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- PDB-5hch: X-ray structure of a lectin-bound DNA duplex containing an unnatu... -

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Basic information

Entry
Database: PDB / ID: 5hch
TitleX-ray structure of a lectin-bound DNA duplex containing an unnatural phenanthrenyl pair
Components
  • DNA (5'-D(*CP*GP*CP*AP*TP*TP*(DF)P*TP*AP*TP*CP*GP*C)-3')
  • DNA (5'-D(P*GP*CP*GP*AP*TP*AP*(DF)P*AP*AP*TP*GP*CP*G)-3')
  • Fucose-binding lectin
KeywordsSUGAR BINDING PROTEIN / LECB / COMPLEX / ARTIFICIAL DNA / PHENANTHRENE
Function / homology
Function and homology information


single-species biofilm formation / carbohydrate binding / metal ion binding
Similarity search - Function
Lectin, sugar-binding / Calcium-mediated lectin / Calcium-mediated lectin / Calcium-mediated lectin superfamily / Fucose-binding lectin II (PA-IIL) / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Chem-61J / DNA / DNA (> 10) / Fucose-binding lectin / Fucose-binding lectin PA-IIL
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.9 Å
AuthorsRoethlisberger, P. / Istrate, A. / Marcaida Lopez, M.J. / Visini, R. / Stocker, A. / Leumann, C.J.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation20020_146646 Switzerland
CitationJournal: Chem.Commun.(Camb.) / Year: 2016
Title: X-ray structure of a lectin-bound DNA duplex containing an unnatural phenanthrenyl pair.
Authors: Roethlisberger, P. / Istrate, A. / Marcaida Lopez, M.J. / Visini, R. / Stocker, A. / Reymond, J.L. / Leumann, C.J.
History
DepositionJan 4, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 2, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 30, 2016Group: Database references
Revision 1.2Sep 13, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / struct_conn / Item: _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _chem_comp.type / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 10, 2024Group: 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: Fucose-binding lectin
B: DNA (5'-D(*CP*GP*CP*AP*TP*TP*(DF)P*TP*AP*TP*CP*GP*C)-3')
E: DNA (5'-D(P*GP*CP*GP*AP*TP*AP*(DF)P*AP*AP*TP*GP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0997
Polymers19,7403
Non-polymers3594
Water46826
1
A: Fucose-binding lectin
B: DNA (5'-D(*CP*GP*CP*AP*TP*TP*(DF)P*TP*AP*TP*CP*GP*C)-3')
E: DNA (5'-D(P*GP*CP*GP*AP*TP*AP*(DF)P*AP*AP*TP*GP*CP*G)-3')
hetero molecules

A: Fucose-binding lectin
B: DNA (5'-D(*CP*GP*CP*AP*TP*TP*(DF)P*TP*AP*TP*CP*GP*C)-3')
E: DNA (5'-D(P*GP*CP*GP*AP*TP*AP*(DF)P*AP*AP*TP*GP*CP*G)-3')
hetero molecules

A: Fucose-binding lectin
B: DNA (5'-D(*CP*GP*CP*AP*TP*TP*(DF)P*TP*AP*TP*CP*GP*C)-3')
E: DNA (5'-D(P*GP*CP*GP*AP*TP*AP*(DF)P*AP*AP*TP*GP*CP*G)-3')
hetero molecules

A: Fucose-binding lectin
B: DNA (5'-D(*CP*GP*CP*AP*TP*TP*(DF)P*TP*AP*TP*CP*GP*C)-3')
E: DNA (5'-D(P*GP*CP*GP*AP*TP*AP*(DF)P*AP*AP*TP*GP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,39828
Polymers78,96112
Non-polymers1,43716
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_585-x,-y+3,z1
crystal symmetry operation9_555-x,-x+y,-z+1/31
crystal symmetry operation12_585x,x-y+3,-z+1/31
MethodPISA
Unit cell
Length a, b, c (Å)60.451, 60.451, 204.828
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number180
Space group name H-MP6222
Components on special symmetry positions
IDModelComponents
11B-101-

NA

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Components

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DNA chain , 2 types, 2 molecules BE

