Blean, E. / Czjzek, M. / Boraston, A.B. / Smith, S.P.
History
DepositionJul 7, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 9, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
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.ptnr2_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Hyaluronoglucosaminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,1374
Polymers18,9951
Non-polymers1423
Water5,459303
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area300 Å2
ΔGint-8 kcal/mol
Surface area7570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.102, 64.709, 37.723
Angle α, β, γ (deg.)90.00, 94.52, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Hyaluronoglucosaminidase / Hyaluronidase


Mass: 18995.051 Da / Num. of mol.: 1 / Fragment: UNP residues 1067-1229
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium perfringens (bacteria) / Strain: ATCC 13124 / NCTC 8237 / Type A / Gene: nagH, CPF_0184 / Production host: Escherichia coli (E. coli)
References: UniProt: Q0TUP2, UniProt: A0A0H2YRL1*PLUS, hyaluronoglucosaminidase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 303 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsFull sequence of expressed protein is: ...Full sequence of expressed protein is: MGSSHHHHHHSSGLVPRGSHMASVYEPSLVDAYVGDDGAKKAVDGDLKTRVKFLGAPSTGDTIVYDLGQEILVDNLKYVVLDTEVDHVRDGKIQLSLDGETWTDAINIGDGVENGVDDMFSTPLKNGYKHGNQSGGIVPIDSAYVEGDNLNQKARYVRILFTAPYRHRWTVINELMINNGEYIPTVNDPT, the sequence "MGSSHHHHHHSSGLVPR" was removed via thrombin cleavage prior to crystallization.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.25 Å3/Da / Density % sol: 45.38 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 12% PEG 20K 0.1M MES pH 6.5

-
Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: ROTATING ANODE / Type: OTHER / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 12, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.4→19.62 Å / Num. obs: 31314 / % possible obs: 94.6 % / Redundancy: 3.58 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 14.2
Reflection shellResolution: 1.4→1.45 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.263 / Mean I/σ(I) obs: 2.4 / % possible all: 75.2

-
Processing

Software
NameVersionClassification
PHENIX1.9_1678refinement
SHARPphasing
RefinementMethod to determine structure: SIRAS / Resolution: 1.4→19.617 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.41 / Phase error: 17.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1706 1586 5.07 %
Rwork0.1489 --
obs0.15 31301 94.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.4→19.617 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1227 0 6 303 1536
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061279
X-RAY DIFFRACTIONf_angle_d1.0731740
X-RAY DIFFRACTIONf_dihedral_angle_d11.795466
X-RAY DIFFRACTIONf_chiral_restr0.077194
X-RAY DIFFRACTIONf_plane_restr0.004229
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4001-1.44520.4221170.39712095X-RAY DIFFRACTION74
1.4452-1.49690.27051510.252613X-RAY DIFFRACTION92
1.4969-1.55680.211380.18462657X-RAY DIFFRACTION94
1.5568-1.62760.18241590.1662686X-RAY DIFFRACTION95
1.6276-1.71340.19551410.16192752X-RAY DIFFRACTION96
1.7134-1.82070.20551370.16452722X-RAY DIFFRACTION96
1.8207-1.96110.16921240.14792796X-RAY DIFFRACTION97
1.9611-2.15820.15761480.13552811X-RAY DIFFRACTION98
2.1582-2.470.16251470.14362830X-RAY DIFFRACTION99
2.47-3.110.15861690.14752853X-RAY DIFFRACTION100
3.11-19.61850.15121550.12672900X-RAY DIFFRACTION100

+
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