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- PDB-8ebf: C-terminal (TPR) domain of LIC11990 from Leptospira interrogans -

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Basic information

Entry
Database: PDB / ID: 8ebf
TitleC-terminal (TPR) domain of LIC11990 from Leptospira interrogans
ComponentsCytoplasmic membrane protein
KeywordsUNKNOWN FUNCTION / tetra-trico-peptide repeats / pathogenesis / virulence / leptospirosis
Function / homology
Function and homology information


membrane => GO:0016020
Similarity search - Function
Tetratricopeptide repeat 1 / Tetratricopeptide repeat / Tetratricopeptide repeat / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
ACETATE ION / Cytoplasmic membrane protein
Similarity search - Component
Biological speciesLeptospira interrogans serovar Copenhageni (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsLarrieux, N. / Buschiazzo, A.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structure and function of a novel membrane-associated protein from Leptospira interrogans (gene LIC11990)
Authors: Wunder, E.A. / Larrieux, N. / Buschiazzo, A.
History
DepositionAug 31, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2022Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytoplasmic membrane protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,8776
Polymers82,5161
Non-polymers3615
Water50428
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.656, 100.093, 170.205
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Cytoplasmic membrane protein


Mass: 82515.867 Da / Num. of mol.: 1 / Fragment: C-terminal (TPR) domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leptospira interrogans serovar Copenhageni (bacteria)
Gene: LIC_11990 / Plasmid: pQE30 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: Q72QW8
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.61 Å3/Da / Density % sol: 52.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9 / Details: 18% (w/v) PEG 3350, 0.3 M magnesium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97948 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 2, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97948 Å / Relative weight: 1
ReflectionResolution: 2.5→43.68 Å / Num. obs: 29774 / % possible obs: 96.5 % / Redundancy: 6.5 % / Biso Wilson estimate: 76.5 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.09 / Net I/σ(I): 11.9
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 6 % / Mean I/σ(I) obs: 1 / Num. unique obs: 1503 / CC1/2: 0.6 / Rrim(I) all: 1.8 / % possible all: 98.8

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Processing

Software
NameVersionClassification
BUSTER2.10.4 (8-JUN-2022)refinement
autoPROCdata processing
XDSdata reduction
Aimlessdata scaling
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 2.5→43.68 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.912 / SU R Cruickshank DPI: 0.48 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.469 / SU Rfree Blow DPI: 0.292 / SU Rfree Cruickshank DPI: 0.298
RfactorNum. reflection% reflectionSelection details
Rfree0.2776 1465 -RANDOM
Rwork0.2355 ---
obs0.2377 29774 96.5 %-
Displacement parametersBiso mean: 85.5 Å2
Baniso -1Baniso -2Baniso -3
1--30.9669 Å20 Å20 Å2
2--12.1431 Å20 Å2
3---18.8238 Å2
Refine analyzeLuzzati coordinate error obs: 0.43 Å
Refinement stepCycle: LAST / Resolution: 2.5→43.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5325 0 24 28 5377
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0075463HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.867371HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1912SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes948HARMONIC5
X-RAY DIFFRACTIONt_it5463HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion688SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact4353SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.6
X-RAY DIFFRACTIONt_other_torsion20.16
LS refinement shellResolution: 2.5→2.52 Å
RfactorNum. reflection% reflection
Rfree0.4442 43 -
Rwork0.3917 --
obs0.3955 596 96.41 %
Refinement TLS params.

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 °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.4519-0.22960.27441.27050.3091.7344-0.18790.433-0.07160.4330.1635-0.0395-0.0716-0.03950.02430.7571-0.002-0.03310.33350.05050.45427.237112.974441.5986
20.6483-0.6528-0.27242.27540.212812.052-0.00030.34240.29150.3424-0.2263-0.38990.2915-0.38990.22660.5207-0.1560.05390.6501-0.02730.477426.664320.3766.3797
33.65250.9061.12375.09332.77966.6590.3250.04551.07390.0455-0.0256-0.16241.0739-0.1624-0.29950.585-0.0179-0.00130.4516-0.03980.510132.58069.0239-16.8995
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|513 - A|944 }A513 - 944
2X-RAY DIFFRACTION2{ A|945 - A|1045 }A945 - 1045
3X-RAY DIFFRACTION3{ A|1046 - A|1191 }A1046 - 1191

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