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- PDB-6yf6: EclA C-terminal domain; sugar-binding protein -

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Basic information

Entry
Database: PDB / ID: 6yf6
TitleEclA C-terminal domain; sugar-binding protein
ComponentsGalactose-binding lectin
KeywordsSUGAR BINDING PROTEIN / EclA C-terminal domain
Function / homologyPA-IL-like / PA-IL-like protein / Galactose-binding-like domain superfamily / metal ion binding / PHOSPHATE ION / methyl 1-seleno-alpha-L-fucopyranoside / CBM-cenC domain-containing protein
Function and homology information
Biological speciesEnterobacter cloacae subsp. cloacae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsKoehnke, J. / Sikandar, A.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)KO4116_3_1 Germany
CitationJournal: To Be Published
Title: EclA C-terminal domain; sugar-binding protein
Authors: Koehnke, J. / Sikandar, A.
History
DepositionMar 26, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 7, 2021Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Galactose-binding lectin
B: Galactose-binding lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5187
Polymers31,8602
Non-polymers6575
Water4,324240
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6070 Å2
ΔGint-29 kcal/mol
Surface area13490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.512, 63.671, 134.009
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Galactose-binding lectin


Mass: 15930.045 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacter cloacae subsp. cloacae (strain ATCC 13047 / DSM 30054 / NBRC 13535 / NCDC 279-56) (bacteria)
Gene: ECL_04191 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0H3CQ33
#2: Sugar ChemComp-SFU / methyl 1-seleno-alpha-L-fucopyranoside / METHYL 6-DEOXY-1-SELENO-ALPHA-L-GALACTOPYRANOSIDE / methyl 1-seleno-alpha-L-fucoside / methyl 1-seleno-L-fucoside / methyl 1-seleno-fucoside


Type: L-saccharide / Mass: 241.144 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H14O4Se
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Ca
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 240 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.63 Å3/Da / Density % sol: 53.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 100-280 mM disodium phosphate, 16-22% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Aug 24, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2→46.16 Å / Num. obs: 22990 / % possible obs: 99.6 % / Redundancy: 25.6 % / Biso Wilson estimate: 22.19 Å2 / CC1/2: 1 / Net I/σ(I): 35.6
Reflection shellResolution: 2→2.05 Å / Num. unique obs: 1594 / CC1/2: 0.994

