[English] 日本語
Yorodumi
- PDB-6kgd: Crystal structure of CaDoc0917(R49D)-CaCohA2 complex at pH 8.0 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6kgd
TitleCrystal structure of CaDoc0917(R49D)-CaCohA2 complex at pH 8.0
Components
  • And cellulose-binding endoglucanase family 9 CelL ortholog dockerin domain
  • Probably cellulosomal scaffolding protein, secreted cellulose-binding and cohesin domain
KeywordsHYDROLASE / cohesin / dockerin / cellulosome / calcium-binding
Function / homology
Function and homology information


cellulose binding / polysaccharide catabolic process / cellulose catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds / metal ion binding
Similarity search - Function
Type 1 dockerin domain / Dockerin domain / Carbohydrate binding X2 domain / Carbohydrate binding domain X2 / Cellulosome anchoring protein, cohesin domain / Cohesin domain / Cellulose binding domain / Carbohydrate-binding module 3 / Cellulose binding domain / CBM3 (carbohydrate binding type-3) domain profile. ...Type 1 dockerin domain / Dockerin domain / Carbohydrate binding X2 domain / Carbohydrate binding domain X2 / Cellulosome anchoring protein, cohesin domain / Cohesin domain / Cellulose binding domain / Carbohydrate-binding module 3 / Cellulose binding domain / CBM3 (carbohydrate binding type-3) domain profile. / Carbohydrate-binding module 3 superfamily / Glycoside hydrolase family 9 / Glycosyl hydrolase family 9 / Parallel beta-helix repeat / Parallel beta-helix repeats / Dockerin domain / Dockerin domain profile. / Dockerin type I domain / Dockerin type I repeat / Dockerin domain superfamily / CBM2/CBM3, carbohydrate-binding domain superfamily / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / Immunoglobulin E-set / Immunoglobulin-like fold / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Probably cellulosomal scaffolding protein, secreted cellulose-binding and cohesin domain / And cellulose-binding endoglucanase family 9 CelL ortholog dockerin domain
Similarity search - Component
Biological speciesClostridium acetobutylicum ATCC 824 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsFeng, Y. / Yao, X.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China31270784 China
National Natural Science Foundation of China31670735 China
CitationJournal: Sci Adv / Year: 2020
Title: Discovery and mechanism of a pH-dependent dual-binding-site switch in the interaction of a pair of protein modules.
Authors: Yao, X. / Chen, C. / Wang, Y. / Dong, S. / Liu, Y.J. / Li, Y. / Cui, Z. / Gong, W. / Perrett, S. / Yao, L. / Lamed, R. / Bayer, E.A. / Cui, Q. / Feng, Y.
History
DepositionJul 11, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 8, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 4, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 22, 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: Probably cellulosomal scaffolding protein, secreted cellulose-binding and cohesin domain
B: And cellulose-binding endoglucanase family 9 CelL ortholog dockerin domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2894
Polymers22,2092
Non-polymers802
Water4,954275
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1360 Å2
ΔGint-7 kcal/mol
Surface area9550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)31.110, 62.500, 100.320
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Probably cellulosomal scaffolding protein, secreted cellulose-binding and cohesin domain


Mass: 15624.421 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium acetobutylicum ATCC 824 (bacteria)
Strain: ATCC 824 / Gene: CA_C0910 / Plasmid: pET28a-SMT3 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q977Y4
#2: Protein And cellulose-binding endoglucanase family 9 CelL ortholog dockerin domain


Mass: 6584.346 Da / Num. of mol.: 1 / Mutation: R49D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium acetobutylicum ATCC 824 (bacteria)
Strain: ATCC 824 / Gene: CA_C0917 / Plasmid: pET28a-SMT3 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): Rosetta / References: UniProt: Q97KK2
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 275 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.29 Å3/Da / Density % sol: 46.18 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop
Details: 0.2 M sodium acetate, 0.1 M Tris-HCl, and 30% (w/v) PEG4000 at pH 8.0

