[English] 日本語
Yorodumi
- PDB-6k53: A variant of metagenome-derived GH6 cellobiohydrolase, HmCel6A (P... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6k53
TitleA variant of metagenome-derived GH6 cellobiohydrolase, HmCel6A (P88S/L230F/F414S)
ComponentsGH6 cellobiohydrolase, HMCEL6A
KeywordsHYDROLASE / glycoside hydrolase / GH6 / thermostable
Function / homology1, 4-beta cellobiohydrolase / TIM Barrel / Alpha-Beta Barrel / Alpha Beta / CITRATE ANION / :
Function and homology information
Biological speciesmetagenome (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsBaba, S. / Takeda, M. / Okuma, J. / Hirose, Y. / Nishimura, A. / Takata, M. / Oda, K. / Shibata, D. / Kondo, Y. / Kumasaka, T.
CitationJournal: To Be Published
Title: A hyperthermophilic GH6 cellobiohydrolase (HmCel6A) from a hot spring metagenomic data
Authors: Takeda, M. / Baba, S. / Okuma, J. / Hirose, Y. / Nishimura, A. / Takata, M. / Oda, K. / Shibata, D. / Kondo, Y. / Kumasaka, T.
History
DepositionMay 28, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 3, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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
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
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: GH6 cellobiohydrolase, HMCEL6A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,0654
Polymers46,8621
Non-polymers2033
Water12,358686
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area750 Å2
ΔGint-11 kcal/mol
Surface area16150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.885, 141.885, 224.099
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-651-

HOH

21A-974-

HOH

31A-1213-

HOH

41A-1217-

HOH

51A-1222-

HOH

61A-1278-

HOH

71A-1280-

HOH

81A-1282-

HOH

-
Components

#1: Protein GH6 cellobiohydrolase, HMCEL6A


Mass: 46862.129 Da / Num. of mol.: 1 / Mutation: P88S/L230F/F414S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) metagenome (others) / Production host: Escherichia coli (E. coli)
References: cellulose 1,4-beta-cellobiosidase (non-reducing end)
#2: Chemical ChemComp-LI / LITHIUM ION


Mass: 6.941 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Li
#3: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 686 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsFIRST MET IS A INITIATING METHIONINE. THIS DNA SEQUENCE HAS BEEN DEPOSITED TO DDBJ WITH A ...FIRST MET IS A INITIATING METHIONINE. THIS DNA SEQUENCE HAS BEEN DEPOSITED TO DDBJ WITH A LOCUS/ACCESSION NUMBER OF LC163906. P88S/ L230F/F414S ARE MUTATIONS.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.63 Å3/Da / Density % sol: 73.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 20% (W/V) PEG 1000, 0.2M LITHIUM SULFATE, 0.1M PHOSPHATE-CITRATE (PH 4.2)

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 29, 2012
RadiationMonochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.89→50 Å / Num. obs: 69369 / % possible obs: 100 % / Redundancy: 10.6 % / Biso Wilson estimate: 20.4113940266 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.025 / Rrim(I) all: 0.08 / Net I/σ(I): 28.1
Reflection shellResolution: 1.89→1.96 Å / Redundancy: 10.2 % / Rmerge(I) obs: 0.578 / Mean I/σ(I) obs: 5.3 / Num. unique obs: 6865 / CC1/2: 0.941 / Rpim(I) all: 0.19 / Rrim(I) all: 0.609 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6K52

6k52


Resolution: 1.89→33.049 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 18.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1887 3473 5.03 %
Rwork0.1601 --
obs0.1615 69101 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.89→33.049 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3303 0 15 686 4004
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073458
X-RAY DIFFRACTIONf_angle_d1.0644743
X-RAY DIFFRACTIONf_dihedral_angle_d20.8451281
X-RAY DIFFRACTIONf_chiral_restr0.078502
X-RAY DIFFRACTIONf_plane_restr0.005643
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.89-1.91590.32371280.24992640X-RAY DIFFRACTION100
1.9159-1.94330.29861340.22222620X-RAY DIFFRACTION100
1.9433-1.97230.22591310.20132595X-RAY DIFFRACTION100
1.9723-2.00310.19811480.17412591X-RAY DIFFRACTION100
2.0031-2.03590.19991480.16972604X-RAY DIFFRACTION100
2.0359-2.0710.19171410.16412620X-RAY DIFFRACTION100
2.071-2.10870.21331350.16532590X-RAY DIFFRACTION100
2.1087-2.14920.20281430.16712628X-RAY DIFFRACTION100
2.1492-2.19310.20321240.16692629X-RAY DIFFRACTION100
2.1931-2.24080.24031290.16392627X-RAY DIFFRACTION100
2.2408-2.29290.22221450.16822611X-RAY DIFFRACTION100
2.2929-2.35020.19311260.17482603X-RAY DIFFRACTION99
2.3502-2.41370.21411490.16992611X-RAY DIFFRACTION99
2.4137-2.48470.21371530.16612570X-RAY DIFFRACTION99
2.4847-2.56490.16941400.16692599X-RAY DIFFRACTION99
2.5649-2.65650.21181460.17052613X-RAY DIFFRACTION99
2.6565-2.76290.22951540.18122592X-RAY DIFFRACTION99
2.7629-2.88850.20211340.17462597X-RAY DIFFRACTION99
2.8885-3.04070.23311380.16952608X-RAY DIFFRACTION99
3.0407-3.23110.20021210.1692651X-RAY DIFFRACTION99
3.2311-3.48030.15261260.14942662X-RAY DIFFRACTION100
3.4803-3.83010.15991520.13182643X-RAY DIFFRACTION100
3.8301-4.38320.1391440.12982654X-RAY DIFFRACTION100
4.3832-5.51820.15211490.13092691X-RAY DIFFRACTION100
5.5182-33.05430.16411350.16242779X-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