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- PDB-2wqw: DOUBLE-DISULFIDE CROSS-LINKED CRYSTAL DIMER of the Listeria monoc... -

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Basic information

Entry
Database: PDB / ID: 2wqw
TitleDOUBLE-DISULFIDE CROSS-LINKED CRYSTAL DIMER of the Listeria monocytogenes InlB internalin domain
ComponentsINTERNALIN B
KeywordsCELL INVASION / HGF RECEPTOR LIGAND / LEUCINE-RICH REPEAT / LEUCINE RICH REPEAT / LRR / C-MET LIGAND / VIRULENCE FACTOR
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
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 ...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 / Immunoglobulin-like - #1220 / : / Copper resistance protein CopC/internalin, immunoglobulin-like / 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, 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 / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Internalin B / Internalin B
Similarity search - Component
Biological speciesLISTERIA MONOCYTOGENES (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.24 Å
AuthorsFerraris, D.M. / Heinz, D.W. / Niemann, H.H.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Ligand-Mediated Dimerization of the met Receptor Tyrosine Kinase by the Bacterial Invasion Protein Inlb.
Authors: Ferraris, D.M. / Gherardi, E. / Di, Y. / Heinz, D.W. / Niemann, H.H.
History
DepositionAug 27, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 10, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 6, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)65,01611
Polymers64,0612
Non-polymers9559
Water2,558142
1
B: INTERNALIN B
hetero molecules

B: INTERNALIN B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,33514
Polymers64,0612
Non-polymers1,27312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_556x-y,-y,-z+11
Buried area3500 Å2
ΔGint17.05 kcal/mol
Surface area27960 Å2
MethodPISA
2
A: INTERNALIN B
hetero molecules

A: INTERNALIN B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,6988
Polymers64,0612
Non-polymers6376
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_556-x,-x+y,-z+11
Buried area2350 Å2
ΔGint2.39 kcal/mol
Surface area27470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)186.990, 186.990, 115.071
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111B1 - 321
2111A1 - 321
DetailsTHE BIOLOGICAL UNITS ARE DIMERS FORMED BY DISULFIDE BONDS BETWEEN CYSTEINES 206 AND 227. THE DIMERS ARE 2-FOLD SYMMETRIC AND CONSIST OF TWO CHAINS A OR TWO CHAINS B.

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Components

#1: Protein INTERNALIN B / INLB


Mass: 32030.586 Da / Num. of mol.: 2 / Fragment: INTERNALIN DOMAIN, RESIDUES 36-321 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: RESIDUES 36-321 OF LISTERIA MONOCYTOGENES INLB CROSS-LINKED INTO DIMERS BY TWO INTERMOLECULAR DISULFIDE BONDS BETWEEN C206 AND C227
Source: (gene. exp.) LISTERIA MONOCYTOGENES (bacteria) / Strain: EGD-E / Plasmid: PETM30 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 CODON PLUS (DE3) / References: UniProt: P25147, UniProt: P0DQD2*PLUS
#2: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C4H10O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, GLY 206 TO CYS ENGINEERED RESIDUE IN CHAIN A, ALA 227 TO CYS ...ENGINEERED RESIDUE IN CHAIN A, GLY 206 TO CYS ENGINEERED RESIDUE IN CHAIN A, ALA 227 TO CYS ENGINEERED RESIDUE IN CHAIN A, CYS 242 TO ALA ENGINEERED RESIDUE IN CHAIN B, GLY 206 TO CYS ENGINEERED RESIDUE IN CHAIN B, ALA 227 TO CYS ENGINEERED RESIDUE IN CHAIN B, CYS 242 TO ALA
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: 2.93 Å3/Da / Density % sol: 57.71 % / Description: NONE
Crystal growTemperature: 293 K / pH: 9.5
Details: 293 K. PROTEIN (6.7 MG/ML) PLUS RESERVOIR = 2 PLUS 1. RESERVOIR SOLUTION IS 44-52% PEG2000, 0.1 M CHES PH=9,5, 0.2M NACL., PH 9.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9535
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9535 Å / Relative weight: 1
ReflectionResolution: 2.24→50 Å / Num. obs: 37017 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Biso Wilson estimate: 37.8 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 10.5
Reflection shellResolution: 2.24→2.36 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.88 / Mean I/σ(I) obs: 2 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1H6T

