PDB-5v77: Crystal structure of an uncharacterized protein from Neisseria go...

ID or keywords:

Entry

Database: PDB / ID: 5v77

Title

Crystal structure of an uncharacterized protein from Neisseria gonorrhoeae

Components

Uncharacterized protein

Keywords

UNKNOWN FUNCTION / SSGCID / Neisseria gonorrhoeae / uncharacterized protein / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease

Function / homology

NGO_1070-like / Uncharacterized protein / Uncharacterized protein

Function and homology information

Biological species

Neisseria gonorrhoeae (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.85 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Citation

Journal: To be Published
Title: Crystal structure of an uncharacterized protein from Neisseria gonorrhoeae
Authors: Abendroth, J. / Mayclin, S.J. / Lorimer, D.D. / Edwards, T.E.

History

Deposition	Mar 18, 2017	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 12, 2017	Provider: repository / Type: Initial release
Revision 1.1	Mar 6, 2024	Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5v77.cif.gz	107.5 KB	Display	PDBx/mmCIF format
PDB format	pdb5v77.ent.gz	84.2 KB	Display	PDB format
PDBx/mmJSON format	5v77.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5v77_validation.pdf.gz	439.2 KB	Display	wwPDB validaton report
Full document	5v77_full_validation.pdf.gz	440.6 KB	Display
Data in XML	5v77_validation.xml.gz	11.3 KB	Display
Data in CIF	5v77_validation.cif.gz	15.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/v7/5v77 ftp://data.pdbj.org/pub/pdb/validation_reports/v7/5v77	HTTPS FTP

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Related structure data

Similar structure data	1zgu-d 1i4g-2 6pgl-3 1i4g-1 6ari-1 3nct-2 1uf9-3 3nct-1 5jj2-d 2gnk-1 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search
Other databases	TargetTrack: NegoA.19180.a

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Uncharacterized protein

B: Uncharacterized protein

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	107.360, 107.360, 87.790
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	179
Space group name H-M	P6₅22

#1: Protein	Uncharacterized protein Mass: 13296.030 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Neisseria gonorrhoeae (bacteria) Gene: WHOF_01246, WHOF_02176, WHOG_00626C, WHOG_02132, WHOK_01205, WHOK_01955, WHOL_01367, WHOL_02114, WHOM_00626C, WHOM_02114, WHON_00630C, WHON_02136, WHOO_00556C, WHOO_02142, WHOP_01206, WHOP_ ...Gene: WHOF_01246, WHOF_02176, WHOG_00626C, WHOG_02132, WHOK_01205, WHOK_01955, WHOL_01367, WHOL_02114, WHOM_00626C, WHOM_02114, WHON_00630C, WHON_02136, WHOO_00556C, WHOO_02142, WHOP_01206, WHOP_02014, WHOU_01273, WHOU_02060, WHOV_00617C, WHOV_01253, WHOW_01270, WHOW_02034, WHOX_00621C, WHOX_02014, WHOY_00665C, WHOY_02132, WHOZ_00621C, WHOZ_00669 Plasmid: NegoA.19180.a.B1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1D3FRT6, UniProt: Q5F7U7*PLUS
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO₄
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 144 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.75 Å³/Da / Density % sol: 55.3 %
Crystal grow	Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 4.5 Details: 18.9 mg/mL NegoA.19180.a.B1.PS38025 + Microlytics MCSG1 screen A5: 1260 mM ammonium sulfate, 200 mM sodium chloride, 100 mM sodium acetate / acetic acid, pH 4.5, tray: 284201 A5, native data ...Details: 18.9 mg/mL NegoA.19180.a.B1.PS38025 + Microlytics MCSG1 screen A5: 1260 mM ammonium sulfate, 200 mM sodium chloride, 100 mM sodium acetate / acetic acid, pH 4.5, tray: 284201 A5, native data set, cryoprotectant: 25% ethylene glycol, puck gsg8-9. For phasing, a crystal from the same condition was incubated for 15 seconds each in 12.5% ethylene glycol, 625 mM potassium iodide in reservoir and 25% ethylene glycol, 1250 mM potassium iodide in reservoir, puck viy9-1. Anomalous data was collected in-house.

