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- PDB-5c9l: Crystal structure of native PLL lectin from Photorhabdus luminesc... -

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Basic information

Entry
Database: PDB / ID: 5c9l
TitleCrystal structure of native PLL lectin from Photorhabdus luminescens at 1.65 A resolution
ComponentsPLL lectin
KeywordsSUGAR BINDING PROTEIN / Lectin / seven-bladed beta-propeller / fucose-specific
Function / homologyProtein of unknown function DUF346 / Repeat of unknown function (DUF346) / metal ion binding / : / Photorhabdus luminescens subsp. laumondii TTO1 complete genome segment 3/17
Function and homology information
Biological speciesPhotorhabdus luminescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.65 Å
AuthorsKumar, A. / Sykorova, P. / Demo, G. / Dobes, P. / Hyrsl, P. / Wimmerova, M.
Funding support Czech Republic, 3items
OrganizationGrant numberCountry
Czech Science Foundation13-25401S Czech Republic
European Regional Development FundCZ.1.05/1.1.00/02.0068 Czech Republic
SYLICACZ.1.05/1.1.00/02.0068 Czech Republic
CitationJournal: J.Biol.Chem. / Year: 2016
Title: A Novel Fucose-binding Lectin from Photorhabdus luminescens (PLL) with an Unusual Heptabladed beta-Propeller Tetrameric Structure.
Authors: Kumar, A. / Sykorova, P. / Demo, G. / Dobes, P. / Hyrsl, P. / Wimmerova, M.
History
DepositionJun 27, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Oct 19, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 2, 2016Group: Database references
Revision 1.2Dec 7, 2016Group: Database references
Revision 1.3Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PLL lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,83916
Polymers40,4371
Non-polymers1,40215
Water6,720373
1
A: PLL lectin
hetero molecules

A: PLL lectin
hetero molecules

A: PLL lectin
hetero molecules

A: PLL lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)167,35764
Polymers161,7494
Non-polymers5,60760
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_655-x+1,y,-z1
crystal symmetry operation4_555x,-y,-z1
Buried area18540 Å2
ΔGint-224 kcal/mol
Surface area44030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.120, 87.677, 157.691
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
SymmetryPoint symmetry: (Schoenflies symbol: C2 (2 fold cyclic))
Components on special symmetry positions
IDModelComponents
11A-402-

HG

21A-862-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein PLL lectin


Mass: 40437.340 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Photorhabdus luminescens (bacteria) / References: UniProt: Q7N8J0

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Non-polymers , 6 types, 388 molecules

#2: Chemical ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Hg
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 373 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.96 Å3/Da / Density meas: 983296.125 Mg/m3 / Density % sol: 58.48 % / Description: prism
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.1 M Tris-HCl, 10% PEG 4000, 0.2 M CaCl2, pH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 1.005 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Aug 27, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.005 Å / Relative weight: 1
ReflectionResolution: 1.65→76.75 Å / Num. obs: 59360 / % possible obs: 99.7 % / Redundancy: 13.5 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 36.2
Reflection shellResolution: 1.65→1.74 Å / Redundancy: 13.7 % / Rmerge(I) obs: 0.154 / Mean I/σ(I) obs: 14.4 / % possible all: 99.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
SHELXDEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.65→39.15 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.962 / SU B: 1.048 / SU ML: 0.037 / Cross valid method: THROUGHOUT / ESU R: 0.065 / ESU R Free: 0.064 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.15894 3001 5.1 %RANDOM
Rwork0.14063 ---
obs0.14158 56352 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.117 Å2
Baniso -1Baniso -2Baniso -3
1-0.28 Å20 Å2-0 Å2
2--0.07 Å20 Å2
3----0.35 Å2
Refinement stepCycle: LAST / Resolution: 1.65→39.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2743 0 63 373 3179
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0680.0192959
X-RAY DIFFRACTIONr_bond_other_d0.0030.022689
X-RAY DIFFRACTIONr_angle_refined_deg2.3971.8844040
X-RAY DIFFRACTIONr_angle_other_deg1.24436158
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7835377
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.51224.275131
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.61515420
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5131514
X-RAY DIFFRACTIONr_chiral_restr0.1690.2446
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.023410
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02746
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.9521.1831448
X-RAY DIFFRACTIONr_mcbond_other1.951.1821447
X-RAY DIFFRACTIONr_mcangle_it2.7621.7721813
X-RAY DIFFRACTIONr_mcangle_other2.7621.7731814
X-RAY DIFFRACTIONr_scbond_it2.8211.41509
X-RAY DIFFRACTIONr_scbond_other2.8121.41509
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.8821.9832217
X-RAY DIFFRACTIONr_long_range_B_refined5.87411.2383721
X-RAY DIFFRACTIONr_long_range_B_other5.56310.4993519
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.178 250 -
Rwork0.14 4029 -
obs--98.53 %

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