#2: DNA chain DNA (5'-D(*CP*GP*CP*AP*TP*TP*(DF)P*TP*AP*TP*CP*GP*C)-3')


Mass: 3953.676 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(P*GP*CP*GP*AP*TP*AP*(DF)P*AP*AP*TP*GP*CP*G)-3')


Mass: 4051.752 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Fucose-binding lectin / Fucose-binding lectin II (PA-IIL) / Fucose-binding lectin PA-IIL / Photopexin A


Mass: 11734.707 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria)
Gene: lecB, AN280_27645, AN399_05715, AN400_17270, AN446_25935, AN447_15925, AOD73_08535, AOX61_23230, AOX62_26425, APG03_22020, APG04_23970, APG05_03535, APG06_28020, APG07_27985, ERS445055_01627, ...Gene: lecB, AN280_27645, AN399_05715, AN400_17270, AN446_25935, AN447_15925, AOD73_08535, AOX61_23230, AOX62_26425, APG03_22020, APG04_23970, APG05_03535, APG06_28020, APG07_27985, ERS445055_01627, PA8380_17510, PAERUG_E15_London_28_01_14_00983, PAERUG_P32_London_17_VIM_2_10_11_00423, PAMH19_1713, PAO1OR1608
Production host: Escherichia coli (E. coli) / References: UniProt: A0A069Q9V4, UniProt: Q9HYN5*PLUS
#6: Sugar ChemComp-61J / (6S)-2,6-anhydro-1-deoxy-6-(2-{[(S)-hydroxy(oxido)-lambda~5~-phosphanyl]oxy}ethyl)-D-galactitol


Type: D-saccharide / Mass: 256.190 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H17O7P

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Non-polymers , 3 types, 29 molecules

#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / 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: 2.84 Å3/Da / Density % sol: 56.68 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.02 M Sodium acetate trihydrate, 0.1 M TRIS hydrochloride, 30% w/v PEG4000
PH range: 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.99995 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99995 Å / Relative weight: 1
ReflectionResolution: 2.9→46.62 Å / Num. obs: 5374 / % possible obs: 98.4 % / Redundancy: 11.4 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 20.54
Reflection shellResolution: 2.9→3.08 Å / Redundancy: 11.4 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 6.08 / % possible all: 90.2

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.96 Å46.6 Å
Translation2.96 Å46.6 Å

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Processing

Software
NameVersionClassification
PHENIXrefinement
PHASER2.5.6phasing
PDB_EXTRACT3.15data extraction
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OXC

1oxc


Resolution: 2.9→46.616 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.41 / Phase error: 25.05
RfactorNum. reflection% reflectionSelection details
Rfree0.2574 538 10.01 %Random Selection
Rwork0.2271 ---
obs0.2302 5373 98.46 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 231.68 Å2 / Biso mean: 91 Å2 / Biso min: 28.67 Å2
Refinement stepCycle: final / Resolution: 2.9→46.616 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms827 537 19 26 1409
Biso mean--86.96 60.73 -
Num. residues----140
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0131457
X-RAY DIFFRACTIONf_angle_d2.1212096
X-RAY DIFFRACTIONf_chiral_restr0.026248
X-RAY DIFFRACTIONf_plane_restr0.022184
X-RAY DIFFRACTIONf_dihedral_angle_d23.367533
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9002-3.19190.36691220.28741095X-RAY DIFFRACTION94
3.1919-3.65370.25361320.23651187X-RAY DIFFRACTION100
3.6537-4.60260.2791350.2381218X-RAY DIFFRACTION100
4.6026-46.62150.22341490.20251335X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -30.2495 Å / Origin y: 76.3711 Å / Origin z: 45.5062 Å
111213212223313233
T0.2992 Å2-0.3256 Å2-0.0147 Å2-0.6137 Å2-0.1619 Å2--0.8695 Å2
L0.9534 °2-0.1726 °20.2247 °2-2.8749 °20.0187 °2--2.9723 °2
S-0.2259 Å °-0.192 Å °0.0235 Å °0.8077 Å °-0.0191 Å °-0.6621 Å °0.0478 Å °0.7103 Å °0.2871 Å °
Refinement TLS groupSelection details: all

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