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- PDB-5hl3: Crystal structure of Listeria monocytogenes InlP -

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Basic information

Entry
Database: PDB / ID: 5hl3
TitleCrystal structure of Listeria monocytogenes InlP
ComponentsLmo2470 protein
KeywordsUNKNOWN FUNCTION / Internalin / LRR / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


extracellular region / metal ion binding
Similarity search - Function
Internalin, N-terminal / Bacterial adhesion/invasion protein N terminal / Leucine rich repeat 4 / Leucine Rich repeats (2 copies) / 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
Biological speciesListeria monocytogenes EGD-e (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.4 Å
AuthorsNocadello, S. / Light, S.H. / Minasov, G. / Kiryukhina, O. / Kwon, K. / Faralla, C. / Bakardjiev, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: Plos Pathog. / Year: 2018
Title: Listeria monocytogenes InlP interacts with afadin and facilitates basement membrane crossing.
Authors: Faralla, C. / Bastounis, E.E. / Ortega, F.E. / Light, S.H. / Rizzuto, G. / Gao, L. / Marciano, D.K. / Nocadello, S. / Anderson, W.F. / Robbins, J.R. / Theriot, J.A. / Bakardjiev, A.I.
History
DepositionJan 14, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 18, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2021Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_struct_conn_angle / struct_conn
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _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.ptnr3_symmetry / _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.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_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_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.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lmo2470 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,94010
Polymers40,5841
Non-polymers3569
Water14,628812
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)72.883, 72.883, 179.449
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-1103-

HOH

21A-1119-

HOH

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Components

#1: Protein Lmo2470 protein


Mass: 40584.180 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes EGD-e (bacteria)
Strain: ATCC BAA-679 / EGD-e / Gene: lmo2470 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8Y4H2
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 812 / 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: 2.98 Å3/Da / Density % sol: 58.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 1/1 ratio of InlP 8.5 mg/ml in 10 mMTrisHCl pH 8.3, 1 mM TCEP and 0.2 M Calcium Chloride, 0.1 M TrisHCl pH 8, 20%(w/v) PEG 6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 22, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.4→30 Å / Num. obs: 180423 / % possible obs: 99.8 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.079 / Rsym value: 0.079 / Net I/σ(I): 30.2
Reflection shellResolution: 1.4→1.42 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.653 / Mean I/σ(I) obs: 2.6 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
BLU-MAXdata collection
RefinementMethod to determine structure: SAD / Resolution: 1.4→30 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.965 / SU B: 1.501 / SU ML: 0.033 / Cross valid method: THROUGHOUT / ESU R: 0.051 / ESU R Free: 0.051 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.176 4635 4.9 %RANDOM
Rwork0.15987 ---
obs0.16064 90409 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.278 Å2
Baniso -1Baniso -2Baniso -3
1-0.51 Å20 Å2-0 Å2
2--0.51 Å2-0 Å2
3----1.01 Å2
Refinement stepCycle: 1 / Resolution: 1.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2779 0 9 812 3600
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.023010
X-RAY DIFFRACTIONr_bond_other_d0.0010.022772
X-RAY DIFFRACTIONr_angle_refined_deg1.5071.994148
X-RAY DIFFRACTIONr_angle_other_deg0.88336428
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3635391
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.37726.923143
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.34515454
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.098156
X-RAY DIFFRACTIONr_chiral_restr0.0950.2489
X-RAY DIFFRACTIONr_gen_planes_refined0.0230.0213553
X-RAY DIFFRACTIONr_gen_planes_other0.0190.02641
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.2460.2431516
X-RAY DIFFRACTIONr_mcbond_other0.2450.2431515
X-RAY DIFFRACTIONr_mcangle_it0.4290.3651923
X-RAY DIFFRACTIONr_mcangle_other0.4290.3651924
X-RAY DIFFRACTIONr_scbond_it0.6710.2821494
X-RAY DIFFRACTIONr_scbond_other0.6710.2821494
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.9390.4062225
X-RAY DIFFRACTIONr_long_range_B_refined9.0117.0464233
X-RAY DIFFRACTIONr_long_range_B_other8.5833.0183545
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.403→1.439 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.223 360 -
Rwork0.21 6483 -
obs--99.16 %
Refinement TLS params.

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 °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
17.8724-4.9464-2.283914.3748-3.499310.41060.24580.6342-0.4452-0.83730.00150.70090.5507-0.9017-0.24720.2448-0.04420.01890.23370.02220.23592.158710.311340.0696
20.6144-0.1258-0.58430.4342-0.06651.6624-0.0130.0079-0.044-0.0085-0.0306-0.01660.05060.04270.04360.12840.0104-0.00290.11250.00870.115712.871516.62534.3347
30.25240.0180.00770.2497-0.19590.6628-0.0088-0.0247-0.0013-0.03840.03650.0230.0321-0.0501-0.02770.1124-0.0017-0.00280.119-0.00260.11746.311528.00768.585
40.57290.0807-0.37610.87930.35921.86820.02330.0650.0361-0.18320.0646-0.0849-0.13790.1726-0.0880.1725-0.02010.01490.1308-0.00650.125123.038440.2184-20.3154
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A33 - 36
2X-RAY DIFFRACTION2A37 - 115
3X-RAY DIFFRACTION3A116 - 267
4X-RAY DIFFRACTION4A268 - 388

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