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- PDB-6mlx: Crystal structure of T. pallidum Leucine Rich Repeat protein (TpLRR) -

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Basic information

Entry
Database: PDB / ID: 6mlx
TitleCrystal structure of T. pallidum Leucine Rich Repeat protein (TpLRR)
ComponentsLeucine-rich repeat protein TpLRR
KeywordsUNKNOWN FUNCTION / Secreted / Leucine Rich Repeat (LRR) / T. pallidum / Periplasmic LRR
Function / homology: / BspA type Leucine rich repeat region / BspA type Leucine rich repeat region (6 copies) / Leucine-rich repeat domain superfamily / Leucine-rich repeat protein TpLRR
Function and homology information
Biological speciesTreponema pallidum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsRamaswamy, R. / Loveless, B.C. / Houston, S. / Cameron, C.E. / Boulanger, M.J.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2019
Title: Structural characterization of Treponema pallidum Tp0225 reveals an unexpected leucine-rich repeat architecture.
Authors: Ramaswamy, R. / Houston, S. / Loveless, B. / Cameron, C.E. / Boulanger, M.J.
History
DepositionSep 28, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Leucine-rich repeat protein TpLRR
B: Leucine-rich repeat protein TpLRR
C: Leucine-rich repeat protein TpLRR
D: Leucine-rich repeat protein TpLRR


Theoretical massNumber of molelcules
Total (without water)93,4134
Polymers93,4134
Non-polymers00
Water9,260514
1
A: Leucine-rich repeat protein TpLRR


Theoretical massNumber of molelcules
Total (without water)23,3531
Polymers23,3531
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Leucine-rich repeat protein TpLRR


Theoretical massNumber of molelcules
Total (without water)23,3531
Polymers23,3531
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Leucine-rich repeat protein TpLRR


Theoretical massNumber of molelcules
Total (without water)23,3531
Polymers23,3531
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Leucine-rich repeat protein TpLRR


Theoretical massNumber of molelcules
Total (without water)23,3531
Polymers23,3531
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)104.079, 104.079, 185.808
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
Leucine-rich repeat protein TpLRR


Mass: 23353.248 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Treponema pallidum (bacteria) / Plasmid: pACGP67b / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: O06686
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 514 / 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

CrystalDensity Matthews: 2.73 Å3/Da / Density % sol: 54.87 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M Bis-Tris HCl, pH 6.5 and 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 0.9202 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Mar 5, 2018
Details: Flat bent collimating Rh coated mirror, toroidal focussing mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9202 Å / Relative weight: 1
ReflectionResolution: 2→92.9 Å / Num. obs: 67107 / % possible obs: 96.2 % / Redundancy: 9.9 % / Net I/σ(I): 15.1
Reflection shellResolution: 2→2.11 Å

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.24data extraction
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2→69.308 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 28.76
RfactorNum. reflection% reflection
Rfree0.2815 3241 4.84 %
Rwork0.2343 --
obs0.2366 66965 96.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 36.28 Å2 / Biso mean: 27.6837 Å2 / Biso min: 19.85 Å2
Refinement stepCycle: final / Resolution: 2→69.308 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6464 0 0 514 6978
Biso mean---27.58 -
Num. residues----852
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086588
X-RAY DIFFRACTIONf_angle_d0.9278904
X-RAY DIFFRACTIONf_chiral_restr0.0571024
X-RAY DIFFRACTIONf_plane_restr0.0061148
X-RAY DIFFRACTIONf_dihedral_angle_d14.753952
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 23

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.02990.3748940.31381968206269
2.0299-2.06160.3191170.2922202231978
2.0616-2.09540.36371210.27812367248884
2.0954-2.13150.33631280.27732564269290
2.1315-2.17030.27441290.27592721285095
2.1703-2.2120.29011400.26952784292498
2.212-2.25720.32671400.27222818295898
2.2572-2.30630.31731460.26462821296799
2.3063-2.35990.34821460.262128192965100
2.3599-2.41890.29711510.273528533004100
2.4189-2.48430.31071430.279328192962100
2.4843-2.55740.30621450.267928743019100
2.5574-2.640.32581490.267928553004100
2.64-2.73430.31671630.271528683031100
2.7343-2.84380.29071650.261628192984100
2.8438-2.97330.31931430.259429033046100
2.9733-3.130.34151600.250128543014100
3.13-3.32610.30771390.244729003039100
3.3261-3.58290.25991460.220529103056100
3.5829-3.94340.23861290.20429313060100
3.9434-4.5140.23351470.179829433090100
4.514-5.68670.25351440.190529893133100
5.6867-69.350.21951560.200931423298100
Refinement TLS params.Method: refined / Origin x: 1.9307 Å / Origin y: 37.8069 Å / Origin z: 60.2567 Å
111213212223313233
T0.2193 Å2-0.0162 Å2-0.0067 Å2-0.1679 Å2-0.0135 Å2--0.1468 Å2
L0.6205 °2-0.298 °2-0.1185 °2-0.2907 °20.0474 °2--0.1785 °2
S-0.0457 Å °-0.0596 Å °-0.0574 Å °0.0463 Å °0.0148 Å °0.0004 Å °0.0504 Å °0.0046 Å °0.0298 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA36 - 247
2X-RAY DIFFRACTION1allB36 - 248
3X-RAY DIFFRACTION1allC36 - 249
4X-RAY DIFFRACTION1allD36 - 248
5X-RAY DIFFRACTION1allS1 - 665

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