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 3, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.65→39.119 Å / Num. obs: 44604 / % possible obs: 98.1 % / Redundancy: 3.514 % / Biso Wilson estimate: 14.19 Å2 / CC1/2: 0.978 / Rmerge(I) obs: 0.125 / Rrim(I) all: 0.147 / Χ2: 1.024 / Net I/σ(I): 7.9 / Num. measured all: 156729
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.65-1.692.2510.1963.97170334831850.9140.25195.1
1.69-1.742.6450.1894.548600328932510.9290.23698.8
1.74-1.793.4860.1855.7811130319531930.950.21999.9
1.79-1.843.7970.1696.7511776310331010.9590.19799.9
1.84-1.913.7720.1647.211263299029860.9550.19199.9
1.91-1.973.7750.1527.7710945290328990.9630.17799.9
1.97-2.053.7740.1468.3710586281028050.9630.17199.8
2.05-2.133.7750.1378.7110073267026680.9650.1699.9
2.13-2.223.7760.1368.979881262026170.9710.15899.9
2.22-2.333.7680.1349.189153243124290.9640.15699.9
2.33-2.463.7550.139.268836235623530.9650.15299.9
2.46-2.613.780.1319.568490224922460.9650.15299.9
2.61-2.793.7650.1279.687835208320810.970.14899.9
2.79-3.013.7490.1249.937202192219210.9720.14599.9
3.01-3.33.6930.1179.986643180317990.9680.13799.8
3.3-3.693.5710.1159.945739162516070.9620.13798.9
3.69-4.263.4280.1089.774638140813530.9630.12896.1
4.26-5.223.1680.1079.373387122410690.9570.12987.3
5.22-7.383.3130.1049.5726809208090.9580.12587.9
7.38-39.1193.0260.0978.997025082320.970.11745.7

-
Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX(1.13_2998: ???)refinement
PHASERphasing
XDSdata reduction
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OHZ

1ohz


Resolution: 1.65→39.119 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.41 / Phase error: 15.93
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I_MINUS AND I_PLUS COLUMNS.
RfactorNum. reflection% reflection
Rfree0.1881 3722 8.34 %
Rwork0.1516 --
obs0.1545 44604 98.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 101.69 Å2 / Biso mean: 23.4857 Å2 / Biso min: 7.41 Å2
Refinement stepCycle: final / Resolution: 1.65→39.119 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1493 0 2 275 1770
Biso mean--17.04 34.68 -
Num. residues----203
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.65-1.67080.23441320.186139992
1.6708-1.69270.20691360.1877151797
1.6927-1.71590.25891370.1776152798
1.7159-1.74040.22221430.1671540100
1.7404-1.76640.16371340.15661504100
1.7664-1.7940.15291450.14831569100
1.794-1.82340.19851410.15391549100
1.8234-1.85490.19071390.15891532100
1.8549-1.88860.19461420.16581521100
1.8886-1.92490.20871420.15411561100
1.9249-1.96420.18391370.16061533100
1.9642-2.00690.22121440.14551549100
2.0069-2.05360.20221380.15481543100
2.0536-2.1050.2121460.15071552100
2.105-2.16190.15941400.15481503100
2.1619-2.22550.22191450.14951591100
2.2255-2.29730.16021370.1441494100
2.2973-2.37940.15321400.13871573100
2.3794-2.47470.17851420.13591530100
2.4747-2.58730.16761360.14031570100
2.5873-2.72360.20631390.14361519100
2.7236-2.89420.18851390.15231539100
2.8942-3.11760.20911430.15211561100
3.1176-3.43120.18571360.1515153899
3.4312-3.92730.17391380.1422152399
3.9273-4.94640.1441270.1311139891
4.9464-39.1190.23871040.1979114774
Refinement TLS params.Method: refined / Origin x: 4.2389 Å / Origin y: -0.3016 Å / Origin z: -30.088 Å
111213212223313233
T0.0798 Å20.0036 Å20.0087 Å2-0.0813 Å2-0.0125 Å2--0.0903 Å2
L0.4042 °20.162 °20.4027 °2-0.2665 °20.0862 °2--0.706 °2
S-0.0112 Å °0.0051 Å °-0.0259 Å °-0.0397 Å °0.0125 Å °0.0002 Å °-0.0453 Å °-0.005 Å °-0.0006 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 146
2X-RAY DIFFRACTION1allA147 - 389
3X-RAY DIFFRACTION1allB5 - 61
4X-RAY DIFFRACTION1allB62 - 118

+
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