PDB-2wqv: Internalin domain of Listeria monocytogenes InlB: rhombohedral cr...

ID or keywords:

Entry

Database: PDB / ID: 2wqv

Title

Internalin domain of Listeria monocytogenes InlB: rhombohedral crystal form

Components

INTERNALIN B

Keywords

CELL INVASION / HGF RECEPTOR LIGAND / 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

Biological species

LISTERIA MONOCYTOGENES (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.8 Å

Authors

Niemann, H.H. / Heinz, D.W.

Citation

Journal: 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

Deposition	Aug 27, 2009	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Nov 10, 2009	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Mar 6, 2019	Group: 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 Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.3	Dec 20, 2023	Group: 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

Remark 700

SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ...

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	2wqv.cif.gz	124 KB	Display	PDBx/mmCIF format
PDB format	pdb2wqv.ent.gz	97.4 KB	Display	PDB format
PDBx/mmJSON format	2wqv.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	2wqv_validation.pdf.gz	451.1 KB	Display	wwPDB validaton report
Full document	2wqv_full_validation.pdf.gz	456.8 KB	Display
Data in XML	2wqv_validation.xml.gz	22.1 KB	Display
Data in CIF	2wqv_validation.cif.gz	29.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/wq/2wqv ftp://data.pdbj.org/pub/pdb/validation_reports/wq/2wqv	HTTPS FTP

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Related structure data

Related structure data	2wquC 2wqwC 2wqxC 1h6tS 1d0b 1m9s 1otm 1otn 1oto 2uzx 2uzy S: Starting model for refinement C: citing same article (ref.)
Similar structure data	2wqu-2 2wqu-1 1all-d 2wqx-2 5h28-d 2wqu-4 2wqx-1 4rmp-d 3m05-2 6jsd-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#143 - Nov 2011 Toll-like Receptors similarity (5) #248 - Aug 2020 Phytosulfokine Receptor similarity (5) #245 - May 2020 Spliceosomes similarity (3) #60 - Dec 2004 Ubiquitin similarity (1) #68 - Aug 2005 Neurotrophins similarity (2) #105 - Sep 2008 Ribonuclease A similarity (2) #234 - Jun 2019 MDM2 and Cancer similarity (1)

Deposited unit

A: INTERNALIN B

B: INTERNALIN B

hetero molecules

65.5 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: INTERNALIN B

hetero molecules

defined by author&software
32.7 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: INTERNALIN B

hetero molecules

defined by author&software
32.7 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	185.900, 185.900, 115.070
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	155
Space group name H-M	H32

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	B
2	1	A
1	2	B
2	2	A
1	3	B
2	3	A
1	4	A
2	4	B

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Refine code	Auth asym-ID	Auth seq-ID
1	1	1	1	B	36 - 243
2	1	1	1	A	36 - 243
1	1	2	1	B	254 - 273
2	1	2	1	A	254 - 273
1	1	3	1	B	279 - 285
2	1	3	1	A	279 - 285
1	1	4	1	A	294 - 318
2	1	4	1	B	294 - 318

NCS ensembles :

ID
1
2
3
4

NCS oper: (Code: given
Matrix: (0.52031, 0.85386, 0.01367), (-0.85373, 0.52048, -0.01568), (-0.0205, -0.00352, 0.99978)
Vector: 0.03024, 0.91133, -0.50046)

#1: Protein	INTERNALIN B Mass: 32243.818 Da / Num. of mol.: 2 / Fragment: INTERNALIN DOMAIN, RESIDUES 36-321 Source method: isolated from a genetically manipulated source 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: Chemical	ChemComp-PG4 / TETRAETHYLENE GLYCOL Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₈H₁₈O₅ / Comment: precipitant*YM
#3: Chemical	ChemComp-PGE / TRIETHYLENE GLYCOL Mass: 150.173 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₆H₁₄O₄
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 31 / Source method: isolated from a natural source / Formula: H₂O
Sequence details	RESIDUE 33-35 (GAM) REMAIN AFTER TEV CLEAVAGE OF GST- FUSION PROTEIN

