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- PDB-4u06: Structure of Leptospira interrogans LRR protein LIC10831 -

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Basic information

Entry
Database: PDB / ID: 4u06
TitleStructure of Leptospira interrogans LRR protein LIC10831
ComponentsLIC10831
KeywordsUNKNOWN FUNCTION / LRR PROTEIN / PATHOGEN / VIRULENCE FACTOR
Function / homology
Function and homology information


Leucine rich repeat 4 / Leucine Rich repeats (2 copies) / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Alpha-Beta Horseshoe / 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 4 / Leucine Rich repeats (2 copies) / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Alpha-Beta Horseshoe / 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 / Alpha Beta
Similarity search - Domain/homology
Uncharacterized protein
Similarity search - Component
Biological speciesLeptospira interrogans serovar Copenhageni str. Fiocruz L1-130 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsShepard, W. / Saul, F.A. / Haouz, A. / Picardeau, M.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2015
Title: Structural characterization of a novel subfamily of leucine-rich repeat proteins from the human pathogen Leptospira interrogans.
Authors: Miras, I. / Saul, F. / Nowakowski, M. / Weber, P. / Haouz, A. / Shepard, W. / Picardeau, M.
History
DepositionJul 11, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 3, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 17, 2015Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LIC10831
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,7788
Polymers40,4101
Non-polymers3687
Water6,557364
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area720 Å2
ΔGint-136 kcal/mol
Surface area15610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.300, 122.300, 58.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11A-531-

HOH

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Components

#1: Protein LIC10831


Mass: 40409.656 Da / Num. of mol.: 1 / Fragment: UNP residues 34-377 / Mutation: E135G, T266(MSE)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leptospira interrogans serovar Copenhageni str. Fiocruz L1-130 (bacteria)
Gene: LIC_10831 / Plasmid: PDEST17 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): PLYSS / References: UniProt: Q72U33
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 364 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.69 Å3/Da / Density % sol: 54.32 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 4000, 2-propanol, 10mM zinc acetate, 100mM HEPES-Na

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 1.28199 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 20, 2012
RadiationMonochromator: CHANNEL CUT SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28199 Å / Relative weight: 1
ReflectionResolution: 1.9→48.23 Å / Num. obs: 35305 / % possible obs: 99.7 % / Redundancy: 6.5 % / Biso Wilson estimate: 36.04 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 16.1
Reflection shellResolution: 1.9→2 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.627 / Mean I/σ(I) obs: 2.1 / % possible all: 98.3

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Processing

Software
NameVersionClassification
BUSTER2.11.4refinement
XDSdata reduction
SCALAdata scaling
SHELXDEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→48.2 Å / Cor.coef. Fo:Fc: 0.9538 / Cor.coef. Fo:Fc free: 0.9465 / SU R Cruickshank DPI: 0.149 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.16 / SU Rfree Blow DPI: 0.143 / SU Rfree Cruickshank DPI: 0.138
RfactorNum. reflection% reflectionSelection details
Rfree0.2355 1757 5.04 %RANDOM
Rwork0.2009 ---
obs0.2027 34851 98.59 %-
Displacement parametersBiso mean: 39.92 Å2
Baniso -1Baniso -2Baniso -3
1-1.8365 Å20 Å20 Å2
2--1.8365 Å20 Å2
3----3.6729 Å2
Refine analyzeLuzzati coordinate error obs: 0.3 Å
Refinement stepCycle: 1 / Resolution: 1.9→48.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2902 0 7 364 3273
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012948HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.124012HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1134SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes113HARMONIC2
X-RAY DIFFRACTIONt_gen_planes396HARMONIC5
X-RAY DIFFRACTIONt_it2948HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.85
X-RAY DIFFRACTIONt_other_torsion17.63
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion394SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3629SEMIHARMONIC4
LS refinement shellResolution: 1.9→1.96 Å / Total num. of bins used: 17
RfactorNum. reflection% reflection
Rfree0.4191 149 5.36 %
Rwork0.4153 2629 -
all0.4155 2778 -
obs--98.59 %

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