[English] 日本語
Yorodumi
- PDB-1h0b: Endoglucanase cel12A from Rhodothermus marinus -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1h0b
TitleEndoglucanase cel12A from Rhodothermus marinus
ComponentsCELLULASE
KeywordsHYDROLASE / CELLULASE / ENDOGLUCANASE
Function / homology
Function and homology information


cellulase / cellulase activity / polysaccharide catabolic process
Similarity search - Function
Glycoside hydrolase family 12 / Glycosyl hydrolase family 12 / Glycoside hydrolase family 11/12, catalytic domain / Glycoside hydrolase family 11/12 / Prokaryotic membrane lipoprotein lipid attachment site profile. / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesRHODOTHERMUS MARINUS (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsCrennell, S.J. / Hreggvidsson, G.O. / Nordberg-Karlsson, E.
CitationJournal: J.Mol.Biol. / Year: 2002
Title: The Structure of Rhodothermus Marinus Cel12A, a Highly Thermostable Family 12 Endoglucanase, at 1.8 A Resolution
Authors: Crennell, S.J. / Hreggvidsson, G.O. / Nordberg Karlsson, E.
History
DepositionJun 17, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 12, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CELLULASE
B: CELLULASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,4844
Polymers57,0072
Non-polymers4772
Water5,044280
1
A: CELLULASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7422
Polymers28,5031
Non-polymers2381
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: CELLULASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7422
Polymers28,5031
Non-polymers2381
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)56.099, 67.779, 132.262
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.999284, 0.030096, -0.0229), (-0.036254, -0.934696, 0.353594), (-0.010762, 0.354171, 0.935119)
Vector: 26.621, 35.091, 3.176)

-
Components

#1: Protein CELLULASE


Mass: 28503.469 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN, RESIDUES 38-260
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RHODOTHERMUS MARINUS (bacteria) / Plasmid: PET25DELTA(SPL) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): LAMBDA(DE3)-LYSOGEN / References: UniProt: O33897, cellulase
#2: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 280 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsCONFLICTS BETWEEN SWISS-PROT ENTRY O33897 AND PDB ENTRY 1H0B ARE AS A RESULT OF RE-SEQUENCING OF ...CONFLICTS BETWEEN SWISS-PROT ENTRY O33897 AND PDB ENTRY 1H0B ARE AS A RESULT OF RE-SEQUENCING OF THE PROTEIN. RESIDUE TRP A 91 AND TRP B 91 ARE ALSO FROM THIS RE-SEQUENCING RUN. HIS-TAG SEQUENCE FROM RESIDUES 226-256, ONLY THE FIRST TWO RESIDUES FROM THESE TAGS WERE VISIBLE IN THE STRUCTURE.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.49 Å3/Da / Density % sol: 46 %
Crystal growpH: 7.5 / Details: 0.1M HEPES, PH7.5, 20% PEG10000, pH 7.50
Crystal grow
*PLUS
Temperature: 291 K / pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
114 mg/mlprotein1drop
20.1 MHEPES1reservoirpH7.5
320 %(w/v)PEG100001reservoir

-
Data collection

DiffractionMean temperature: 291 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 15, 2001 / Details: OSMIC MIRRORS
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. obs: 44464 / % possible obs: 93.4 % / Redundancy: 6.9 % / Biso Wilson estimate: 17.2 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 27.7
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.275 / Mean I/σ(I) obs: 5.5 / % possible all: 88.1
Reflection
*PLUS
Highest resolution: 1.8 Å / Num. measured all: 308104 / Rmerge(I) obs: 0.074
Reflection shell
*PLUS
% possible obs: 88.1 % / Rmerge(I) obs: 0.275 / Mean I/σ(I) obs: 5.3

-
Processing

Software
NameVersionClassification
CNS0.5refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1NLR

1nlr


Resolution: 1.8→28.49 Å / Rfactor Rfree error: 0.004 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.194 2258 5.1 %RANDOM
Rwork0.173 ---
obs0.173 44412 93.4 %-
Solvent computationSolvent model: BULK SOLVENT MODEL / Bsol: 38.3243 Å2 / ksol: 0.380923 e/Å3
Displacement parametersBiso mean: 22.38 Å2
Baniso -1Baniso -2Baniso -3
1-1.2 Å2--
2--1.17 Å2-
3----2.37 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.18 Å
Luzzati d res low-30 Å
Luzzati sigma a0.15 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 1.8→28.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3548 0 30 280 3858
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.33766
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.45402
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.92555
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.511.5
X-RAY DIFFRACTIONc_mcangle_it0.9162
X-RAY DIFFRACTIONc_scbond_it0.6392
X-RAY DIFFRACTIONc_scangle_it1.0472.5
LS refinement shellResolution: 1.8→1.88 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.255 265 5.1 %
Rwork0.237 4922 -
obs--88.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN.PARAMPROTEIN_REP.TOP
X-RAY DIFFRACTION2WATER.PARAMWATER_REP.TOP
X-RAY DIFFRACTION3EPE_XPLOR.PAREPE_XPLOR.TOP
Refinement
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 30 Å / Num. reflection obs: 42154
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.34
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.45402
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.92555

+
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