Crystal

Density Matthews: 2.75 Å³/Da / Density % sol: 55.3 %

Crystal grow

Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 18.9 mg/mL NegoA.19180.a.B1.PS38025 + Microlytics MCSG1 screen A5: 1260 mM ammonium sulfate, 200 mM sodium chloride, 100 mM sodium acetate / acetic acid, pH 4.5, tray: 284201 A5, native data ...

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Data collection

Diffraction

ID	Mean temperature (K)	Crystal-ID
1	100	1
2	100	1

Diffraction source

Source	Site	Beamline	Type	ID	Wavelength (Å)
SYNCHROTRON	APS	21-ID-F		1	0.97872
ROTATING ANODE			RIGAKU FR-E+ SUPERBRIGHT	2	1.5418

Detector

Type	ID	Detector	Date
RAYONIX MX-300	1	CCD	Feb 24, 2017
RIGAKU SATURN 944+	2	CCD	Feb 27, 2017

Radiation

ID	Monochromator	Protocol	Monochromatic (M) / Laue (L)	Scattering type	Wavelength-ID
1	diamond(111)	SINGLE WAVELENGTH	M	x-ray	1
2	diamond(111)	SINGLE WAVELENGTH	M	x-ray	2

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.97872	1
2	1.5418	1

Reflection

Resolution: 1.85→39.694 Å / Num. obs: 26041 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 14.369 % / B_iso Wilson estimate: 27.21 Å² / CC_1/2: 1 / R_merge(I) obs: 0.041 / R_rim(I) all: 0.043 / Χ²: 1.022 / Net I/σ(I): 39.24

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. unique all	Num. unique obs	CC_1/2	R_rim(I) all	% possible all
1.85-1.9	14.645	0.499	6.4	27694	1891	1891	0.967	0.517	100
1.9-1.95	14.63	0.354	9			1837	0.98	0.367	100
1.95-2.01	14.646	0.254	12.07			1778	0.99	0.263	100
2.01-2.07	14.598	0.208	14.48			1745	0.992	0.216	100
2.07-2.14	14.681	0.165	17.44			1696	0.996	0.171	100
2.14-2.21	14.627	0.122	22.84			1630	0.998	0.127	100
2.21-2.29	14.618	0.101	26.5			1582	0.999	0.105	100
2.29-2.39	14.575	0.095	28.79			1546	0.998	0.098	100
2.39-2.49	14.648	0.081	33.09			1447	0.999	0.084	100
2.49-2.62	14.504	0.065	39.23			1414	0.999	0.068	100
2.62-2.76	14.563	0.057	44.66			1340	0.999	0.059	100
2.76-2.93	14.409	0.045	55.4			1268	0.999	0.046	100
2.93-3.13	14.347	0.039	63.61			1210	0.999	0.041	100
3.13-3.38	14.197	0.033	73.05			1136	1	0.034	100
3.38-3.7	14.108	0.026	84.41			1031	1	0.027	99.9
3.7-4.14	13.941	0.023	89.09			958	1	0.024	100
4.14-4.78	13.651	0.022	92.05			852	1	0.022	99.9
4.78-5.85	13.54	0.022	93.28			732	1	0.023	99.7
5.85-8.27	12.838	0.025	86.68			591	1	0.026	100
8.27-39.694	10.387	0.024	82.88			357	0.999	0.026	96.5

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Phasing

Phasing	Method: SAD

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Processing

Software

Name	Classification
XDS	data reduction
XSCALE	data scaling
PHASER	phasing
ARP	model building
Coot	model building
PHENIX	refinement

Refinement

Method to determine structure:

