[English] 日本語
Yorodumi
- PDB-6wni: Crystal structure of CldA, the first cyclomaltodextrin glucanotra... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6wni
TitleCrystal structure of CldA, the first cyclomaltodextrin glucanotransferase with a three-domain ABC distribution
ComponentsCyclomaltodextrin glucanotransferase
KeywordsTRANSFERASE / Cyclodextrin / Extremozyme / GH13 family / Starch
Function / homology
Function and homology information


alpha-amylase / alpha-amylase activity / carbohydrate metabolic process / calcium ion binding
Similarity search - Function
Alpha-amylase-like / Alpha-amylase, C-terminal domain / Aamy_C / Alpha-amylase/branching enzyme, C-terminal all beta / Alpha amylase, C-terminal all-beta domain / Alpha amylase / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Glycosyl hydrolase, all-beta ...Alpha-amylase-like / Alpha-amylase, C-terminal domain / Aamy_C / Alpha-amylase/branching enzyme, C-terminal all beta / Alpha amylase, C-terminal all-beta domain / Alpha amylase / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Glycosyl hydrolase, all-beta / Prokaryotic membrane lipoprotein lipid attachment site profile. / Glycoside hydrolase superfamily
Similarity search - Domain/homology
CITRATE ANION / DI(HYDROXYETHYL)ETHER / Alpha-amylase
Similarity search - Component
Biological speciesCaldanaerobacter subterraneus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.66 Å
AuthorsMagana-Cuevas, E. / Centeno-Leija, S. / Serrano-Posada, H.
Funding support Mexico, 3items
OrganizationGrant numberCountry
Consejo Nacional de Ciencia y Tecnologia (CONACYT)CB-2018-A1-S-18011 Mexico
Consejo Nacional de Ciencia y Tecnologia (CONACYT)CB-2016-01-285001 Mexico
Consejo Nacional de Ciencia y Tecnologia (CONACYT)INFR-2017-01-280608 Mexico
CitationJournal: To Be Published
Title: Discovery of a novel group of three-domain thermophilic cyclomaltodextrin glucanotransferases: structural and functional implications.
Authors: Centeno-Leija, S. / Lopez-Munguia, A. / Cardenas-Conejo, Y. / Mancilla-Margalli, N.A. / Velazquez-Cruz, B. / Magana-Cuevas, E. / Guerra-Borrego, Y. / Zatarain-Palacios, R. / Marin-Tovar, Y. ...Authors: Centeno-Leija, S. / Lopez-Munguia, A. / Cardenas-Conejo, Y. / Mancilla-Margalli, N.A. / Velazquez-Cruz, B. / Magana-Cuevas, E. / Guerra-Borrego, Y. / Zatarain-Palacios, R. / Marin-Tovar, Y. / Gomez-Manzo, S. / Marcial-Quino, J. / Hernandez-Ochoa, B. / Osuna-Castro, J.A. / Rudino-Pinera, E. / Serrano-Posada, H.
History
DepositionApr 22, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 28, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cyclomaltodextrin glucanotransferase
B: Cyclomaltodextrin glucanotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,20929
Polymers122,4082
Non-polymers2,80127
Water15,277848
1
A: Cyclomaltodextrin glucanotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,78717
Polymers61,2041
Non-polymers1,58316
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cyclomaltodextrin glucanotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,42212
Polymers61,2041
Non-polymers1,21811
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.440, 66.440, 209.500
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32

-
Components

#1: Protein Cyclomaltodextrin glucanotransferase


Mass: 61203.836 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caldanaerobacter subterraneus (bacteria)
Gene: O163_00610 / Plasmid: PET-22B / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS
References: UniProt: U5CJP3, cyclomaltodextrin glucanotransferase
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H5O7
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 848 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.28 Å3/Da / Density % sol: 46 %
Crystal growTemperature: 291 K / Method: microbatch / pH: 5.1 / Details: 0.2 M ammonium citrate dibasic, 20%(w/v) PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 1.19499 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Feb 8, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.19499 Å / Relative weight: 1
ReflectionResolution: 1.66→28.54 Å / Num. obs: 121677 / % possible obs: 99.5 % / Redundancy: 7.4 % / Biso Wilson estimate: 20.2 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.06 / Net I/σ(I): 16.3
Reflection shellResolution: 1.66→1.69 Å / Redundancy: 4 % / Rmerge(I) obs: 0.565 / Mean I/σ(I) obs: 2 / Num. unique obs: 5577 / CC1/2: 0.674 / % possible all: 92.8

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1QHO

1qho


Resolution: 1.66→28.502 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 24.5
RfactorNum. reflection% reflection
Rfree0.2119 6062 4.99 %
Rwork0.1884 --
obs0.1895 121556 99.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 75.81 Å2 / Biso mean: 24.2611 Å2 / Biso min: 10.21 Å2
Refinement stepCycle: final / Resolution: 1.66→28.502 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7979 0 177 848 9004
Biso mean--32.44 33.54 -
Num. residues----987
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.66-1.67890.34271670.3038348292
1.6789-1.69860.29061820.2901379396
1.6986-1.71940.27482190.2853381299
1.7194-1.74110.34511580.27653912100
1.7411-1.7640.27872480.2673790100
1.764-1.78820.29332060.2623922100
1.7882-1.81370.28221730.26813830100
1.8137-1.84080.31621920.26363892100
1.8408-1.86950.2582040.2523860100
1.8695-1.90020.31162400.25363849100
1.9002-1.9330.28921780.25873877100
1.933-1.96810.29881780.24413934100
1.9681-2.00590.23891580.24033922100
2.0059-2.04690.26231500.23673872100
2.0469-2.09140.30242300.2293901100
2.0914-2.140.24982080.22323882100
2.14-2.19350.24312610.22173758100
2.1935-2.25280.24352110.21393854100
2.2528-2.3190.2131740.20293911100
2.319-2.39390.21392080.19593884100
2.3939-2.47940.21432550.19753799100
2.4794-2.57860.23491920.19493883100
2.5786-2.69580.21322150.18413858100
2.6958-2.83790.22122240.18813843100
2.8379-3.01550.18422350.17863873100
3.0155-3.2480.19461900.16893849100
3.248-3.57430.17932450.15013849100
3.5743-4.09020.14952000.13363871100
4.0902-5.14830.13081580.1273903100
5.1483-28.5020.16522030.1537382999

+
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