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- PDB-4aw4: Engineered variant of Listeria monocytogenes InlB internalin doma... -

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Basic information

Entry
Database: PDB / ID: 4aw4
TitleEngineered variant of Listeria monocytogenes InlB internalin domain with an additional leucine rich repeat inserted
ComponentsINTERNALIN B
KeywordsPROTEIN BINDING / LRR / PROTEIN ENGINEERING / RECEPTOR BINDING / PROTEIN PROTEIN INTERACTION / CELL INVASION / VIRULENCE FACTOR / HGF RECEPTOR LIGAND / C-MET LIGAND
Function / homology
Function and homology information


entry of bacterium into host cell / 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
Similarity search - Function
Internalin N-terminal Cap domain-like / 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 Cap domain-like / 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 / Leucine-rich repeat, SDS22-like subfamily / Alpha-Beta Horseshoe / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / Helicase, Ruva Protein; domain 3 / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Immunoglobulin E-set / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Internalin B / Internalin B
Similarity search - Component
Biological speciesLISTERIA MONOCYTOGENES (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsNiemann, H.H. / Heinz, D.W.
CitationJournal: Protein Sci. / Year: 2012
Title: Engineered Variants of Inlb with an Additional Leucine-Rich Repeat Discriminate between Physiologically Relevant and Packing Contacts in Crystal Structures of the Inlb:Met Complex.
Authors: Niemann, H.H. / Gherardi, E. / Bleymuller, W.M. / Heinz, D.W.
History
DepositionMay 31, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 15, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 29, 2012Group: Database references
Revision 1.2Oct 3, 2012Group: Database references
Revision 1.3May 8, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / pdbx_struct_special_symmetry
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.4May 22, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.5Jul 17, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.6Dec 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_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
C: INTERNALIN B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,18036
Polymers104,0543
Non-polymers3,12633
Water8,341463
1
A: INTERNALIN B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,01015
Polymers34,6851
Non-polymers1,32514
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: INTERNALIN B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,72512
Polymers34,6851
Non-polymers1,04111
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: INTERNALIN B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4459
Polymers34,6851
Non-polymers7618
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)179.080, 102.150, 69.810
Angle α, β, γ (deg.)90.00, 90.23, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-1345-

GOL

21A-2045-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: _ / Auth seq-ID: 36 - 342 / Label seq-ID: 4 - 310

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13BB
23CC

NCS ensembles :
ID
1
2
3

NCS oper:
IDCodeMatrixVector
1given(-0.5091, 0.86054, 0.01704), (-0.8607, -0.50891, -0.01408), (-0.00344, -0.02184, 0.99976)47.72824, 20.26614, -0.07956
2given(0.50147, 0.86512, -0.00988), (0.86513, -0.50131, 0.01526), (0.00825, -0.0162, -0.99983)47.72829, 20.30023, -0.06249