SAD / Resolution: 1.85→39.694 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.51

	R_factor	Num. reflection	% reflection
R_free	0.2027	2015	7.75 %
R_work	0.1759	-	-
obs	0.1781	25994	99.94 %

Solvent computation

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

Displacement parameters

B_iso max: 149.65 Å² / B_iso mean: 39.6539 Å² / B_iso min: 15.86 Å²

Refinement step

Cycle: final / Resolution: 1.85→39.694 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1703	0	5	149	1857
B_iso mean	-	-	84.82	47.28	-
Num. residues	-	-	-	-	210

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	1811
X-RAY DIFFRACTION	f_angle_d	0.88	2475
X-RAY DIFFRACTION	f_chiral_restr	0.069	276
X-RAY DIFFRACTION	f_plane_restr	0.005	319
X-RAY DIFFRACTION	f_dihedral_angle_d	13.918	1054

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 14

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.85-1.8963	0.287	130	0.231	1687	1817	100
1.8963-1.9476	0.2307	158	0.1935	1659	1817	100
1.9476-2.0049	0.1966	149	0.1745	1665	1814	100
2.0049-2.0696	0.2081	146	0.1802	1687	1833	100
2.0696-2.1436	0.1992	125	0.1846	1703	1828	100
2.1436-2.2294	0.2097	151	0.1697	1660	1811	100
2.2294-2.3308	0.2155	134	0.1883	1705	1839	100
2.3308-2.4537	0.2629	137	0.197	1708	1845	100
2.4537-2.6074	0.2701	133	0.1998	1718	1851	100
2.6074-2.8087	0.2527	135	0.1912	1718	1853	100
2.8087-3.0912	0.1999	152	0.196	1709	1861	100
3.0912-3.5383	0.1848	163	0.1699	1722	1885	100
3.5383-4.4569	0.1584	151	0.1429	1766	1917	100
4.4569-39.7029	0.1965	151	0.1735	1872	2023	99

