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- PDB-6kgf: Crystal structure of CaDoc0917(R16D)-CaCohA2 complex at pH 8.2 -

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Basic information

Entry
Database: PDB / ID: 6kgf
TitleCrystal structure of CaDoc0917(R16D)-CaCohA2 complex at pH 8.2
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: 2.3 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 / Structure summary / Category: audit_author / citation / citation_author
Item: _audit_author.name / _citation.country ..._audit_author.name / _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
C: Probably cellulosomal scaffolding protein, secreted cellulose-binding and cohesin domain
D: And cellulose-binding endoglucanase family 9 CelL ortholog dockerin domain
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)44,5788
Polymers44,4184
Non-polymers1604
Water3,549197
1
C: Probably cellulosomal scaffolding protein, secreted cellulose-binding and cohesin domain
D: 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
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1400 Å2
ΔGint-8 kcal/mol
Surface area9860 Å2
MethodPISA
2
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
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1430 Å2
ΔGint-23 kcal/mol
Surface area9680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.650, 75.970, 120.330
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.: 2
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.: 2 / Mutation: R16D
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.: 4 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 197 / 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: 2.17 Å3/Da / Density % sol: 43.26 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop
Details: crystals were obtained with 0.2 M MgCl2, 0.1 M sodium acetate, and 25% (w/v) PEG 3350 at pH 5.5, and soaked into 0.2 M sodium acetate, 0.1 M Tris-HCl, and 30% (w/v) PEG 4000 at pH 8.2 for 10 minutes.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97852 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97852 Å / Relative weight: 1
ReflectionResolution: 2.3→47.165 Å / Num. obs: 32350 / % possible obs: 98.7 % / Redundancy: 3.271 % / Biso Wilson estimate: 32.92 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.112 / Rrim(I) all: 0.134 / Χ2: 1.124 / Net I/σ(I): 7.31 / Num. measured all: 105812 / Scaling rejects: 56
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
2.3-2.363.3960.4892.548207242524170.8630.58299.7
2.36-2.423.360.4762.657873235923430.8680.56899.3
2.42-2.493.3940.442.917762229322870.8880.52399.7
2.49-2.573.3290.3373.527428224022310.9350.40399.6
2.57-2.663.30.347086217221470.9410.35998.8
2.66-2.753.0590.2554.446385210920870.940.30999
2.75-2.852.9430.2174.85772198819610.9640.26498.6
2.85-2.973.4490.1826.316774198119640.9720.21599.1
2.97-3.13.4250.1557.246189182218070.9770.18499.2
3.1-3.253.3960.1278.546014178417710.9810.15199.3
3.25-3.433.260.1069.985509171916900.9830.12798.3
3.43-3.643.2770.09511.155125159415640.9850.11498.1
3.64-3.893.0910.08811.554476149714480.9860.10796.7
3.89-4.22.770.07711.683681141313290.9840.09594.1
4.2-4.63.4090.07414.074336129312720.9880.08998.4
4.6-5.143.3360.0714.133850116611540.990.08499
5.14-5.943.370.06714.073421102110150.9920.0899.4
5.94-7.273.1360.06513.4626288548380.990.07898.1
7.27-10.293.0920.06414.5920596786660.9870.07698.2
10.29-47.1653.4460.07116.112373613590.9890.08499.4

