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- PDB-6lx0: Structure of Leptospira santarosai serovar shermani LRR protein L... -

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Basic information

Entry
Database: PDB / ID: 6lx0
TitleStructure of Leptospira santarosai serovar shermani LRR protein LSS11580
ComponentsMembrane protein
KeywordsUNKNOWN FUNCTION / Leptospira / Leptospirosis / Leucine-rich repeat / CELL ADHESION / MEMBRANE PROTEIN
Function / homology: / Leucine-rich repeats, bacterial type / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Membrane protein
Function and homology information
Biological speciesLeptospira santarosai serovar Shermani str. LT 821 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsChu, C.H. / Hsu, S.H. / Yang, C.W. / Sun, Y.J.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, Taiwan) Taiwan
CitationJournal: Biochem.J. / Year: 2020
Title: Crystal structure of Leptospira leucine-rich repeat 20 reveals a novel E-cadherin binding protein to induce NGAL expression in HK2 cells.
Authors: Hsu, S.H. / Chu, C.H. / Tian, Y.C. / Chang, M.Y. / Chou, L.F. / Sun, Y.J. / Yang, C.W.
History
DepositionFeb 10, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 23, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: 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

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Assembly

Deposited unit
A: Membrane protein


Theoretical massNumber of molelcules
Total (without water)24,5821
Polymers24,5821
Non-polymers00
Water1,38777
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7330 Å2
Unit cell
Length a, b, c (Å)47.301, 47.301, 120.500
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Membrane protein / leucine-rich repeat 20


Mass: 24581.539 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leptospira santarosai serovar Shermani str. LT 821 (bacteria)
Gene: LSS_11580 / Plasmid: pET30b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: K8Y7G8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / 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

Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1M Tris hydrochloride (pH 8.5), 0.2M Sodium acetate trihydrate, 30% (w/v) Polyethylene glycol 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Oct 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.99→44.03 Å / Num. obs: 10011 / % possible obs: 99.7 % / Redundancy: 12.6 % / CC1/2: 0.998 / CC star: 0.999 / Net I/σ(I): 3.4
Reflection shellResolution: 1.99→2.02 Å / Redundancy: 13.2 % / Num. unique obs: 486 / CC1/2: 0.896 / CC star: 0.972 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
SCALEPACKdata scaling
PDB_EXTRACT3.25data extraction
ADDREFdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4PQ8

4pq8


Resolution: 1.99→19.959 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 22.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2316 511 5.13 %RANDOM
Rwork0.1972 9445 --
obs0.199 9956 99.64 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 61.37 Å2 / Biso mean: 25.1418 Å2 / Biso min: 10.5 Å2
Refinement stepCycle: final / Resolution: 1.99→19.959 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1090 0 0 77 1167
Biso mean---32.84 -
Num. residues----135
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071099
X-RAY DIFFRACTIONf_angle_d0.9011482
X-RAY DIFFRACTIONf_chiral_restr0.049182
X-RAY DIFFRACTIONf_plane_restr0.005189
X-RAY DIFFRACTIONf_dihedral_angle_d16.014712
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9903-2.19040.25751400.1862283100
2.1904-2.50680.23181160.2012330100
2.5068-3.15630.29561130.22182374100
3.1563-19.9590.2031420.1873245899

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