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- PDB-6t96: Photorhabdus laumondii subsp. laumondii lectin PLL3 -

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Basic information

Entry
Database: PDB / ID: 6t96
TitlePhotorhabdus laumondii subsp. laumondii lectin PLL3
ComponentsLectin PLL3
KeywordsSUGAR BINDING PROTEIN / lectin / beta-propeller / carbohydrate-binding protein
Function / homologyPhotorhabdus luminescens subsp. laumondii TTO1 complete genome segment 3/17
Function and homology information
Biological speciesPhotorhabdus laumondii subsp. laumondii TTO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsMelicher, F. / Houser, J. / Fujdiarova, E. / Faltinek, L. / Wimmerova, M.
CitationJournal: Molecules / Year: 2019
Title: Lectin PLL3, a Novel Monomeric Member of the Seven-Bladed beta-Propeller Lectin Family.
Authors: Faltinek, L. / Fujdiarova, E. / Melicher, F. / Houser, J. / Kasakova, M. / Kondakov, N. / Kononov, L. / Parkan, K. / Vidal, S. / Wimmerova, M.
History
DepositionOct 26, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 25, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_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_type.id
Revision 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lectin PLL3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,5482
Polymers40,5251
Non-polymers231
Water5,855325
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation, analytical centrifugation, sedimentation velocity
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-13 kcal/mol
Surface area13630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.582, 69.416, 76.706
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Lectin PLL3


Mass: 40525.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: CYS at position 347 is found to be oxidized in the X-ray structure
Source: (gene. exp.) Photorhabdus laumondii subsp. laumondii TTO1 (bacteria)
Gene: plu0735 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7N8I7
#2: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 325 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 1.86 Å3/Da / Density % sol: 33.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M NaF, 14% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.65→45.53 Å / Num. all: 37089 / Num. obs: 37089 / % possible obs: 99.9 % / Redundancy: 7.3 % / CC1/2: 0.997 / Rmerge(I) obs: 0.143 / Rpim(I) all: 0.057 / Rrim(I) all: 0.154 / Rsym value: 0.143 / Net I/σ(I): 8.2 / Num. measured all: 271406
Reflection shellResolution: 1.65→1.74 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.989 / Num. unique obs: 5293 / CC1/2: 0.708 / Rpim(I) all: 0.024 / Rrim(I) all: 0.065 / Rsym value: 0.06 / % possible all: 99.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
SCALA3.3.22data scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5C9P

5c9p


Resolution: 1.65→45.53 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.959 / SU B: 2.568 / SU ML: 0.082 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.105 / ESU R Free: 0.098 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.196 1804 4.9 %RANDOM
Rwork0.1693 ---
obs0.1706 35215 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 70.58 Å2 / Biso mean: 18.29 Å2 / Biso min: 10.09 Å2
Baniso -1Baniso -2Baniso -3
1--0.87 Å2-0 Å2-0 Å2
2---1.12 Å20 Å2
3---1.99 Å2
Refinement stepCycle: final / Resolution: 1.65→45.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2695 0 1 327 3023
Biso mean--45.22 29.1 -
Num. residues----348
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0122887
X-RAY DIFFRACTIONr_bond_other_d0.0010.0182432
X-RAY DIFFRACTIONr_angle_refined_deg1.4761.6153992
X-RAY DIFFRACTIONr_angle_other_deg1.4331.5655645
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.3245374
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.04822.986144
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.90915391
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.1071513
X-RAY DIFFRACTIONr_chiral_restr0.0730.2377
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023396
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02655
LS refinement shellResolution: 1.65→1.693 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.263 130 -
Rwork0.269 2552 -
all-2682 -
obs--99.96 %

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