PDB-6d7y: 1.75 Angstrom Resolution Crystal Structure of the Toxic C-Termina...

ID or keywords:

Entry

Database: PDB / ID: 6d7y

Title

1.75 Angstrom Resolution Crystal Structure of the Toxic C-Terminal Tip of CdiA from Pseudomonas aeruginosa in Complex with Immune Protein

Components

Hemagglutinin
immune protein

Keywords

TOXIN / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID

Function / homology

Uncharacterized protein / :

Function and homology information

Biological species

Pseudomonas aeruginosa (bacteria)

Enterobacter cloacae (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.75 Å

Authors

Minasov, G. / Shuvalova, L. / Wawrzak, Z. / Kiryukhina, O. / Allen, J.P. / Hauser, A.R. / Anderson, W.F. / Satchell, K.J.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: A comparative genomics approach identifies contact-dependent growth inhibition as a virulence determinant.
Authors: Allen, J.P. / Ozer, E.A. / Minasov, G. / Shuvalova, L. / Kiryukhina, O. / Satchell, K.J.F. / Hauser, A.R.

History

Deposition	Apr 25, 2018	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 1, 2019	Provider: repository / Type: Initial release
Revision 1.1	Mar 11, 2020	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2	Mar 25, 2020	Group: Database references / Category: citation / citation_author Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.3	Apr 15, 2020	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4	Oct 16, 2024	Group: Data collection / Database references / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6d7y.cif.gz	119.1 KB	Display	PDBx/mmCIF format
PDB format	pdb6d7y.ent.gz	92.4 KB	Display	PDB format
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Validation report

Summary document	6d7y_validation.pdf.gz	428 KB	Display	wwPDB validaton report
Full document	6d7y_full_validation.pdf.gz	430.3 KB	Display
Data in XML	6d7y_validation.xml.gz	12 KB	Display
Data in CIF	6d7y_validation.cif.gz	16.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/d7/6d7y ftp://data.pdbj.org/pub/pdb/validation_reports/d7/6d7y	HTTPS FTP

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Related structure data

Similar structure data	4hv0-1 6pqm-d 3nsu-2 3imj-1 2bf2-1 4r55-d 2h3m-d 1igq-1 1bfe-d 1poq-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 - HomologyF&H Search
Other databases	TargetTrack: CSGID-IDP95525

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Hemagglutinin

B: immune protein

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

1

A: Hemagglutinin

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

2

B: immune protein

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

Unit cell

Length a, b, c (Å)	76.579, 76.579, 61.441
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	173
Space group name H-M	P6₃

#1: Protein	Hemagglutinin Mass: 10866.086 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: BKN49_19035 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL-21(DE3) magic / References: UniProt: A0A1X0SIL3
#2: Protein	immune protein Mass: 17926.510 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacter cloacae (bacteria) / Gene: SAMEA2273162_06031 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)-Magic / References: UniProt: A0A157WHH8
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 98 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 1.85 Å³/Da / Density % sol: 33.5 %
Crystal grow	Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: Protein: 6.4mg/ml, 0.5 Sodium chloride, 0.01M Tris pH 8.3; Screen: Clasics II (D6), 0.1M Bis-Tris pH 5.5, 25% (w/v) PEG 3350;

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
Detector	Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 20, 2017
Radiation	Monochromator: Be / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97872 Å / Relative weight: 1
Reflection	Resolution: 1.75→30 Å / Num. obs: 20855 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 6.6 % / B_iso Wilson estimate: 27.7 Å² / R_merge(I) obs: 0.075 / R_pim(I) all: 0.032 / R_rim(I) all: 0.082 / R_sym value: 0.075 / Χ²: 1.803 / Net I/σ(I): 30.7
Reflection shell	Resolution: 1.75→1.78 Å / Redundancy: 6.6 % / R_merge(I) obs: 0.799 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 1035 / CC_1/2: 0.722 / R_pim(I) all: 0.34 / R_rim(I) all: 0.868 / R_sym value: 0.799 / Χ²: 1.006 / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0189	refinement
HKL-3000		data reduction
HKL-3000		data scaling
HKL-3000		phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.75→29.18 Å / Cor.coef. F_o:F_c: 0.965 / Cor.coef. F_o:F_c free: 0.95 / SU B: 7.205 / SU ML: 0.109 / Cross valid method: THROUGHOUT / ESU R: 0.141 / ESU R Free: 0.13 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.22364	1012	4.9 %	RANDOM
R_work	0.18302	-	-	-
obs	0.185	19733	99.91 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å

