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- PDB-7t7y: The crystal structure of family 8 carbohydrate-binding module fro... -

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Basic information

Entry
Database: PDB / ID: 7t7y
TitleThe crystal structure of family 8 carbohydrate-binding module from Dictyostelium discoideum complexed with iodine atoms
ComponentsEndoglucanase
KeywordsSUGAR BINDING PROTEIN / Carbohydrate-binding protein / ligand specificity / cellulose / CAZymes
Function / homology
Function and homology information


spore germination / cellulose binding / cellulase / cellulase activity / sporulation resulting in formation of a cellular spore / cellulose catabolic process / extracellular region
Similarity search - Function
Glycosyl hydrolases family 9 (GH9) active site signature 1. / Glycoside hydrolase family 9, His active site / Glycosyl hydrolases family 9 (GH9) active site signature 2. / Glycosyl hydrolases family 9, Asp/Glu active sites / Glycosyl hydrolases family 9 (GH9) active site signature 3. / Glycoside hydrolase family 9 / Glycosyl hydrolase family 9 / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily
Similarity search - Domain/homology
IODIDE ION / Endoglucanase
Similarity search - Component
Biological speciesDictyostelium discoideum (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.81 Å
AuthorsMarcelo, M.V. / Campos, B.M. / Squina, F.M.
Funding support Brazil, 3items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2014/04105-4 Brazil
Sao Paulo Research Foundation (FAPESP)2015/50590-4 Brazil
Brazilian National Council for Scientific and Technological Development (CNPq)310177/2011-1 Brazil
CitationJournal: J.Biol.Chem. / Year: 2022
Title: Unique properties of a Dictyostelium discoideum carbohydrate-binding module expand our understanding of CBM-ligand interactions.
Authors: Liberato, M.V. / Campos, B.M. / Tomazetto, G. / Crouch, L.I. / Garcia, W. / Zeri, A.C.M. / Bolam, D.N. / Squina, F.M.
History
DepositionDec 15, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 20, 2022Provider: repository / Type: Initial release
Revision 1.1May 18, 2022Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Endoglucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,4948
Polymers16,6051
Non-polymers8887
Water1,00956
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area940 Å2
ΔGint-2 kcal/mol
Surface area7050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.788, 47.267, 79.344
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11A-801-

IOD

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Components

#1: Protein Endoglucanase / Cellulase / Endo-1 / 4-beta-glucanase / Spore germination protein 270-6


Mass: 16605.338 Da / Num. of mol.: 1
Fragment: carbohydrate-binding module (UNP residues 555-705)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dictyostelium discoideum (eukaryote) / Gene: celA, DDB_G0271134 / Production host: Escherichia coli (E. coli) / References: UniProt: P22699
#2: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: I / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 2.08 Å3/Da / Density % sol: 40.78 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 1.6 M di-sodium DL-malate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.8 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.8 Å / Relative weight: 1
ReflectionResolution: 1.81→47.27 Å / Num. obs: 12778 / % possible obs: 96.9 % / Redundancy: 8.3 % / Biso Wilson estimate: 4.06 Å2 / CC1/2: 0.973 / Rmerge(I) obs: 0.171 / Rpim(I) all: 0.062 / Rrim(I) all: 0.183 / Net I/σ(I): 12 / Num. measured all: 106102
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.81-1.853.20.49819096050.6510.3140.5933.278.9
9.05-47.278.90.1112401390.9880.0370.11621.399.7

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Processing

Software
NameVersionClassification
Aimless0.5.8data scaling
PHENIX1.19.2refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
CRANK22.0.281phasing
RefinementMethod to determine structure: SAD / Resolution: 1.81→40.61 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.39 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2475 655 5.24 %
Rwork0.2315 11855 -
obs0.2324 12510 94.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 21.84 Å2 / Biso mean: 4.2789 Å2 / Biso min: 0.6 Å2
Refinement stepCycle: final / Resolution: 1.81→40.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1165 0 7 56 1228
Biso mean--10.24 12.17 -
Num. residues----154
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.81-1.950.28711110.27092029214083
1.95-2.150.22271210.23242442256399
2.15-2.460.25781430.23112428257199
2.46-3.090.26591420.23122438258098
3.1-40.610.22421380.21572518265696
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)
10.72610.21480.2610.81090.26460.8892-0.05520.0706-0.0756-0.05860.02430.20860.1176-0.1813-0.0314-0.0028-0.03750.00690.04380.01060.09390.77985.943413.92
20.3396-0.0875-0.09770.1807-0.00130.3218-0.0181-0.02-0.0017-0.0134-0.0474-0.02050.0490.0308-0.11720.01040.00930.00590.0349-0.00250.027713.363314.95220.5353
30.3701-0.01690.01770.2476-0.04960.18240.063-0.0211-0.0498-0.0348-0.00790.01690.0177-0.01440.04250.0104-0.0011-0.00650.05460.0090.02489.965910.530522.6914
40.1069-0.0532-0.15870.31370.07120.2618-0.0231-0.0231-0.00370.069-0.0094-0.05170.04230.0795-0.2115-0.00360.0157-0.0183-0.0299-0.0073-0.012513.18221.330927.6589
51.4825-0.9955-0.08481.01390.06290.1665-0.0394-0.12720.00760.03790.04060.0782-0.0396-0.0809-0.1327-0.00150.01290.0260.0650.00040.04723.366613.266632.1918
60.3424-0.0868-0.020.2502-0.06370.25780.01150.0136-0.01190.00110.0150.0457-0.0031-0.01770.0910.02040.00180.01870.05520.02510.05019.10340.646532.7397
70.5525-0.0251-0.03920.6085-0.08750.1709-0.0291-0.020.02910.03840.02430.1106-0.0325-0.0298-0.05620.0260.0045-0.02340.08620.04040.04320.17275.504927.5123
80.11320.0679-0.0670.32910.07240.3817-0.004-0.0374-0.02320.0910.0036-0.01480.00690.09420.0199-0.02420.01090.00930.00330.0120.030712.62857.285928.5951
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 552 through 561 )A552 - 561
2X-RAY DIFFRACTION2chain 'A' and (resid 562 through 581 )A562 - 581
3X-RAY DIFFRACTION3chain 'A' and (resid 582 through 617 )A582 - 617
4X-RAY DIFFRACTION4chain 'A' and (resid 618 through 632 )A618 - 632
5X-RAY DIFFRACTION5chain 'A' and (resid 633 through 641 )A633 - 641
6X-RAY DIFFRACTION6chain 'A' and (resid 642 through 662 )A642 - 662
7X-RAY DIFFRACTION7chain 'A' and (resid 663 through 681 )A663 - 681
8X-RAY DIFFRACTION8chain 'A' and (resid 682 through 705 )A682 - 705

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