PDB-4w64: Hcp1 protein from Acinetobacter baumannii AB0057

ID or keywords:

Entry

Database: PDB / ID: 4w64

Title

Hcp1 protein from Acinetobacter baumannii AB0057

Components

Type VI secretion system effector, Hcp1 family

Keywords

UNKNOWN FUNCTION / Type VI secretion system effector / Hcp1 family

Function / homology

Hcp1-like / Type VI secretion system effector Hcp / Hcp1-like superfamily / Type VI secretion system effector, Hcp / Pnp Oxidase; Chain A / Roll / Mainly Beta / Type VI secretion system effector, Hcp1 family / Uncharacterized protein

Function and homology information

Biological species

Acinetobacter baumannii (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.55 Å

Authors

Ruiz, F.M. / Romero, A.

Citation

Journal: Plos One / Year: 2015
Title: Crystal Structure of Hcp from Acinetobacter baumannii: A Component of the Type VI Secretion System.
Authors: Ruiz, F.M. / Santillana, E. / Spinola-Amilibia, M. / Torreira, E. / Culebras, E. / Romero, A.

History

Deposition	Aug 20, 2014	Deposition site: RCSB / Processing site: PDBE
Revision 1.0	Jul 1, 2015	Provider: repository / Type: Initial release
Revision 2.0	Jan 10, 2024	Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Refinement description Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4w64.cif.gz	222 KB	Display	PDBx/mmCIF format
PDB format	pdb4w64.ent.gz	179.4 KB	Display	PDB format
PDBx/mmJSON format	4w64.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4w64_validation.pdf.gz	450.4 KB	Display	wwPDB validaton report
Full document	4w64_full_validation.pdf.gz	453.2 KB	Display
Data in XML	4w64_validation.xml.gz	25.2 KB	Display
Data in CIF	4w64_validation.cif.gz	37 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/w6/4w64 ftp://data.pdbj.org/pub/pdb/validation_reports/w6/4w64	HTTPS FTP

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Related structure data

Related structure data	1y12S S: Starting model for refinement
Similar structure data	3eaa-1 3kti-d 3kth-d 6w9t-d 3ktg-d 1y12-1 3ktj-d 1tg6-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) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Type VI secretion system effector, Hcp1 family

B: Type VI secretion system effector, Hcp1 family

C: Type VI secretion system effector, Hcp1 family

hetero molecules

57.7 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Type VI secretion system effector, Hcp1 family

hetero molecules

x 6

defined by author&software
116 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1
crystal symmetry operation	2_555	-y,x-y,z	1
crystal symmetry operation	3_555	-x+y,-x,z	1
crystal symmetry operation	4_555	-x,-y,z	1
crystal symmetry operation	5_555	y,-x+y,z	1
crystal symmetry operation	6_555	x-y,x,z	1

2

B: Type VI secretion system effector, Hcp1 family

hetero molecules

x 6

defined by author&software
115 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1
crystal symmetry operation	2_555	-y,x-y,z	1
crystal symmetry operation	3_555	-x+y,-x,z	1
crystal symmetry operation	4_555	-x,-y,z	1
crystal symmetry operation	5_555	y,-x+y,z	1
crystal symmetry operation	6_555	x-y,x,z	1

3

C: Type VI secretion system effector, Hcp1 family

hetero molecules

x 6

defined by author&software
115 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1
crystal symmetry operation	2_555	-y,x-y,z	1
crystal symmetry operation	3_555	-x+y,-x,z	1
crystal symmetry operation	4_555	-x,-y,z	1
crystal symmetry operation	5_555	y,-x+y,z	1
crystal symmetry operation	6_555	x-y,x,z	1

Unit cell

Length a, b, c (Å)	87.001, 87.001, 128.809
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	168
Space group name H-M	P6

