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- PDB-6kgd: Crystal structure of CaDoc0917(R49D)-CaCohA2 complex at pH 8.0 -

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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 / hydrolase activity, hydrolyzing O-glycosyl compounds / metal ion binding
Similarity search - Function
Carbohydrate binding X2 domain / Carbohydrate binding domain X2 / Type 1 dockerin domain / Dockerin domain / Cellulosome anchoring protein, cohesin domain / Cohesin domain / Cellulose binding domain / Cellulose binding domain / Carbohydrate-binding module 3 / Carbohydrate-binding module 3 superfamily ...Carbohydrate binding X2 domain / Carbohydrate binding domain X2 / Type 1 dockerin domain / Dockerin domain / Cellulosome anchoring protein, cohesin domain / Cohesin domain / Cellulose binding domain / Cellulose binding domain / Carbohydrate-binding module 3 / Carbohydrate-binding module 3 superfamily / CBM3 (carbohydrate binding type-3) domain profile. / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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

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Experimental details

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Experiment

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

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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

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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

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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

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