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- PDB-7yjw: Structure of Leptospira santarosai serovar shermani LRR protein L... -

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Basic information

Entry
Database: PDB / ID: 7yjw
TitleStructure of Leptospira santarosai serovar shermani LRR protein LSS01692
ComponentsMembrane protein
KeywordsMEMBRANE PROTEIN / Leptospira / Leptospirosis / Leucine-rich repeat / CELL ADHESION
Function / homology
Function and homology information


Leucine rich repeat 4 / Leucine Rich repeats (2 copies) / Leucine-rich repeats, bacterial type / Leucine-rich repeat, SDS22-like subfamily / 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
Similarity search - Domain/homology
Leucine rich repeat protein
Similarity search - Component
Biological speciesLeptospira santarosai serovar Shermani (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsWu, C.T. / Hsu, S.H. / Yang, C.W. / Sun, Y.J.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, Taiwan) Taiwan
CitationJournal: Febs J. / Year: 2023
Title: Crystal structure of Leptospira LSS_01692 reveals a dimeric structure and induces inflammatory responses through Toll-like receptor 2-dependent NF-kappa B and MAPK signal transduction pathways.
Authors: Hsu, S.H. / Wu, C.T. / Sun, Y.J. / Chang, M.Y. / Li, C. / Ko, Y.C. / Chou, L.F. / Yang, C.W.
History
DepositionJul 20, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 28, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Nov 29, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Membrane protein
B: Membrane protein


Theoretical massNumber of molelcules
Total (without water)76,5562
Polymers76,5562
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1320 Å2
ΔGint1 kcal/mol
Surface area28490 Å2
Unit cell
Length a, b, c (Å)65.713, 78.862, 66.578
Angle α, β, γ (deg.)90.000, 106.030, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 30 through 36 or resid 38 through 240 or resid 242 through 330))
21(chain B and (resid 30 through 36 or resid 38...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYGLUGLU(chain A and (resid 30 through 36 or resid 38 through 240 or resid 242 through 330))AA30 - 3630 - 36
12ALAALASERSER(chain A and (resid 30 through 36 or resid 38 through 240 or resid 242 through 330))AA38 - 24038 - 240
13LEULEUPHEPHE(chain A and (resid 30 through 36 or resid 38 through 240 or resid 242 through 330))AA242 - 330242 - 330
21GLYGLYGLUGLU(chain B and (resid 30 through 36 or resid 38...BB30 - 3630 - 36
22ALAALAASNASN(chain B and (resid 30 through 36 or resid 38...BB38 - 4138 - 41
23VALVALSERSER(chain B and (resid 30 through 36 or resid 38...BB45 - 24045 - 240
24LEULEUPHEPHE(chain B and (resid 30 through 36 or resid 38...BB242 - 330242 - 330

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Components

#1: Protein Membrane protein


Mass: 38277.754 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leptospira santarosai serovar Shermani (bacteria)
Gene: LSS_01692 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: K8Y546

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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: 2.17 Å3/Da / Density % sol: 43.21 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M Tris-HCl (pH=8.5), 2% Tasimate pH, and 16% PEG3350

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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: RAYONIX MX300HE / Detector: CCD / Date: Jun 27, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.2→30 Å / Num. obs: 10860 / % possible obs: 99 % / Redundancy: 3.7 % / Biso Wilson estimate: 47.6 Å2 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.049 / Rrim(I) all: 0.094 / Χ2: 0.923 / Net I/σ(I): 10.5 / Num. measured all: 39710
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.2-3.263.20.6195020.8630.3980.7380.80498.2
3.26-3.313.40.6295720.7140.3910.7420.80198.3
3.31-3.383.60.5685120.7630.3530.6710.923100
3.38-3.453.70.4485540.8580.2720.5250.86299.3
3.45-3.523.70.4185470.8590.2540.490.911100
3.52-3.63.80.2865260.9310.170.3330.88399.6
3.6-3.693.80.2355640.9590.140.2740.97599.8
3.69-3.793.80.1865390.9660.1110.2170.98299.4
3.79-3.93.70.1315390.9860.0790.1541.03799.8
3.9-4.033.80.1215450.9830.0720.1410.96299.8
4.03-4.173.80.1045570.990.0620.1210.97399.3
4.17-4.343.80.0955320.9890.0560.1110.93399.3
4.34-4.543.70.0785440.9920.0470.0911.01399.1
4.54-4.783.70.0635450.9940.0380.0740.91499.1
4.78-5.073.70.0565520.9960.0340.0661.01899.1
5.07-5.463.70.0625340.9970.0370.0721.0998
5.46-6.013.70.0555510.9960.0330.0651.01899.1
6.01-6.873.60.0395490.9980.0240.0460.89798.6
6.87-8.623.60.0295570.9990.0180.0340.79698.9
8.62-303.40.01453910.0090.0160.59594.7

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
SCALEPACKdata scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4U06

4u06


Resolution: 3.2→29.65 Å / SU ML: 0.46 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 31.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3039 983 10.01 %
Rwork0.2528 8835 -
obs0.2578 9818 90.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 113.28 Å2 / Biso mean: 45.3715 Å2 / Biso min: 9.37 Å2
Refinement stepCycle: final / Resolution: 3.2→29.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4824 0 0 0 4824
Num. residues----599
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1778X-RAY DIFFRACTION1.744TORSIONAL
12B1778X-RAY DIFFRACTION1.744TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.2-3.370.3356870.347875684355
3.37-3.580.39061240.31631148127282
3.58-3.850.34531580.26211373153199
3.86-4.240.27881540.239113881542100
4.24-4.850.27481490.21891384153399
4.85-6.10.27971500.24991412156299
6.11-29.650.29121610.23751374153597
Refinement TLS params.

S33: -0 Å ° / Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.0007-0.0011-0.00310.0109-0.0023-0.00340.0270.008-0.0634-0.0220.05060.01970.0472-0.01790.29310.0423-0.03940.1007-0.23220.3298-14.5404-3.747387.4467
2-0.00910.00680.0250.01020.0230.0060.05960.1659-0.0895-0.02750.0151-0.0214-0.02190.08250.0202-0.0072-0.0057-0.1123-0.357-0.3216-3.494329.762685.581
3-0.0001-0.0007-0.0001-0.00010.00050.00010.0136-0.00040.0011-0.00840.0070.0011-0.0058-0.00640.49620.0705-0.00870.5233-0.04570.5621-34.203963.6788111.4715
40.0058-0.0035-0.00050.0073-0.00450.0012-0.00020.0210.01050.0213-0.00670.0204-0.03610.01250.2420.00710.04070.232-0.09150.4076-20.99457.5931109.4933
5-0.00370.00760.00220.0070.0040.0094-0.0133-0.06460.04310.0081-0.10790.0782-0.01220.04850.0571-0.0391-0.00580.0517-0.1736-0.1413-10.258637.949116.3302
60.00230.0001-0.00170.00720.00440.0071-0.0080.015-0.03670.0012-0.05250.0342-0.00730.02930.21790.0201-0.01430.09360.01090.0454-16.54512.3259119.2055
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 30 through 144 )A30 - 144
2X-RAY DIFFRACTION2chain 'A' and (resid 145 through 330 )A145 - 330
3X-RAY DIFFRACTION3chain 'B' and (resid 30 through 51 )B30 - 51
4X-RAY DIFFRACTION4chain 'B' and (resid 52 through 118 )B52 - 118
5X-RAY DIFFRACTION5chain 'B' and (resid 119 through 233 )B119 - 233
6X-RAY DIFFRACTION6chain 'B' and (resid 234 through 330 )B234 - 330

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