Displacement parameters

B_iso mean: 37.575 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.84 Å²	-0.42 Å²	0 Å²
2-	-	-0.84 Å²	0 Å²
3-	-	-	2.73 Å²

Refinement step

Cycle: 1 / Resolution: 1.75→29.18 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1974	0	0	98	2072

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.019	2065
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	1903
X-RAY DIFFRACTION	r_angle_refined_deg	1.507	1.966	2776
X-RAY DIFFRACTION	r_angle_other_deg	0.88	3	4417
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	2.871	5	255
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	24.142	24.02	102
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	9.372	15	337
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	13.449	15	11
X-RAY DIFFRACTION	r_chiral_restr	0.093	0.2	286
X-RAY DIFFRACTION	r_gen_planes_refined	0.023	0.02	2336
X-RAY DIFFRACTION	r_gen_planes_other	0.019	0.02	471
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
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
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
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	1.536	1.826	1011
X-RAY DIFFRACTION	r_mcbond_other	1.528	1.824	1010
X-RAY DIFFRACTION	r_mcangle_it	2.507	2.727	1269
X-RAY DIFFRACTION	r_mcangle_other	2.508	2.729	1270
X-RAY DIFFRACTION	r_scbond_it	1.989	2.058	1054
X-RAY DIFFRACTION	r_scbond_other	1.988	2.058	1054
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	3.108	3.012	1507
X-RAY DIFFRACTION	r_long_range_B_refined	5.219	22.398	2284
X-RAY DIFFRACTION	r_long_range_B_other	5.183	22.213	2269
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.75→1.795 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.28	85	-
R_work	0.288	1442	-
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	2.9473	0.7849	0.6525	3.4615	0.1372	5.3315	-0.0058	-0.0274	0.1867	0.0332	-0.0349	0.5038	0.2586	-0.4456	0.0407	0.0309	-0.0589	0.005	0.1242	-0.0162	0.0901	18.81	50.0394	9.2394
2	5.2368	4.5873	6.2621	4.2225	6.0391	9.9531	-0.1603	0.0045	0.617	-0.1141	-0.0863	0.5678	-0.5121	-0.3292	0.2466	0.2459	0.0622	0.1296	0.2922	-0.0082	0.4914	18.9431	60.6565	15.1102
3	7.5069	-4.9037	-2.8644	8.7542	3.9889	6.1155	-0.1248	-0.2051	0.0806	0.4637	0.2264	-0.4092	0.2152	0.2644	-0.1016	0.0555	-0.0218	-0.0066	0.096	0.0056	0.064	39.3531	56.8545	13.6825
4	2.3218	0.7916	-0.2742	3.9003	-0.0556	3.5898	-0.0624	-0.1163	0.1737	0.1442	-0.089	0.1811	0.0192	-0.1918	0.1514	0.0327	-0.0052	0.0059	0.0766	-0.0337	0.0289	30.1094	57.3193	13.7823
5	3.0012	0.2644	0.1563	2.7939	-0.4438	1.1485	-0.1561	0.1493	-0.2333	0.0319	-0.0241	0.3244	0.5834	-0.2115	0.1802	0.4324	-0.1263	0.1488	0.2157	-0.0652	0.1203	23.4127	33.0467	5.7599
6	1.4895	0.6188	0.4337	8.7836	-3.1109	1.4015	0.0807	-0.2038	0.1132	0.0748	0.0067	0.3754	0.029	-0.1247	-0.0874	0.1809	-0.0998	0.0605	0.2296	-0.0418	0.1363	9.0639	33.4167	9.1809
7	3.4586	0.4078	0.8407	2.9079	0.0001	3.2172	-0.1967	0.1936	-0.2972	-0.0781	-0.0296	0.2225	0.4878	-0.2607	0.2263	0.2852	-0.1407	0.0638	0.1973	-0.0349	0.0825	19.5472	34.6659	4.8941
8	2.5464	0.337	0.0067	3.0191	1.3147	3.3239	-0.0707	0.2823	-0.1418	-0.0583	0.0879	-0.2335	0.4631	-0.0342	-0.0172	0.2536	-0.0005	0.0479	0.1298	-0.0139	0.0301	34.9448	38.9295	2.4586

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	3352 - 3390
2	X-RAY DIFFRACTION	2	A	3391 - 3406
3	X-RAY DIFFRACTION	3	A	3407 - 3417
4	X-RAY DIFFRACTION	4	A	3418 - 3443
5	X-RAY DIFFRACTION	5	B	1 - 35
6	X-RAY DIFFRACTION	6	B	36 - 48
7	X-RAY DIFFRACTION	7	B	49 - 96
8	X-RAY DIFFRACTION	8	B	97 - 155

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