Components on special symmetry positions

ID	Model	Components
1	1	A-380- HOH
2	1	A-387- HOH
3	1	A-405- HOH

#1: Protein	Type VI secretion system effector, Hcp1 family Mass: 19111.244 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Strain: AB0057 / Gene: AB57_1481 / Production host: Escherichia coli (E. coli) / References: UniProt: B7I1Z0, UniProt: A0A0M3KKY9*PLUS
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO₄
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 513 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 2.45 Å³/Da / Density % sol: 52 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop / Details: 2.0 M Ammonium Sulfate and 0.1 M Hepes / PH range: 7.5

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98011 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 24, 2011
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.98011 Å / Relative weight: 1
Reflection	Resolution: 1.55→48.96 Å / Num. obs: 79939 / % possible obs: 99.8 % / Redundancy: 10.8 % / R_sym value: 0.026 / Net I/σ(I): 20.8
Reflection shell	Resolution: 1.55→1.6 Å / Redundancy: 8.3 % / Mean I/σ(I) obs: 1.8 / % possible all: 98.06

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Processing

Software

Name	Version	Classification
PHENIX	(phenix.refine: 1.8_1069)	refinement
XDS		data reduction
Aimless		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1Y12

1y12

Resolution: 1.55→48.956 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.05 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1977	4033	5.05 %
R_work	0.1681	-	-
obs	0.1695	79916	99.77 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.55→48.956 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3928	0	20	513	4461

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	4111
X-RAY DIFFRACTION	f_angle_d	1.088	5594
X-RAY DIFFRACTION	f_dihedral_angle_d	14.847	1487
X-RAY DIFFRACTION	f_chiral_restr	0.076	607
X-RAY DIFFRACTION	f_plane_restr	0.005	708

