PDB-5w5p: Crystal structure of Acinetobacter baumannii phage AM24 tailspike...

ID or keywords:

Entry

Database: PDB / ID: 5w5p

Title

Crystal structure of Acinetobacter baumannii phage AM24 tailspike protein

Components

Tail fiber protein

Keywords

VIRAL PROTEIN / AM27 / Tailspike protein / Bacteriophage / capsular polysaccharide

Function / homology

metal ion binding / Tail fiber protein

Function and homology information

Biological species

Acinetobacter phage AM24 (virus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.429 Å

Authors

Plattner, M. / Shneider, M.M. / Leiman, P.G.

Funding support

Switzerland, 1items

Citation

Journal: To be Published
Title: Crystal structure of Acinetobacter baumannii phage AM24 tailspike protein
Authors: Plattner, M. / Shneider, M.M. / Leiman, P.G.

History

Deposition	Jun 15, 2017	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 19, 2018	Provider: repository / Type: Initial release
Revision 1.1	Oct 23, 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	5w5p.cif.gz	246.2 KB	Display	PDBx/mmCIF format
PDB format	pdb5w5p.ent.gz	196.9 KB	Display	PDB format
PDBx/mmJSON format	5w5p.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	5w5p_validation.pdf.gz	429.6 KB	Display	wwPDB validaton report
Full document	5w5p_full_validation.pdf.gz	431 KB	Display
Data in XML	5w5p_validation.xml.gz	24.3 KB	Display
Data in CIF	5w5p_validation.cif.gz	35.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/w5/5w5p ftp://data.pdbj.org/pub/pdb/validation_reports/w5/5w5p	HTTPS FTP

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Related structure data

Similar structure data	1wp1-1 6e1r-2 3gq8-1 5xeb-1 5xeb-2 3gq7-1 5azo-1 2vde-d 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

Deposited unit

A: Tail fiber protein

hetero molecules

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

1

A: Tail fiber protein

hetero molecules

A: Tail fiber protein

hetero molecules

A: Tail fiber protein

hetero molecules

defined by author&software
Evidence: gel filtration
202 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	100.657, 100.657, 307.836
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	182
Space group name H-M	P6₃22

Components on special symmetry positions

ID	Model	Components
1	1	A-905- HOH
2	1	A-960- HOH
3	1	A-1013- HOH
4	1	A-1026- HOH

#1: Protein	Tail fiber protein Mass: 67334.359 Da / Num. of mol.: 1 / Fragment: UNP residues 230-848 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acinetobacter phage AM24 (virus) / Production host: Escherichia coli B (bacteria) / Strain (production host): 834 / References: UniProt: A0A1J0MGR2
#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 251 / 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: 3.34 Å³/Da / Density % sol: 63.21 %
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 38% PEG1000, 120 mM magnesium sulfate, 100 mM sodium citrate

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.979 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 18, 2015
Radiation	Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.979 Å / Relative weight: 1
Reflection	Resolution: 2.429→50 Å / Num. obs: 64571 / % possible obs: 97.9 % / Redundancy: 20 % / Net I/σ(I): 21.04
Reflection shell	Highest resolution: 2.429 Å

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Processing

Software

Name	Version	Classification
PHENIX	(dev_2666: ???)	refinement
XDS		data reduction
XSCALE		data scaling
SHELXDE		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.429→47.836 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.71

	R_factor	Num. reflection	% reflection
R_free	0.2171	3243	5.03 %
R_work	0.1802	-	-
obs	0.182	64470	97.81 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 2.429→47.836 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4606	0	2	251	4859

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	4690
X-RAY DIFFRACTION	f_angle_d	0.554	6366
X-RAY DIFFRACTION	f_dihedral_angle_d	6.545	2735
X-RAY DIFFRACTION	f_chiral_restr	0.045	727
X-RAY DIFFRACTION	f_plane_restr	0.003	825

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.4286-2.4649	0.3126	80	0.3133	1467	X-RAY DIFFRACTION	53
2.4649-2.5034	0.3169	141	0.2725	2680	X-RAY DIFFRACTION	100
2.5034-2.5444	0.2912	142	0.2621	2703	X-RAY DIFFRACTION	100
2.5444-2.5883	0.2751	147	0.256	2750	X-RAY DIFFRACTION	100
2.5883-2.6354	0.2966	143	0.2426	2702	X-RAY DIFFRACTION	100
2.6354-2.6861	0.2972	140	0.2355	2702	X-RAY DIFFRACTION	100
2.6861-2.7409	0.2173	145	0.2259	2715	X-RAY DIFFRACTION	100
2.7409-2.8005	0.2474	147	0.2186	2764	X-RAY DIFFRACTION	100
2.8005-2.8656	0.2445	147	0.2266	2720	X-RAY DIFFRACTION	100
2.8656-2.9373	0.2642	143	0.2258	2657	X-RAY DIFFRACTION	100
2.9373-3.0167	0.2951	150	0.2257	2738	X-RAY DIFFRACTION	100
3.0167-3.1054	0.2774	144	0.2217	2704	X-RAY DIFFRACTION	100
3.1054-3.2056	0.2545	142	0.2072	2736	X-RAY DIFFRACTION	100
3.2056-3.3202	0.2405	142	0.2037	2696	X-RAY DIFFRACTION	100
3.3202-3.4531	0.2258	149	0.1921	2742	X-RAY DIFFRACTION	100
3.4531-3.6102	0.2175	137	0.1688	2718	X-RAY DIFFRACTION	100
3.6102-3.8004	0.1763	144	0.1562	2708	X-RAY DIFFRACTION	100
3.8004-4.0384	0.1791	145	0.1464	2731	X-RAY DIFFRACTION	100
4.0384-4.3501	0.1688	143	0.1342	2715	X-RAY DIFFRACTION	100
4.3501-4.7875	0.182	144	0.1251	2705	X-RAY DIFFRACTION	99
4.7875-5.4793	0.1658	140	0.1421	2720	X-RAY DIFFRACTION	100
5.4793-6.9001	0.188	141	0.1651	2716	X-RAY DIFFRACTION	100
6.9001-47.8454	0.2196	147	0.1775	2738	X-RAY DIFFRACTION	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	1.6603	0.2932	1.4023	1.5365	1.2949	2.8888	0.0143	-0.3055	-0.0504	0.1815	-0.0167	0.0505	0.1574	-0.3088	-0.0019	0.5525	-0.0223	0.056	0.5706	0.06	0.4369	38.1975	26.1915	47.4937
2	0.6444	-0.1592	-0.152	0.4125	0.2866	2.1387	0.0668	-0.0178	-0.0913	0.0928	0.0462	0.0447	0.1604	-0.2337	-0.1157	0.417	-0.0248	-0.0167	0.4091	0.0418	0.4287	36.6139	18.8791	5.8157
3	0.5638	-0.1193	-0.107	0.5417	-0.1276	1.2797	0.0596	0.2455	0.108	-0.1233	0.0275	-0.1298	-0.1632	0.1246	-0.0878	0.5059	-0.0113	0.0242	0.5241	0.0031	0.3972	56.4601	35.9113	-39.7236

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 12 through 117 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 118 through 396 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 397 through 619 )

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