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Components

#1: Protein INTERNALIN B


Mass: 34684.504 Da / Num. of mol.: 3 / Fragment: INTERNALIN DOMAIN, RESIDUES 36-321
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) LISTERIA MONOCYTOGENES (bacteria) / Strain: EGD-E / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): CODONPLUS RIL / References: UniProt: P25147, UniProt: P0DQD3*PLUS
#2: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 463 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsSULFATE ION (SO4): FROM RESERVOIR SOLUTION GLYCEROL (GOL): FROM CRYO PROTECTION
Sequence detailsBETWEEN PRO98 AND ASN99 THERE IS AN INSERTION OF A CONSENSUS LEUCINE RICH REPEAT OF 22 AMINO ACIDS ...BETWEEN PRO98 AND ASN99 THERE IS AN INSERTION OF A CONSENSUS LEUCINE RICH REPEAT OF 22 AMINO ACIDS WITH SEQUENCE NLTSLNLSNNQITDISPIQYLP. SO THAT AFTER PRO98 THE SEQUENCE NUMBERING IS OFFSET BY PLUS 22. THE N-TERMINAL RESIDUES GLY-ALA-MET REMAIN AFTER TEV CLEAVAGE OF 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: 3.07 Å3/Da / Density % sol: 60 %
Description: DATA INDEXES AND SCALES REASONABLY WELL IN C2 AND P321. SCALING IS BETTER IN C2 THAN IN P321. IN C2 RMEAS OF 0.09, I OVER SIGI OF 15.5. IN P321 RMEAS OF 0.18, I OVER SIGI OF 10.8. WHILE ...Description: DATA INDEXES AND SCALES REASONABLY WELL IN C2 AND P321. SCALING IS BETTER IN C2 THAN IN P321. IN C2 RMEAS OF 0.09, I OVER SIGI OF 15.5. IN P321 RMEAS OF 0.18, I OVER SIGI OF 10.8. WHILE THE STRUCTURE CAN BE SOLVED AND REFINED IN P321, DATA ANALYSIS SUGGESTS THAT THE CRYSTAL IS ACTUALLY IN C2 WITH A NON-CRYSTALLOGRAPHIC 3-FOLD AXIS AND PROBABLY NON-MEROHEDRAL TWINNING PARALLEL TO THE 3- FOLD NCS AXIS.
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: SITTING DROP VAPOUR DIFFUSION IN 96-WELL PLATES AT 20 DEGREE C. 17 MG/ML PROTEIN IN 25 MM TRIS, PH 8, 20 MM NACL. RESERVOIR SOLUTION WAS 2M AMMONIUM SULFATE. DROPS WERE SET UP WITH EQUAL ...Details: SITTING DROP VAPOUR DIFFUSION IN 96-WELL PLATES AT 20 DEGREE C. 17 MG/ML PROTEIN IN 25 MM TRIS, PH 8, 20 MM NACL. RESERVOIR SOLUTION WAS 2M AMMONIUM SULFATE. DROPS WERE SET UP WITH EQUAL VOLUMES OF PROTEIN AND RESERVOIR SOLUTION.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 0.9204
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 21, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9204 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.664
111/2H-3/2K, -1/2H-1/2K, -L20.192
111/2H+3/2K, 1/2H-1/2K, -L30.144
ReflectionResolution: 1.95→19.7 Å / Num. obs: 89100 / % possible obs: 97.4 % / Observed criterion σ(I): -3 / Redundancy: 5.7 % / Biso Wilson estimate: 35.8 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 15.5
Reflection shellResolution: 1.95→2 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.84 / Mean I/σ(I) obs: 2.85 / % possible all: 96.6

