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- PDB-2wqx: InlB321_4R: S199R, D200R, G206R, A227R, C242A mutant of the Liste... -

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Basic information

Entry
Database: PDB / ID: 2wqx
TitleInlB321_4R: S199R, D200R, G206R, A227R, C242A mutant 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
Internalin B / Internalin B
Similarity search - Component
Biological speciesLISTERIA MONOCYTOGENES (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.03 Å
AuthorsNiemann, H.H. / Ferraris, D.M. / Heinz, D.W.
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 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Mar 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 1.3May 8, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
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

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Assembly

Deposited unit
A: INTERNALIN B
B: INTERNALIN B


Theoretical massNumber of molelcules
Total (without water)65,0202
Polymers65,0202
Non-polymers00
Water6,648369
1
A: INTERNALIN B


Theoretical massNumber of molelcules
Total (without water)32,5101
Polymers32,5101
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: INTERNALIN B


Theoretical massNumber of molelcules
Total (without water)32,5101
Polymers32,5101
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.700, 57.450, 64.300
Angle α, β, γ (deg.)102.99, 90.21, 93.56
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A1 - 45
2111B1 - 45
1211A47 - 50
2211B47 - 50
1311A52 - 88
2311B52 - 88
1411A90 - 108
2411B90 - 108
1511A110 - 130
2511B110 - 130
1611A134 - 150
2611B134 - 150
1711A151 - 174
2711B151 - 174
1811A176 - 211
2811B176 - 211
1911A213 - 237
2911B213 - 237
11011A239 - 321
21011B239 - 321

NCS oper: (Code: given
Matrix: (0.99991, -0.01073, 0.00801), (-0.01071, -0.99994, -0.00264), (0.00804, 0.00256, -0.99996)
Vector: -19.4099, -18.48323, -28.31996)

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Components

#1: Protein INTERNALIN B / INLB


Mass: 32510.229 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 4R MUTANT
Source: (gene. exp.) LISTERIA MONOCYTOGENES (bacteria) / Strain: EGD-E / Plasmid: PETM30 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): CODONPLUS / References: UniProt: P25147, UniProt: P0DQD2*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 369 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, SER 199 TO ARG ENGINEERED RESIDUE IN CHAIN A, ASP 200 TO ARG ...ENGINEERED RESIDUE IN CHAIN A, SER 199 TO ARG ENGINEERED RESIDUE IN CHAIN A, ASP 200 TO ARG ENGINEERED RESIDUE IN CHAIN A, GLY 206 TO ARG ENGINEERED RESIDUE IN CHAIN A, ALA 227 TO ARG ENGINEERED RESIDUE IN CHAIN A, CYS 242 TO ALA ENGINEERED RESIDUE IN CHAIN B, SER 199 TO ARG ENGINEERED RESIDUE IN CHAIN B, ASP 200 TO ARG ENGINEERED RESIDUE IN CHAIN B, GLY 206 TO ARG ENGINEERED RESIDUE IN CHAIN B, ALA 227 TO ARG ENGINEERED RESIDUE IN CHAIN B, CYS 242 TO ALA
Sequence detailsRESIDUES 33-35 REMAIN AFTER TEV CLEAVAGE OF THE GST-FUSION PROTEIN

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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: 2.14 Å3/Da / Density % sol: 0.42 % / Description: NONE
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: SITTING DROP VAPOUR DIFFUSION AT 293K WITH 1 UL PROTEIN (3.8 MG/ML IN 50 MM HEPES, PH 7.0, 100 MM NACL) PLUS 0.5 UL RESERVOIR (17% PEG1000MME, 90 MM NA-CITRATE).

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.541
DetectorType: RIGAKU SATURN 944PLUS / Detector: CCD / Date: Apr 8, 2009 / Details: VARIMAX HF
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.541 Å / Relative weight: 1
ReflectionResolution: 2.03→20 Å / Num. obs: 33525 / % possible obs: 96.8 % / Observed criterion σ(I): -3 / Redundancy: 5.1 % / Biso Wilson estimate: 20.09 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 12.65
Reflection shellResolution: 2.03→2.09 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 4.02 / % possible all: 68.5

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Processing

Software
NameVersionClassification
REFMAC5.5.0088refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1H6T

1h6t


Resolution: 2.03→38.63 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.881 / SU B: 11.832 / SU ML: 0.146 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.258 / ESU R Free: 0.209 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES ARE RESIDUAL ONLY. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2567 1677 5 %RANDOM
Rwork0.19423 ---
obs0.19729 31849 100 %-
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: 12.299 Å2
Baniso -1Baniso -2Baniso -3
1--0.38 Å20.24 Å20.15 Å2
2--0.93 Å2-0.01 Å2
3----0.52 Å2
Refinement stepCycle: LAST / Resolution: 2.03→38.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4546 0 0 369 4915
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0224671
X-RAY DIFFRACTIONr_bond_other_d0.0030.023164
X-RAY DIFFRACTIONr_angle_refined_deg1.7991.9836346
X-RAY DIFFRACTIONr_angle_other_deg1.08137856
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9695586
X-RAY DIFFRACTIONr_dihedral_angle_2_deg45.14626.143210
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.75215898
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1171518
X-RAY DIFFRACTIONr_chiral_restr0.1090.2762
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0215074
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02800
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_it0.851.52886
X-RAY DIFFRACTIONr_mcbond_other0.2741.51146
X-RAY DIFFRACTIONr_mcangle_it1.4624728
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.54331785
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.0984.51610
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: 3675 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Atight positional0.070.05
2Btight positional0.070.05
1Atight thermal0.170.5
2Btight thermal0.170.5
LS refinement shellResolution: 2.033→2.086 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 86 -
Rwork0.239 1630 -
obs--100 %
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)
10.3166-0.04030.44170.33360.35982.14260.0325-0.0045-0.0774-0.0174-0.02660.00790.1779-0.0517-0.00580.02670.00230.01020.05330.02050.04212.878-22.491-10.168
20.36060.0164-0.4610.29010.33341.91510.0305-0.00950.07950.0062-0.02370.0058-0.1768-0.0723-0.00680.02660.0148-0.00560.07120.01490.0355-6.4183.946-18.168
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 321
2X-RAY DIFFRACTION2B1 - 321

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