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 (%)
1.549-1.5672	0.3099	129	0.2991	2465	X-RAY DIFFRACTION	94
1.5672-1.5863	0.282	125	0.2419	2663	X-RAY DIFFRACTION	100
1.5863-1.6064	0.2492	155	0.2199	2559	X-RAY DIFFRACTION	100
1.6064-1.6275	0.2591	124	0.2198	2614	X-RAY DIFFRACTION	100
1.6275-1.6498	0.2513	133	0.2053	2641	X-RAY DIFFRACTION	100
1.6498-1.6734	0.233	136	0.2041	2620	X-RAY DIFFRACTION	100
1.6734-1.6984	0.2454	145	0.2001	2596	X-RAY DIFFRACTION	100
1.6984-1.7249	0.2665	139	0.1972	2615	X-RAY DIFFRACTION	100
1.7249-1.7532	0.2408	147	0.1967	2616	X-RAY DIFFRACTION	100
1.7532-1.7834	0.2293	152	0.1823	2604	X-RAY DIFFRACTION	100
1.7834-1.8158	0.244	128	0.1827	2634	X-RAY DIFFRACTION	100
1.8158-1.8508	0.2182	146	0.1816	2628	X-RAY DIFFRACTION	100
1.8508-1.8885	0.2211	149	0.174	2597	X-RAY DIFFRACTION	100
1.8885-1.9296	0.1946	137	0.1683	2587	X-RAY DIFFRACTION	100
1.9296-1.9745	0.2002	143	0.1688	2638	X-RAY DIFFRACTION	100
1.9745-2.0239	0.2172	146	0.1605	2617	X-RAY DIFFRACTION	100
2.0239-2.0786	0.2129	128	0.1647	2617	X-RAY DIFFRACTION	100
2.0786-2.1398	0.2149	142	0.1625	2602	X-RAY DIFFRACTION	100
2.1398-2.2088	0.1885	122	0.1628	2637	X-RAY DIFFRACTION	100
2.2088-2.2878	0.2036	133	0.1661	2653	X-RAY DIFFRACTION	100
2.2878-2.3794	0.2282	131	0.1639	2586	X-RAY DIFFRACTION	100
2.3794-2.4877	0.1938	156	0.1688	2642	X-RAY DIFFRACTION	100
2.4877-2.6188	0.1979	142	0.1724	2604	X-RAY DIFFRACTION	100
2.6188-2.7829	0.1748	135	0.1715	2630	X-RAY DIFFRACTION	100
2.7829-2.9977	0.2048	140	0.1682	2636	X-RAY DIFFRACTION	100
2.9977-3.2993	0.1717	146	0.162	2622	X-RAY DIFFRACTION	100
3.2993-3.7766	0.1656	147	0.1465	2641	X-RAY DIFFRACTION	100
3.7766-4.7575	0.1628	136	0.1419	2627	X-RAY DIFFRACTION	100
4.7575-48.9808	0.2097	141	0.1806	2692	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	2.7462	-0.2383	0.5371	3.7287	-0.1979	3.4245	-0.0659	-0.3426	-0.1612	0.2474	-0.0241	-0.1444	0.0348	0.0806	0.0837	0.1038	0.0012	0.0048	0.0798	0.0162	0.1309	19.2787	-27.9309	-24.8844
2	2.0421	-0.1826	2.0931	0.4275	-0.1655	6.576	-0.2515	0.5681	0.2461	-0.068	0.0563	-0.0409	-0.1305	0.4427	0.3314	0.1536	0.0031	-0.0117	0.1124	-0.0159	0.1348	-4.9899	-22.7685	-42.7232
3	9.777	-2.1112	-4.3737	7.8569	-2.5867	3.698	-0.1552	-1.3633	-0.0444	0.6376	0.1779	-0.7526	0.0381	1.583	-0.0359	0.5093	0.0501	-0.0439	0.6017	-0.0142	0.3225	-8.8478	-28.6275	-54.8886
4	5.7006	0.9674	2.5743	1.5281	0.3054	2.5624	-0.0671	0.458	-0.0278	-0.1183	0.0407	0.0319	0.0185	0.2265	-0.0074	0.1016	0.0037	0.0251	0.0866	0.0001	0.0954	11.6817	-20.59	-34.2794
5	1.4939	0.9635	0.7034	2.9769	-0.6197	0.8439	-0.0892	0.2825	-0.1649	-0.3297	-0.0078	-0.2766	0.0297	0.0748	0.0266	0.0733	0.0054	0.0405	0.0756	-0.0202	0.127	24.6576	-21.0062	-37.2178
6	3.1309	0.6209	-1.5621	2.5818	-0.4523	2.5617	0.0854	-0.2766	-0.0996	0.2104	0.0002	-0.0078	0.2832	-0.0928	-0.0116	0.1176	-0.0023	0.0022	0.1179	0.0041	0.122	10.25	-32.9212	-24.1388
7	3.9259	4.0035	3.4823	6.0414	3.6565	3.122	-0.0316	0.0701	-0.0545	0.084	-0.0231	-0.0277	0.1792	-0.041	0.008	0.0935	0.0002	0.0187	0.0724	0.0105	0.0574	17.7237	-18.2052	-37.0531
8	1.5084	1.5021	0.3303	1.8432	0.1137	1.2425	0.021	-0.0855	0.0331	0.0143	-0.0012	0.1019	-0.1143	0.028	0.0545	0.0688	0.0391	0.041	0.0562	-0.0182	0.07	13.2912	-20.4451	-29.3388
9	3.0511	0.3148	-0.8161	3.0724	-0.8283	4.5223	-0.105	-0.2856	-0.2908	0.1788	-0.0217	0.1435	0.4176	-0.2066	0.1969	0.1741	-0.0039	0.0258	0.1348	-0.0167	0.1824	3.496	-37.1511	-34.4449
10	3.1621	0.0729	-0.4009	4.3939	-0.2531	3.6166	-0.0653	0.2372	-0.3873	-0.3362	-0.0555	0.0793	0.2357	-0.0778	0.0586	0.1172	0.0172	-0.0077	0.1058	-0.0191	0.1428	13.9045	-31.2954	-84.6202
11	5.0757	4.7341	4.9108	4.4	4.6038	4.7627	-0.0959	-0.2586	0.2457	-0.0786	-0.1348	0.2153	-0.364	-0.1016	0.226	0.2101	-0.0146	-0.0102	0.198	-0.0066	0.1445	22.3487	-6.9832	-67.5774
12	6.0274	3.8859	-6.2311	6.3724	-4.6116	6.6725	-0.4284	0.6457	-0.7264	-0.9301	0.1471	0.1605	1.3908	-1.1923	0.3488	0.5786	-0.0013	0.0048	0.5474	-0.0486	0.3065	29.502	-6.2206	-55.1097
13	6.3432	4.4409	4.8034	5.1137	3.897	5.1674	0.0144	-0.2693	0.2204	0.2056	-0.265	0.1947	0.0875	-0.165	0.2173	0.114	0.0195	0.0017	0.1075	0.0029	0.1127	11.895	-20.5067	-75.9528
14	2.3471	0.6433	-0.0964	0.9865	0.1702	0.8663	-0.0275	0.0592	-0.0829	-0.0234	0.0254	-0.1017	0.0195	0.0748	-0.0004	0.1011	0.0294	-0.0005	0.0686	0.0173	0.0733	16.4688	-25.0163	-76.8673
15	3.5088	0.216	0.4168	4.0266	0.6181	4.1238	-0.0973	0.2318	-0.4541	-0.117	0.0492	0.2087	0.3665	-0.2651	0.015	0.1556	-0.0134	0.0118	0.1586	-0.0458	0.2025	1.2775	-34.519	-123.8504
16	4.5289	4.2015	1.8324	3.8378	2.1328	3.5033	0.1815	-0.7552	0.1317	0.4051	-0.3339	-0.0583	0.1247	0.0419	0.0939	0.2242	-0.004	-0.0024	0.2847	-0.0126	0.1952	19.0025	-15.787	-103.6706
17	2.6812	-0.5656	0.2028	0.6984	0.1521	1.1668	-0.0175	0.1687	-0.0627	-0.0753	-0.0017	-0.0611	0.0347	0.06	0.0203	0.1345	-0.0137	0.0053	0.0945	0.0018	0.134	4.3904	-28.8826	-121.0774
18	4.491	-2.0102	-0.5851	6.945	4.359	4.921	0.0752	-0.2271	-0.1349	0.3844	0.0851	-0.1389	0.1903	0.3204	-0.0554	0.1721	-0.0081	-0.047	0.1494	0.0387	0.198	19.2345	-31.1049	-111.0843