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1H6T

1h6t


Resolution: 1.93→19.69 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.938 / SU B: 6.338 / SU ML: 0.086 / Cross valid method: THROUGHOUT / ESU R: 0.027 / ESU R Free: 0.026 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.20535 2016 2.3 %TAKING HIGHER LATTICE SYMMETRY INTO ACCOUNT USING PHENIX_REFLECTION_FILE_CONVERTE
Rwork0.16685 ---
obs0.16771 87083 94.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 29.952 Å2
Baniso -1Baniso -2Baniso -3
1-3.28 Å20 Å2-4.52 Å2
2--21.74 Å20 Å2
3----25.02 Å2
Refinement stepCycle: LAST / Resolution: 1.93→19.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7196 0 176 463 7835
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.027740
X-RAY DIFFRACTIONr_bond_other_d0.0060.025122
X-RAY DIFFRACTIONr_angle_refined_deg1.7151.99910561
X-RAY DIFFRACTIONr_angle_other_deg1.312312803
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7895979
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.85827.088340
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.631151449
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3751513
X-RAY DIFFRACTIONr_chiral_restr0.1010.21279
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0218331
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021262
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A111270.06
12B111270.06
21A111480.07
22C111480.07
31B114220.07
32C114220.07
LS refinement shellResolution: 1.928→1.978 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.258 70 -
Rwork0.222 3701 -
obs--54.7 %
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)
14.84742.1705-0.734.7755-2.4481.66070.03640.1335-0.0593-0.0521-0.1918-0.4021-0.12860.01370.15540.1468-0.06480.03650.2360.0540.225918.03174.0816-13.4641
21.72950.8243-0.92641.5217-0.61462.47650.0370.1150.13690.088-0.0314-0.0299-0.26540.1086-0.00560.0627-0.06410.02580.16670.04160.195713.21943.825-7.685
32.210.3618-0.98751.78910.56692.5359-0.0929-0.3075-0.07220.11630.0142-0.2724-0.1880.54190.07860.0833-0.02680.01140.23040.04880.176213.4343-2.27957.8437
42.35980.9987-0.02792.0516-0.5762.42390.1034-0.6466-0.1204-0.0513-0.2826-0.2458-0.15280.15360.17920.0287-0.01820.00990.34390.07520.16571.868-9.074321.3448
52.69791.3178-0.28963.3316-0.37241.99310.1233-1.0607-0.7007-0.1436-0.2268-0.11320.3851-0.23140.10350.1024-0.1145-0.01660.57260.31890.3157-13.8374-25.299628.1838
63.4084-0.2219-0.264610.7976-0.29842.75630.1737-0.8637-0.39480.0421-0.3582-0.17510.0696-0.24670.18450.0141-0.05280.00160.4330.14270.2003-13.5656-18.210125.0136
73.5497-2.528-3.229.66754.16143.4445-0.47910.2404-0.45180.33410.02040.45430.3137-0.1370.45860.2877-0.04040.09820.0881-0.02750.303439.9949-0.8102-14.0547
80.8081-0.6944-0.42551.97641.65093.2984-0.0968-0.0071-0.07840.10650.0458-0.05970.28460.13990.0510.17180.01490.05530.0470.00470.197744.40347.4363-8.6584
92.4077-0.8090.53773.4835-0.01472.73530.0086-0.0452-0.17760.0404-0.04220.15180.5918-0.08370.03370.2404-0.02580.05360.1011-0.0060.165438.902410.70556.0696
101.5474-0.8043-0.33881.51080.59222.9138-0.0749-0.0553-0.30150.1219-0.05760.10970.5493-0.0750.13260.1712-0.03360.05850.0790.03050.196438.526516.459418.015
110.97220.2062-0.09642.02740.3071.87850.0647-0.03570.13360.2091-0.06450.1984-0.1703-0.1177-0.00020.1332-0.01430.0680.10650.02670.190336.990836.893226.7784
124.6827-1.6462-0.88694.16560.70542.34130.12030.010.29540.2003-0.1960.5164-0.3813-0.32430.07580.19970.01880.09540.0926-0.02070.276233.182146.521126.8091
1313.38812.84093.98884.4782-0.17232.5294-0.23730.08690.57350.1045-0.0756-0.1142-0.1030.12440.31290.0665-0.0397-0.01640.20870.02660.24162.187936.952913.8854
141.86350.19711.08550.63740.45762.5836-0.03440.018-0.07290.00020.0453-0.09160.09220.2892-0.01090.0674-0.02650.01760.18580.02920.209857.788229.43348.2237
153.64030.2195-0.00880.95861.18863.1185-0.05380.11560.3264-0.17740.005-0.0838-0.43280.35770.04880.1474-0.06020.01190.15040.03940.170652.406433.051-7.5832
161.3912-0.96890.32251.7071-0.17554.0051-0.1040.01680.2987-0.0776-0.0267-0.2355-0.39070.27960.13070.1627-0.04080.02490.0760.00730.229543.597730.6928-17.4616
171.99470.39590.32971.0078-0.20022.0586-0.10550.04170.1131-0.10010.1190.1147-0.0903-0.2941-0.01360.1609-0.00750.03420.11460.04110.181728.589322.3663-26.1012
185.7986-1.10651.48582.4356-0.72762.3939-0.2395-0.08050.2385-0.0130.22960.3116-0.1031-0.66680.00990.0937-0.0210.01050.27230.07180.19616.926820.7526-26.072
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A36 - 59
2X-RAY DIFFRACTION2A60 - 115
3X-RAY DIFFRACTION3A116 - 166
4X-RAY DIFFRACTION4A167 - 250
5X-RAY DIFFRACTION5A251 - 321
6X-RAY DIFFRACTION6A322 - 342
7X-RAY DIFFRACTION7B36 - 51
8X-RAY DIFFRACTION8B52 - 115
9X-RAY DIFFRACTION9B116 - 158
10X-RAY DIFFRACTION10B159 - 211
11X-RAY DIFFRACTION11B212 - 300
12X-RAY DIFFRACTION12B301 - 342
13X-RAY DIFFRACTION13C36 - 51
14X-RAY DIFFRACTION14C52 - 115
15X-RAY DIFFRACTION15C116 - 166
16X-RAY DIFFRACTION16C167 - 206
17X-RAY DIFFRACTION17C207 - 300
18X-RAY DIFFRACTION18C301 - 342

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