1h6t


Resolution: 2.24→46.88 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.927 / SU B: 12.37 / SU ML: 0.14 / Cross valid method: THROUGHOUT / ESU R: 0.244 / ESU R Free: 0.199 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.239 1849 5 %RANDOM
Rwork0.199 ---
obs0.201 35166 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.45 Å2
Baniso -1Baniso -2Baniso -3
1--1.09 Å2-0.55 Å2-0 Å2
2---1.09 Å20 Å2
3---1.64 Å2
Refinement stepCycle: LAST / Resolution: 2.24→46.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4512 0 63 142 4717
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0224640
X-RAY DIFFRACTIONr_bond_other_d0.0040.023129
X-RAY DIFFRACTIONr_angle_refined_deg1.9091.9936269
X-RAY DIFFRACTIONr_angle_other_deg1.25937789
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9525570
X-RAY DIFFRACTIONr_dihedral_angle_2_deg47.1226.97198
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.59315870
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.839158
X-RAY DIFFRACTIONr_chiral_restr0.130.2754
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0214966
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02750
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_it0.6821.52864
X-RAY DIFFRACTIONr_mcbond_other0.2581.51138
X-RAY DIFFRACTIONr_mcangle_it1.1224684
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.16531776
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.2334.51585
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 3780 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
2Atight positional0.080.05
1Btight positional0.080.05
2Atight thermal0.180.5
1Btight thermal0.180.5
LS refinement shellResolution: 2.24→2.3 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 126 -
Rwork0.264 2554 -
obs--99.22 %
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)
14.4623.27692.18898.50062.22224.7914-0.53210.53540.0362-1.03250.51450.0977-0.24290.16150.01760.3744-0.1557-0.05020.29750.03160.0959-21.492214.54278.5138
21.59210.43050.20233.59391.74682.9444-0.11210.0980.0753-0.09440.01370.2258-0.1545-0.27120.09840.08650.0095-0.03830.12480.0190.1346-20.996518.682222.4895
31.06791.04530.22982.11190.73983.1377-0.07620.04080.0741-0.2019-0.00290.2295-0.0564-0.32290.07910.06250.0326-0.03080.06350.00310.1742-20.17325.223240.1145
43.519-2.2833-0.12213.69091.34384.8727-0.0061-0.004-0.0113-0.09250.01180.0706-0.16830.2824-0.00570.0165-0.0072-0.03720.0187-0.00610.1428-9.480331.226148.5058
53.05650.38620.62858.6039-1.28116.7935-0.29670.06880.65710.03120.18610.3664-1.3158-0.26360.11060.37590.0514-0.10050.0691-0.0140.3372-10.637853.455155.131
62.6733-4.30061.9718.506-3.39153.9497-0.4041-0.1780.17120.02610.3457-0.3343-0.68850.07650.05840.2247-0.0368-0.04980.0459-0.02310.1227-7.706442.20250.2931
75.3419-3.19340.10119.81230.93433.71150.3070.734-0.0671-1.2996-0.4020.25750.29550.09430.0950.45780.0627-0.0160.3036-0.04280.0903-22.9107-11.26528.5235
82.9005-1.53-1.01033.04340.45864.125-0.04390.0377-0.179-0.16920.00190.1910.2078-0.24940.0420.0578-0.0482-0.01520.0974-0.03610.1435-26.54-8.756522.469
91.2561-0.9881-0.66921.3650.96374.13210.03470.0692-0.1301-0.0375-0.07980.16680.3577-0.28060.04520.0455-0.0327-0.01760.0995-0.02620.1784-31.9788-4.76639.9753
104.8850.6089-1.05432.16870.76735.67970.02990.1916-0.10290.063-0.11140.0274-0.4079-0.08880.08140.0379-0.0025-0.00760.0234-0.04070.1648-31.72087.330148.4229
118.5589-3.49562.71543.7953-0.36823.6422-0.0479-0.17110.03740.0627-0.07630.4587-0.0328-0.61430.12420.05160.06540.04830.2741-0.0970.3035-51.475117.514154.8855
1215.6693-3.65243.66744.1004-0.45022.81940.3731-0.18190.9931-0.0901-0.4475-0.0001-0.1708-0.39280.07440.08990.07360.01370.1712-0.07730.1691-40.325714.432850.1348
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A33 - 70
2X-RAY DIFFRACTION2A71 - 135
3X-RAY DIFFRACTION3A136 - 207
4X-RAY DIFFRACTION4A208 - 241
5X-RAY DIFFRACTION5A242 - 299
6X-RAY DIFFRACTION6A300 - 321
7X-RAY DIFFRACTION7B33 - 70
8X-RAY DIFFRACTION8B71 - 135
9X-RAY DIFFRACTION9B136 - 207
10X-RAY DIFFRACTION10B208 - 241
11X-RAY DIFFRACTION11B242 - 299
12X-RAY DIFFRACTION12B300 - 321

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