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resseq -1:33)
2	X-RAY DIFFRACTION	2	chain 'A' and (resseq 34:43)
3	X-RAY DIFFRACTION	3	chain 'A' and (resseq 44:53)
4	X-RAY DIFFRACTION	4	chain 'A' and (resseq 54:68)
5	X-RAY DIFFRACTION	5	chain 'A' and (resseq 69:84)
6	X-RAY DIFFRACTION	6	chain 'A' and (resseq 85:107)
7	X-RAY DIFFRACTION	7	chain 'A' and (resseq 108:117)
8	X-RAY DIFFRACTION	8	chain 'A' and (resseq 118:140)
9	X-RAY DIFFRACTION	9	chain 'A' and (resseq 141:169)
10	X-RAY DIFFRACTION	10	chain 'B' and (resseq 0:33)
11	X-RAY DIFFRACTION	11	chain 'B' and (resseq 34:43)
12	X-RAY DIFFRACTION	12	chain 'B' and (resseq 44:53)
13	X-RAY DIFFRACTION	13	chain 'B' and (resseq 54:68)
14	X-RAY DIFFRACTION	14	chain 'B' and (resseq 69:169)
15	X-RAY DIFFRACTION	15	chain 'C' and (resseq 1:33)
16	X-RAY DIFFRACTION	16	chain 'C' and (resseq 34:59)
17	X-RAY DIFFRACTION	17	chain 'C' and (resseq 60:147)
18	X-RAY DIFFRACTION	18	chain 'C' and (resseq 148:166)

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