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- PDB-2y5p: B-repeat of Listeria monocytogenes InlB (internalin B) -

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Basic information

Entry
Database: PDB / ID: 2y5p
TitleB-repeat of Listeria monocytogenes InlB (internalin B)
ComponentsINTERNALIN B
KeywordsPROTEIN BINDING / VIRULENCE FACTOR / PATHOGENICITY FACTOR / BETA-GRASP FOLD
Function / homology
Function and homology information


peptidoglycan-based cell wall / InlB-mediated entry of Listeria monocytogenes into host cell / heparin binding / lipid binding / cell surface / extracellular region / metal ion binding / plasma membrane / cytoplasm
Similarity search - Function
Listeria-Bacteroides repeat domain / GW domain / GW domain superfamily / GW (Gly-Tryp) dipeptide domain / GW domain profile. / Listeria/Bacterioides repeat / Listeria-Bacteroides repeat domain superfamily / Listeria-Bacteroides repeat domain (List_Bact_rpt) / Leucine-rich repeat-containing adjacent domain / LRR adjacent ...Listeria-Bacteroides repeat domain / GW domain / GW domain superfamily / GW (Gly-Tryp) dipeptide domain / GW domain profile. / Listeria/Bacterioides repeat / Listeria-Bacteroides repeat domain superfamily / Listeria-Bacteroides repeat domain (List_Bact_rpt) / Leucine-rich repeat-containing adjacent domain / LRR adjacent / Internalin, N-terminal / Bacterial adhesion/invasion protein N terminal / Copper resistance protein CopC/internalin, immunoglobulin-like / Leucine rich repeat 4 / Leucine Rich repeats (2 copies) / Leucine-rich repeat, SDS22-like subfamily / 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 / Immunoglobulin E-set / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Internalin B / Internalin B
Similarity search - Component
Biological speciesLISTERIA MONOCYTOGENES EGD (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.3 Å
AuthorsEbbes, M. / Niemann, H.H.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Fold and Function of the Inlb B-Repeat.
Authors: Ebbes, M. / Bleymuller, W.M. / Cernescu, M. / Nolker, R. / Brutschy, B. / Niemann, H.H.
History
DepositionJan 17, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 23, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 10, 2014Group: Data collection / Source and taxonomy / Version format compliance
Revision 1.2May 8, 2019Group: Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_biol
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.3Jul 17, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: INTERNALIN B
B: INTERNALIN B
C: INTERNALIN B
D: INTERNALIN B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,64015
Polymers33,2134
Non-polymers42711
Water7,134396
1
A: INTERNALIN B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,3833
Polymers8,3031
Non-polymers802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: INTERNALIN B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,3833
Polymers8,3031
Non-polymers802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: INTERNALIN B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,4946
Polymers8,3031
Non-polymers1915
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: INTERNALIN B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,3793
Polymers8,3031
Non-polymers762
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4190 Å2
ΔGint-90.8 kcal/mol
Surface area16330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)28.610, 58.340, 158.070
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.395, -0.903, 0.17), (-0.916, 0.371, -0.157), (0.079, -0.217, -0.973)-5.49415, -12.08115, -21.476
2given(0.96314, 0.25222, 0.09354), (-0.19788, 0.89984, -0.38876), (-0.18223, 0.35592, 0.91658)1.98639, -6.43393, -40.44755
3given(-0.44894, -0.89146, -0.06122), (-0.88352, 0.43261, 0.17954), (-0.13357, 0.13469, -0.98184)-8.1784, -8.9221, -62.89132

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Components

#1: Protein
INTERNALIN B / INLB


Mass: 8303.241 Da / Num. of mol.: 4 / Fragment: B-REPEAT, RESIDUES 322-392
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) LISTERIA MONOCYTOGENES EGD (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): CODON PLUS / References: UniProt: P25147, UniProt: P0DQD2*PLUS
#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 / Chloride


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


Mass: 18.015 Da / Num. of mol.: 396 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsCALCIUM ION (CA): CA2+ IONS FROM CRYSTALLIZATION SOLUTION. POSITION VERIFIED BY ANOMALOUS ...CALCIUM ION (CA): CA2+ IONS FROM CRYSTALLIZATION SOLUTION. POSITION VERIFIED BY ANOMALOUS DIFFERENCE DENSITY. IDENTITY INFERRED FROM SURROUNDINGS. CHLORIDE ION (CL): CL- IONS FROM CRYSTALLIZATION SOLUTION. POSITION VERIFIED BY ANOMALOUS DIFFERENCE DENSITY. IDENTITY INFERRED FROM SURROUNDINGS.
Sequence detailsFIRST THREE RESIDUES GAM DERIVE FROM TEV CLEAVAGE OF GST TAG.

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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: 2.03 Å3/Da / Density % sol: 39.3 %
Description: DATA MERGED FROM THREE DIFFERENT WAVELENGTHS COLLECTED FROM THE SAME CRYSTAL. 0.81 A COLLECTED ON X11 WITH FLATPANEL DETECTOR. 0.95 A AND 1.9 A COLLECTED ON X12 WITH MAR 225 CCD DETECTOR.
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 20 DEG C IN HANGING OR SITTING-DROPS WITH 2 UL PROTEIN (17.3 MG/ML) PLUS 1 UL RESERVOIR (0.1 M NA-ACETATE PH 5.0, 0.2 M CACL2, 18 % PEG 6000).

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONEMBL/DESY, HAMBURG X1110.81
SYNCHROTRONEMBL/DESY, HAMBURG X122
Detector
TypeIDDetector
MAR555 FLAT PANEL1IMAGE PLATE
MARMOSAIC 225 mm CCD2CCD
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1MADMx-ray1
2Mx-ray1
Radiation wavelengthWavelength: 0.81 Å / Relative weight: 1
ReflectionResolution: 1.3→47 Å / Num. obs: 66287 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 22.7 % / Biso Wilson estimate: 21 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 31.8
Reflection shellResolution: 1.3→1.33 Å / Rmerge(I) obs: 0.72 / Mean I/σ(I) obs: 2.98 / % possible all: 99.3

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
XDSdata reduction
XSCALEdata scaling
SHELXDphasing
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 1.3→47 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.964 / SU B: 2.556 / SU ML: 0.047 / Cross valid method: THROUGHOUT / ESU R: 0.057 / ESU R Free: 0.055 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.19559 1989 3 %RANDOM
Rwork0.15709 ---
obs0.15827 64294 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 18.105 Å2
Baniso -1Baniso -2Baniso -3
1-3.24 Å20 Å20 Å2
2---1.85 Å20 Å2
3----1.4 Å2
Refinement stepCycle: LAST / Resolution: 1.3→47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2313 0 11 396 2720
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0222597
X-RAY DIFFRACTIONr_bond_other_d0.0010.021743
X-RAY DIFFRACTIONr_angle_refined_deg2.0971.9313564
X-RAY DIFFRACTIONr_angle_other_deg1.00334286
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3555340
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.5724.672122
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.6715434
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.013156
X-RAY DIFFRACTIONr_chiral_restr0.1270.2373
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0212946
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02556
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_it2.6931.51539
X-RAY DIFFRACTIONr_mcbond_other1.1121.5626
X-RAY DIFFRACTIONr_mcangle_it3.84122526
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.14831058
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it7.0144.51014
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr2.40934340
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.3→1.334 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 140 -
Rwork0.263 4576 -
obs--99.24 %

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