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- PDB-6f37: Fusion protein of RSL and trimeric coiled coil -

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Basic information

Entry
Database: PDB / ID: 6f37
TitleFusion protein of RSL and trimeric coiled coil
ComponentsNano3,Fucose-binding lectin protein
KeywordsSUGAR BINDING PROTEIN / genetic fusion / coiled-coil / lectin / trimer
Function / homologyFucose-specific lectin / Fungal fucose-specific lectin / carbohydrate binding / beta-D-mannopyranose / Fucose-binding lectin protein
Function and homology information
Biological speciesRalstonia solanacearum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsWronska, M.A. / Rennie, M.L. / Crowley, P.B.
Funding support Ireland, 1items
OrganizationGrant numberCountry
Science Foundation Ireland13/CDA/2168 Ireland
CitationJournal: To Be Published
Title: Fusion protein of RSL and trimeric coiled coil
Authors: Wronska, M.A. / Rennie, M.L. / Crowley, P.B.
History
DepositionNov 28, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 12, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nano3,Fucose-binding lectin protein
B: Nano3,Fucose-binding lectin protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2437
Polymers24,3152
Non-polymers9285
Water1,33374
1
A: Nano3,Fucose-binding lectin protein
hetero molecules

A: Nano3,Fucose-binding lectin protein
hetero molecules

A: Nano3,Fucose-binding lectin protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,17512
Polymers36,4723
Non-polymers1,7039
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area10840 Å2
ΔGint-16 kcal/mol
Surface area15280 Å2
MethodPISA
2
B: Nano3,Fucose-binding lectin protein
hetero molecules

B: Nano3,Fucose-binding lectin protein
hetero molecules

B: Nano3,Fucose-binding lectin protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5539
Polymers36,4723
Non-polymers1,0816
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_544z+1/2,-x-1/2,-y-11
crystal symmetry operation12_444-y-1/2,-z-1,x-1/21
Buried area9250 Å2
ΔGint-27 kcal/mol
Surface area15500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.760, 88.760, 88.760
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11A-247-

HOH

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Components

#1: Protein Nano3,Fucose-binding lectin protein / Putative fucose-binding lectin protein


Mass: 12157.452 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ralstonia solanacearum (bacteria) / Plasmid: pET-25b(+) / Gene: RSP795_21825, RSP799_05830, RUN39_v1_50103 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0S4TLR1
#2: Sugar
ChemComp-BMA / beta-D-mannopyranose / beta-D-mannose / D-mannose / mannose / Mannose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DManpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-mannopyranoseCOMMON NAMEGMML 1.0
b-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-NHE / 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID / N-CYCLOHEXYLTAURINE / CHES / CHES (buffer)


Mass: 207.290 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H17NO3S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 74 / Source method: isolated from a natural source / Formula: H2O

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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: 2.4 Å3/Da / Density % sol: 48.68 % / Description: Cubic
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 9.5 / Details: 20% PEG 8000, 0.1 M CHES pH 9.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 11, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.2→88.76 Å / Num. obs: 12123 / % possible obs: 100 % / Redundancy: 13.2 % / CC1/2: 0.997 / Rmerge(I) obs: 0.178 / Rpim(I) all: 0.051 / Rrim(I) all: 0.185 / Net I/σ(I): 21.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.2-2.27140.51110190.5540.1410.531100
9.07-88.7690.0652040.9980.0230.06999.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
MxCuBEdata collection
MOSFLMdata reduction
Aimless0.5.27data scaling
PHASERphasing
Cootmodel building
REFMACrefinement
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BT9 chain A

2bt9


Resolution: 2.2→62.81 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.928 / SU B: 7.352 / SU ML: 0.178 / SU R Cruickshank DPI: 0.3069 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.307 / ESU R Free: 0.22
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2469 605 5 %RANDOM
Rwork0.2076 ---
obs0.2096 11491 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 291.94 Å2 / Biso mean: 61.227 Å2 / Biso min: 20.12 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 2.2→62.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1691 0 61 74 1826
Biso mean--70.06 41.78 -
Num. residues----225
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.021794
X-RAY DIFFRACTIONr_bond_other_d0.0010.021628
X-RAY DIFFRACTIONr_angle_refined_deg1.0131.9292451
X-RAY DIFFRACTIONr_angle_other_deg0.78833752
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0955223
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.83824.06264
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.60315257
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.495156
X-RAY DIFFRACTIONr_chiral_restr0.0550.2288
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021976
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02406
LS refinement shellResolution: 2.201→2.258 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 44 -
Rwork0.335 840 -
all-884 -
obs--100 %

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