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Processing

Software
NameVersionClassification
Aimless1.16_3549refinement
PHENIX1.16_3549refinement
xia2data reduction
Aimlessdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2→36.57 Å / SU ML: 0.1801 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.7532
RfactorNum. reflection% reflection
Rfree0.2371 1131 4.94 %
Rwork0.1901 --
obs0.1923 22899 99.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 39.17 Å2
Refinement stepCycle: LAST / Resolution: 2→36.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2200 0 31 240 2471
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00332275
X-RAY DIFFRACTIONf_angle_d0.60563080
X-RAY DIFFRACTIONf_chiral_restr0.0466345
X-RAY DIFFRACTIONf_plane_restr0.0031387
X-RAY DIFFRACTIONf_dihedral_angle_d2.88871336
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.090.27921340.2352588X-RAY DIFFRACTION97.04
2.09-2.20.27341430.20822694X-RAY DIFFRACTION99.79
2.2-2.340.25211550.20542655X-RAY DIFFRACTION99.86
2.34-2.520.24611300.20552722X-RAY DIFFRACTION99.93
2.52-2.770.3161550.21392724X-RAY DIFFRACTION99.86
2.77-3.170.2581500.20212710X-RAY DIFFRACTION99.76
3.17-40.17921210.17262751X-RAY DIFFRACTION98.49
4-36.570.211430.16792924X-RAY DIFFRACTION99.9
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)
12.55524374299-0.1761950362270.04411756404810.17772050118-1.032540795396.708250152610.2358520669230.0462058347093-0.379552279611.34931177066-0.112040283480.1740547684810.243817045123-0.0455827162303-0.2505123017960.818402729811-0.01551196928120.09751689650660.2067172483740.08301028635450.320323915663-9.2212632930134.7192642474-15.7718356896
20.283968936001-0.3562188677560.2266673820891.02040161844-1.201044702911.36261921664-0.0238264950857-0.05794285558170.01740554111960.02570229801430.04403469583590.0494383685721-0.06900990134050.0018818206231-0.03612710712590.255069405345-0.0250832876695-0.003592598153910.226971920434-0.0116074361640.2174178362384.4537814257423.2553895091-20.6039149962
38.522833597840.4924734042617.420629834222.1040573293-0.3072577407947.931192254090.254516355805-0.0358146126677-0.2253090482240.164966636622-0.07010612758120.1946729598150.442355287158-0.0482548956446-0.2283283101140.2012756363360.02681078575080.06507358959970.173136841298-0.008555509733390.1647867513481.9359074464714.0619381897-14.3395764219
42.252718528151.019988389992.604243841571.826214542920.8276895969097.029187796480.109719088316-0.124598640097-0.02053675362030.170871375894-0.0552658967420.09429304169590.155603135482-0.191076488963-0.05012793655040.1893466446940.0189850272510.0429943370310.168453499175-0.005543051714290.1700491181593.3197662689715.815879866-14.5471447705
57.399114276860.6046172621483.893727170910.952878456056-0.7470548167845.16933250693-0.3178045535040.3087960941340.3385802085320.22116725371-0.0725184262948-0.0169418384584-1.084302494040.5379374716110.3567832469460.32836729327-0.06289535585030.005197537310650.2122864708730.01539191638890.22440573750814.479843310524.6764397954-17.2807430614
60.684993309491-1.54561638809-0.1122655307646.57983409013-0.4153784466410.693393043262-0.0760710428281-0.008485268558650.07020803020930.3350982812260.0584078939036-0.0559908466794-0.2339737193650.06394865255720.003249858668390.318038391829-0.0276263901222-0.03822275980130.206023681976-0.002093188239710.1594191406682.2343671252133.1911957458-26.5852985456
70.594998106629-0.233513117670.03048619372490.2783720077540.01106753810493.427043915360.192049490567-0.126093450512-0.01645122195651.58643991284-0.0182079046057-0.360950122152-0.2789828628880.0741181186199-0.04320190964881.18452807874-0.0715788804527-0.05377016323720.3062012537330.001833813488180.2869823268340.9403064865345.3595002477-13.4901871475
86.20428698799-2.7750501346-6.126652474551.354714024693.222559077398.04686322173-0.0419154519815-0.6506001259080.06004319428841.239084921970.0837826432388-0.0897722198616-0.05494432572470.583615362403-0.1266905074691.31265020257-0.170538915269-0.1563168032650.4104910828960.01309551727690.4189452457991.9980115666742.1097297245-5.83973373115
90.6679828340890.0327086145614-0.5076628527440.159638614677-0.6486967064184.695420286420.155890689264-0.177719529319-0.05878153479141.29468339638-0.0186458501146-0.0474242020676-0.15582690443-0.0564508280611-0.05135714559261.00173368533-0.0390937898409-0.01458838970160.2768041561490.03440850973250.262459752321-2.5478033092545.756055211-15.0948022309
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 144 through 158 )
2X-RAY DIFFRACTION2chain 'A' and (resid 159 through 203 )
3X-RAY DIFFRACTION3chain 'A' and (resid 204 through 232 )
4X-RAY DIFFRACTION4chain 'A' and (resid 233 through 283 )
5X-RAY DIFFRACTION5chain 'B' and (resid 143 through 158 )
6X-RAY DIFFRACTION6chain 'B' and (resid 159 through 188 )
7X-RAY DIFFRACTION7chain 'B' and (resid 189 through 244 )
8X-RAY DIFFRACTION8chain 'B' and (resid 245 through 252 )
9X-RAY DIFFRACTION9chain 'B' and (resid 253 through 283 )

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