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Processing

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

1ohz


Resolution: 2.3→47.165 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 27.81
RfactorNum. reflection% reflection
Rfree0.2486 3234 10 %
Rwork0.2005 --
obs0.2054 32327 98.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 141.37 Å2 / Biso mean: 49.5384 Å2 / Biso min: 19 Å2
Refinement stepCycle: final / Resolution: 2.3→47.165 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3032 0 4 197 3233
Biso mean--32.81 37.75 -
Num. residues----413
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.3-2.33430.34281470.2611128599
2.3343-2.37070.26211370.26211260100
2.3707-2.40960.35051440.2703128099
2.4096-2.45120.36411450.2746130299
2.4512-2.49570.34851360.2613123199
2.4957-2.54370.27731450.2619128599
2.5437-2.59560.3281410.25841272100
2.5956-2.65210.37421420.2756126598
2.6521-2.71380.32931410.2701128299
2.7138-2.78160.32241410.251126199
2.7816-2.85680.25811370.2495125099
2.8568-2.94090.35461380.2348130199
2.9409-3.03580.32821410.2542127099
3.0358-3.14430.29231390.2345125199
3.1443-3.27010.29471420.2123127899
3.2701-3.41890.26831390.2019125598
3.4189-3.59910.20341430.1818126498
3.5991-3.82450.24261360.1722124097
3.8245-4.11960.20061360.1598122694
4.1196-4.53390.21431310.1485123598
4.5339-5.18930.1531440.1465127299
5.1893-6.53520.21761410.159126499
6.5352-47.1650.17341480.1672126499
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.2769-5.06080.48535.24950.60082.6030.1351-0.4482-0.1036-0.4046-0.30830.3186-1.7952-0.59140.13150.552-0.00670.04310.3994-0.04460.4877-20.10145.9949-5.9272
22.0053-0.00270.92185.59161.20250.89290.00710.1138-0.0292-0.5986-0.16150.4703-0.0075-0.11010.14160.3607-0.0088-0.04130.22820.03690.2125-11.3596-0.5765-21.1738
38.7254-3.39720.83438.28931.2344.15210.18260.36730.542-1.2372-0.247-0.111-0.3979-0.21090.08780.5031-0.01740.02840.2458-0.0110.2235-7.641510.3218-20.236
40.4401-0.06450.47343.92772.18362.23960.0654-0.0135-0.0021-0.4352-0.2920.5311-0.2682-0.36140.29710.50130.0731-0.08560.29580.02370.3555-14.436610.1277-19.6226
50.91960.18880.39544.66552.20523.16280.0209-0.0314-0.0203-0.0242-0.0194-0.245-0.01530.2868-0.02490.26930.05870.06240.27160.06340.1741-9.51590.0494-13.1362
65.7458-3.6507-3.04985.83383.09042.97460.4686-0.01730.20410.4947-0.07880.2681-0.0113-0.2112-0.10210.648-0.14550.02810.2150.02780.2864-14.4672-7.1457-16.7006
76.69492.88780.1917.72293.76882.5099-0.303-0.06540.5023-0.24570.3488-0.1166-0.55240.7342-0.05080.4748-0.0161-0.0640.3066-0.0150.30739.249924.739-8.149
87.51343.58141.28446.64784.69167.8739-0.19720.70570.2934-0.79810.16190.4099-0.1860.32920.19270.381-0.01930.01860.2410.02170.24413.138618.2641-16.274
96.55542.88980.03476.61674.97364.6291-0.3163-0.2605-0.4228-0.34840.181-0.6455-0.16230.58350.21050.35160.0716-0.02490.22550.0630.3446.494613.2653-10.4825
105.999-1.02360.14658.71793.70175.6003-0.4919-0.14270.25760.0027-0.13220.6725-0.7922-0.04280.580.41970.0425-0.13220.3149-0.02960.3032-3.511321.5318-7.3787
113.8165-2.47160.0914.5170.10462.32370.26310.2788-0.265-0.5746-0.17960.11040.0484-0.1202-0.07410.4369-0.0501-0.08030.2701-0.01990.22686.429711.0673-48.5361
124.5761-6.31642.56459.5104-3.36976.1710.06081.0041-0.7861-0.6657-0.38190.02720.00140.50080.43740.4423-0.13310.00630.3253-0.03410.554114.632314.0243-49.6589
135.9724-2.3159-1.42568.31820.83421.67810.3224-0.4113-0.75960.29450.18180.43340.6072-0.2746-0.42930.4431-0.114-0.12470.28580.07820.349312.4967-5.096-29.1806
140.4533-0.3241-0.38972.7759-1.34751.37190.4568-0.0870.10070.4313-0.33260.4879-0.1190.0829-0.09460.469-0.03340.03330.27540.01510.52458.03171.6482-26.9156
157.30444.63573.54417.30695.90097.79380.31260.3267-0.29110.308-0.1855-0.63360.29110.36320.01240.3835-0.0114-0.12710.37160.06160.368419.2475-1.3365-35.7865
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'C' and (resid 0 through 10 )C0 - 10
2X-RAY DIFFRACTION2chain 'C' and (resid 11 through 55 )C11 - 55
3X-RAY DIFFRACTION3chain 'C' and (resid 56 through 83 )C56 - 83
4X-RAY DIFFRACTION4chain 'C' and (resid 84 through 105 )C84 - 105
5X-RAY DIFFRACTION5chain 'C' and (resid 106 through 133 )C106 - 133
6X-RAY DIFFRACTION6chain 'C' and (resid 134 through 146 )C134 - 146
7X-RAY DIFFRACTION7chain 'D' and (resid 0 through 14 )D0 - 14
8X-RAY DIFFRACTION8chain 'D' and (resid 15 through 25 )D15 - 25
9X-RAY DIFFRACTION9chain 'D' and (resid 26 through 47 )D26 - 47
10X-RAY DIFFRACTION10chain 'D' and (resid 48 through 61 )D48 - 61
11X-RAY DIFFRACTION11chain 'A' and (resid 4 through 126 )A4 - 126
12X-RAY DIFFRACTION12chain 'A' and (resid 127 through 146 )A127 - 146
13X-RAY DIFFRACTION13chain 'B' and (resid 1 through 25 )B1 - 25
14X-RAY DIFFRACTION14chain 'B' and (resid 26 through 37 )B26 - 37
15X-RAY DIFFRACTION15chain 'B' and (resid 38 through 61 )B38 - 61

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