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- PDB-4u09: Structure of Leptospira interrogans LRR protein LIC12759 -

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Basic information

Entry
Database: PDB / ID: 4u09
TitleStructure of Leptospira interrogans LRR protein LIC12759
ComponentsLIC12759
KeywordsUNKNOWN FUNCTION / LRR PROTEIN / PATHOGEN / VIRULENCE FACTOR
Function / homology
Function and homology information


: / Leucine-rich repeats, bacterial type / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Leucine-rich repeat, SDS22-like subfamily / Alpha-Beta Horseshoe / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. ...: / Leucine-rich repeats, bacterial type / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Leucine-rich repeat, SDS22-like subfamily / 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
DI(HYDROXYETHYL)ETHER / Cytoplasmic membrane protein
Similarity search - Component
Biological speciesLeptospira interrogans serovar Copenhageni str. Fiocruz L1-130 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.95 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
Revision 1.2Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LIC12759
B: LIC12759
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,58417
Polymers92,2622
Non-polymers1,32215
Water10,971609
1
A: LIC12759
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,7908
Polymers46,1311
Non-polymers6597
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: LIC12759
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,7949
Polymers46,1311
Non-polymers6638
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.166, 104.796, 116.597
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein LIC12759 / LIC12759


Mass: 46131.152 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leptospira interrogans serovar Copenhageni str. Fiocruz L1-130 (bacteria)
Gene: LIC_12759 / Plasmid: PDEST17 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): PLYSS / References: UniProt: Q72NS0

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Non-polymers , 6 types, 624 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical
ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 609 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.49 Å3/Da / Density % sol: 50.63 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 4000, 125 mM zinc acetate, 200 mM magnesium chloride, 100 mM MES

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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: Oct 8, 2011
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: 1.95→47.79 Å / Num. obs: 67851 / % possible obs: 100 % / Redundancy: 10.9 % / Biso Wilson estimate: 33.52 Å2 / Rmerge(I) obs: 0.097 / Net I/σ(I): 13.6
Reflection shellResolution: 1.95→2.06 Å / Redundancy: 11 % / Rmerge(I) obs: 0.974 / Mean I/σ(I) obs: 2.4 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.11.4refinement
XDSdata reduction
SCALAdata scaling
SHELXDEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.95→47.79 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.8992 / SU R Cruickshank DPI: 0.154 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.16 / SU Rfree Blow DPI: 0.136 / SU Rfree Cruickshank DPI: 0.134
RfactorNum. reflection% reflectionSelection details
Rfree0.2132 984 1.45 %RANDOM
Rwork0.1869 ---
obs0.1873 67774 99.99 %-
Displacement parametersBiso mean: 43.7 Å2
Baniso -1Baniso -2Baniso -3
1--22.4237 Å20 Å20 Å2
2--9.15 Å20 Å2
3---13.2737 Å2
Refine analyzeLuzzati coordinate error obs: 0.246 Å
Refinement stepCycle: 1 / Resolution: 1.95→47.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6379 0 58 609 7046
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.016503HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.158774HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2506SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes237HARMONIC2
X-RAY DIFFRACTIONt_gen_planes838HARMONIC5
X-RAY DIFFRACTIONt_it6503HARMONIC20
X-RAY DIFFRACTIONt_nbd3SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.98
X-RAY DIFFRACTIONt_other_torsion18.35
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion841SEMIHARMONIC5
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_contact7791SEMIHARMONIC4
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 65 1.32 %
Rwork0.2518 4854 -
all0.2521 4919 -
obs--99.99 %

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