[English] 日本語
Yorodumi
- PDB-1mac: CRYSTAL STRUCTURE AND SITE-DIRECTED MUTAGENESIS OF BACILLUS MACER... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1mac
TitleCRYSTAL STRUCTURE AND SITE-DIRECTED MUTAGENESIS OF BACILLUS MACERANS ENDO-1,3-1,4-BETA-GLUCANASE
Components1,3-1,4-BETA-D-GLUCAN 4-GLUCANOHYDROLASE
KeywordsHYDROLASE (GLUCANASE)
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 speciesPaenibacillus macerans (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.3 Å
AuthorsHahn, M. / Heinemann, U.
Citation
Journal: J.Biol.Chem. / Year: 1995
Title: Crystal structure and site-directed mutagenesis of Bacillus macerans endo-1,3-1,4-beta-glucanase.
Authors: Hahn, M. / Olsen, O. / Politz, O. / Borriss, R. / Heinemann, U.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1993
Title: Molecular and Active-Site Structure of a Bacillus 1,3-1,4-Beta-Glucanase
Authors: Keitel, T. / Simon, O. / Borriss, R. / Heinemann, U.
History
DepositionDec 22, 1994Processing site: BNL
Revision 1.0Feb 27, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / 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.process_site / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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_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: 1,3-1,4-BETA-D-GLUCAN 4-GLUCANOHYDROLASE
B: 1,3-1,4-BETA-D-GLUCAN 4-GLUCANOHYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,7334
Polymers47,6522
Non-polymers802
Water3,153175
1
A: 1,3-1,4-BETA-D-GLUCAN 4-GLUCANOHYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8662
Polymers23,8261
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 1,3-1,4-BETA-D-GLUCAN 4-GLUCANOHYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8662
Polymers23,8261
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)203.680, 42.410, 60.700
Angle α, β, γ (deg.)90.00, 101.27, 90.00
Int Tables number5
Space group name H-MC121
Atom site foot note1: CIS PROLINE - PRO A 199 / 2: CIS PROLINE - PRO B 199
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.3583, -0.69916, 0.61871), (-0.76118, -0.60249, -0.24003), (0.54058, -0.38494, -0.74806)
Vector: 83.36453, 85.95627, -4.24362)
DetailsMTRIX THE TRANSFORMATIONS PRESENTED ON MTRIX RECORDS BELOW DESCRIBE NON-CRYSTALLOGRAPHIC RELATIONSHIPS AMONG THE VARIOUS DOMAINS IN THIS ENTRY. APPLYING THE APPROPRIATE MTRIX TRANSFORMATION TO THE RESIDUES LISTED FIRST WILL YIELD APPROXIMATE COORDINATES FOR THE RESIDUES LISTED SECOND. APPLIED TO TRANSFORMED TO MTRIX RESIDUES RESIDUES RMSD M1 B 1 .. B 212 A 1 .. A 212 0.422 ROTATION AND TRANSLATION MATRIX OF LEAST-SQUARES FIT OF ALL C-ALPHA POSITIONS.

-
Components

#1: Protein 1,3-1,4-BETA-D-GLUCAN 4-GLUCANOHYDROLASE


Mass: 23826.232 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paenibacillus macerans (bacteria) / Plasmid: PBR322 PUC19 / Production host: Escherichia coli (E. coli) / References: UniProt: P23904, 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.: 175 / Source method: isolated from a natural source / Formula: H2O
Source detailsBETA-GLUCANASE FROM BACILLUS MACERANS.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 54.39 %
Crystal grow
*PLUS
pH: 4.3 / Method: vapor diffusion, hanging drop / Details: using macroseeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
16 mg/mlB.macerans beta-glucanase1drop
210 mMsodium acetate1drop
35 mM1dropCaCl2
430 %(w/v)ammonium sulfate1reservoir
520 mM1reservoirMgCl2

-
Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 16.9 Å / Num. obs: 16928 / % possible obs: 72.9 % / Rmerge(I) obs: 0.106

-
Processing

SoftwareName: TNT / Classification: refinement
RefinementResolution: 2.3→8 Å / σ(F): 2 /
RfactorNum. reflection
obs0.163 16417
Refinement stepCycle: LAST / Resolution: 2.3→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3380 0 2 175 3557
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 35.3 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONt_bond_d0.0090.011
X-RAY DIFFRACTIONt_angle_d
X-RAY DIFFRACTIONt_angle_deg2.292.41
X-RAY DIFFRACTIONt_dihedral_angle_d28.4226.89

+
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