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

Crystal	Density Matthews: 2.97 Å³/Da / Density % sol: 58.6 % / Description: NONE
Crystal grow	Temperature: 293 K / Method: vapor diffusion Details: SITTING VAPOR DIFFUSION AT 293 K. 200 NL PROTEIN PLUS 100 NL OF RESERVOIR SOLUTION CONSISTING OF 0.1 M NACL, 0.1 M CHES PH 9.5, 40% PEG300. THE PROTEIN WAS ACTUALLY A COMPLEX OF MET741 WITH ...Details: SITTING VAPOR DIFFUSION AT 293 K. 200 NL PROTEIN PLUS 100 NL OF RESERVOIR SOLUTION CONSISTING OF 0.1 M NACL, 0.1 M CHES PH 9.5, 40% PEG300. THE PROTEIN WAS ACTUALLY A COMPLEX OF MET741 WITH INLB321 AT 5 MG/ML, I.E. INLB321 WAS AT 1.4 MG/ML. CRYSTAL GROWTH TIME: SEVERAL WEEKS TO MONTHS.

Crystal

Density Matthews: 2.97 Å³/Da / Density % sol: 58.6 % / Description: NONE

Crystal grow

Temperature: 293 K / Method: vapor diffusion
Details: SITTING VAPOR DIFFUSION AT 293 K. 200 NL PROTEIN PLUS 100 NL OF RESERVOIR SOLUTION CONSISTING OF 0.1 M NACL, 0.1 M CHES PH 9.5, 40% PEG300. THE PROTEIN WAS ACTUALLY A COMPLEX OF MET741 WITH ...

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873
Detector	Type: MARRESEARCH / Detector: CCD / Date: May 19, 2006
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.873 Å / Relative weight: 1
Reflection	Resolution: 2.8→20 Å / Num. obs: 18763 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 6.96 % / B_iso Wilson estimate: 45.1 Å² / R_merge(I) obs: 0.16 / Net I/σ(I): 10.98
Reflection shell	Resolution: 2.8→2.87 Å / Redundancy: 7.08 % / R_merge(I) obs: 0.91 / Mean I/σ(I) obs: 2.58 / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0019	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1H6T

1h6t

Resolution: 2.8→19.822 Å / Cor.coef. F_o:F_c: 0.933 / Cor.coef. F_o:F_c free: 0.917 / SU B: 24.703 / SU ML: 0.233 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.343 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTOR

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2378	941	5.05 %	RANDOM
R_work	0.2033	-	-	-
obs	0.205	18762	99.692 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 40.35 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	2.278 Å²	1.139 Å²	0 Å²
2-	-	2.278 Å²	0 Å²
3-	-	-	-3.417 Å²

Refinement step

Cycle: LAST / Resolution: 2.8→19.822 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4436	0	66	31	4533

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.022	4582
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	3089
X-RAY DIFFRACTION	r_angle_refined_deg	1.072	1.994	6189
X-RAY DIFFRACTION	r_angle_other_deg	0.815	3	7696
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.979	5	565
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	44.594		192
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.609		858
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	13.99	15	8
X-RAY DIFFRACTION	r_chiral_restr	0.057	0.2	745
X-RAY DIFFRACTION	r_gen_planes_refined	0.003	0.02	4881
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	739
X-RAY DIFFRACTION	r_nbd_refined	0.195	0.2	867
X-RAY DIFFRACTION	r_nbd_other	0.185		3188
X-RAY DIFFRACTION	r_nbtor_refined	0.168	0.2	2147
X-RAY DIFFRACTION	r_nbtor_other	0.082	0.2	2472
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.137	0.2	116
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.125	0.2	18
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.212	0.2	64
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.162	0.2	7
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.334	1.5	3747
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	0.387	2	4615
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	0.771	3	2086
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	1.11	4.5	1572
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-ID	Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	1	B	2705	tight positional	0.02	0.05
1	2	A	2705	tight positional	0.02	0.05
2	1	B	234	tight positional	0.02	0.05
2	2	A	234	tight positional	0.02	0.05
3	1	B	113	tight positional	0.01	0.05
3	2	A	113	tight positional	0.01	0.05
4	1	A	354	tight positional	0.02	0.05
4	2	B	354	tight positional	0.02	0.05
1	1	B	2705	tight thermal	0.03	0.5
1	2	A	2705	tight thermal	0.03	0.5
2	1	B	234	tight thermal	0.03	0.5
2	2	A	234	tight thermal	0.03	0.5
3	1	B	113	tight thermal	0.03	0.5
3	2	A	113	tight thermal	0.03	0.5
4	1	A	354	tight thermal	0.03	0.5
4	2	B	354	tight thermal	0.03	0.5

LS refinement shell

Resolution: 2.8→2.871 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.384	69	-
R_work	0.294	1287	-
obs	-	-	100 %

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°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)
1	1.4088	1.5003	0.3544	4.6008	0.5305	3.769	-0.233	0.385	-0.0222	-0.5181	0.1505	-0.0167	-0.0358	-0.1252	0.0824	0.1452	-0.0112	-0.0452	0.253	-0.0008	0.1385	-20.824	16.041	14.792
2	1.3932	0.2639	1.195	2.0771	0.7029	3.703	-0.1116	0.2064	0.0361	-0.2096	-0.0143	0.061	-0.1772	-0.1735	0.1259	0.0515	0.0434	0.0146	0.0898	0.0002	0.1158	-17.22	25.974	40.275
3	1.1965	0.9573	0.637	7.4779	-1.6735	3.8701	-0.1194	-0.1409	0.3934	0.0885	0.0257	0.8181	-0.766	-0.2959	0.0938	0.4433	0.0282	-0.0534	0.1715	-0.0614	0.3545	-11.584	50.743	54.841
4	2.0857	0.1529	0.5767	7.4359	0.1913	1.76	-0.1909	-0.0296	0.7861	-0.0591	0.0714	-0.3642	-0.5768	0.0591	0.1195	0.35	0.0289	-0.0911	0.1184	-0.0128	0.2775	-7.23	48.359	52.889
5	2.5002	-1.5276	-1.3011	3.4075	1.3982	4.8776	0.064	0.2596	-0.0778	-0.4706	-0.042	-0.0483	0.0511	0.0353	-0.0221	0.1545	-0.0282	-0.0045	0.1947	-0.0003	0.1064	-24.178	-9.911	14.769
6	1.2264	-0.0858	-0.1548	1.8008	1.3037	4.1768	-0.0359	0.1682	-0.0213	-0.1431	-0.0517	0.0673	0.1268	-0.185	0.0875	0.0101	-0.0242	-0.0034	0.0866	0.0145	0.1124	-31.149	-1.87	40.219
7	7.3563	-3.6914	0.0755	3.6104	0.0485	2.1424	-0.1263	0.1167	-0.4227	-0.0609	0.0149	0.4504	-0.2087	-0.5908	0.1115	0.1568	0.0746	0.0434	0.317	-0.043	0.2659	-49.775	17.213	55.12
8	7.6324	-4.0759	-1.118	2.58	0.4098	2.5753	0.0611	0.3476	0.2327	-0.1049	-0.1954	0.2153	-0.2513	-0.6183	0.1344	0.1307	0.0384	0.0102	0.2606	-0.1067	0.1954	-46.495	18	50.792

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	37 - 115
2	X-RAY DIFFRACTION	2	A	116 - 240
3	X-RAY DIFFRACTION	3	A	241 - 274
4	X-RAY DIFFRACTION	4	A	275 - 320
5	X-RAY DIFFRACTION	5	B	37 - 115
6	X-RAY DIFFRACTION	6	B	116 - 240
7	X-RAY DIFFRACTION	7	B	241 - 280
8	X-RAY DIFFRACTION	8	B	281 - 320

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