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	7.3049	2.833	0.403	5.1265	-0.6708	5.324	-0.1355	-0.0742	0.7309	0.0769	-0.0395	0.3098	-0.647	-0.6012	0.1467	0.1665	0.0049	0.0021	0.2268	-0.0457	0.2427	62.0852	58.8762	4.4552
2	8.3455	-2.5923	7.0249	4.2431	-1.6572	9.2617	0.4238	-1.1192	-1.1897	1.1301	0.2794	1.0165	1.1312	-1.7401	0.0502	0.0814	-0.1613	0.2238	0.7904	-0.0533	0.3379	55.2475	47.8065	11.033
3	1.5623	-3.6199	-2.2416	9.7552	4.806	3.1876	0.3433	0.9515	0.4028	-2.1275	-0.6676	-0.1759	-1.5088	0.3545	0.2183	0.659	-0.0769	-0.069	0.6718	0.1643	0.3406	66.6022	55.129	-25.086
4	5.4476	0.4607	1.7713	2.5684	1.9583	7.0358	0.0427	0.193	-0.1384	0.1204	-0.1395	0.0645	0.2984	-0.0439	0.2055	0.1612	-0.068	0.0034	0.264	0.007	0.246	68.0508	45.6732	-10.9366
5	3.6381	-1.5192	-2.3279	5.5055	-1.2144	2.148	0.0524	0.6351	-0.29	-0.651	-0.2475	0.8192	0.2881	-0.6829	-0.0353	0.1872	-0.0829	-0.0739	0.3809	-0.0616	0.2646	67.2539	42.0181	-19.376
6	2.1895	3.21	0.0547	4.7715	-0.1395	4.7196	0.261	0.4384	0.218	-0.0588	-0.2809	-0.0011	-0.3902	-0.153	0.0545	0.1846	-0.0418	-0.0153	0.2244	-0.0147	0.2025	66.3236	56.8213	-7.4733
7	5.9925	-1.8325	-3.2444	6.7508	-0.2521	2.0362	0.1903	1.0259	0.8449	-1.3148	0.5551	1.0784	0.4438	-2.6075	-0.3725	0.1516	0.0378	-0.0848	1.258	0.0991	0.5543	49.4087	54.1783	-9.7688
8	4.9031	-1.9831	-0.4891	3.6812	0.2447	0.5903	0.136	-0.1258	-0.0605	-0.0854	0.0497	1.2306	0.0543	-1.2177	-0.0607	0.2666	-0.1561	-0.0865	0.8049	-0.0767	0.543	52.2921	45.8272	-12.9834
9	8.4766	6.2313	4.1034	6.2858	5.8108	6.8537	-0.3445	0.3238	1.0661	-0.8578	0.035	0.5374	-1.9576	0.0281	0.191	0.604	-0.1016	-0.0267	0.3098	0.1119	0.338	71.5309	61.8351	-18.7683
10	7.4011	3.5365	1.5212	5.64	1.2898	1.7908	0.1585	0.5913	0.7159	-0.5862	-0.3499	0.4438	-1.1366	-0.8932	0.2278	0.2347	0.0572	-0.0807	0.4527	0.0107	0.2188	62.3771	56.734	-14.5205
11	6.8432	3.0612	2.79	4.865	4.8249	7.0214	-0.0731	0.5613	-0.0932	-1.0516	0.4397	-0.6755	-0.8385	1.1432	-0.5337	0.2516	-0.1159	0.0424	0.3855	0.0394	0.2327	74.7167	50.3472	-19.8719
12	6.3224	-6.3614	4.6159	6.6968	-4.6895	3.473	-0.4754	-1.2168	0.7136	0.9565	-0.0043	0.3264	-0.6363	-1.6746	0.0697	0.3866	0.0556	0.0592	0.8082	-0.2538	0.3988	59.6058	57.5438	15.4539
13	8.6542	0.0572	1.9357	1.9226	-0.1737	4.4659	-0.0121	-0.1607	-0.1777	0.1481	-0.0974	0.1848	0.4486	-0.5869	0.0628	0.1545	-0.072	0.0355	0.2273	-0.0374	0.1911	64.5373	46.0701	3.3099
14	4.0599	-5.381	3.9778	7.3144	-3.6147	8.6934	-0.3379	-0.2382	0.5364	0.7056	-0.1412	-0.2306	0.3326	0.0471	0.38	0.2537	-0.0482	0.0557	0.2798	-0.0208	0.2051	66.709	45.66	12.206
15	8.7927	4.7705	1.0798	6.6125	0.842	5.9383	-0.1512	0.1347	0.3839	-0.0352	0.1384	0.1968	-0.6044	-0.1527	-0.0208	0.1928	-0.0051	-0.0091	0.2353	-0.0175	0.1943	64.9324	58.127	-1.6241
16	5.3896	0.6902	-0.8081	5.4489	-2.2725	2.7714	-0.4614	-0.3278	0.5857	-0.2121	0.4265	-0.7906	-0.3458	1.3568	0.0653	0.2225	-0.1494	-0.0451	0.4512	-0.0847	0.3403	77.0701	56.2364	3.9369
17	3.2563	-0.8935	2.8875	1.2908	-0.8613	2.6798	0.006	-0.0959	0.7255	-0.0426	-0.1891	0.2115	-0.9338	-0.9555	0.0006	0.2716	0.1226	0.0036	0.6992	-0.1725	0.4106	51.5355	58.4282	8.4668

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'B' and (resid 81 through 95 )	B	81 - 95
2	X-RAY DIFFRACTION	2	chain 'B' and (resid 96 through 103 )	B	96 - 103
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 0 through 8 )	A	0 - 8
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 9 through 29 )	A	9 - 29
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 30 through 42 )	A	30 - 42
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 43 through 50 )	A	43 - 50
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 51 through 55 )	A	51 - 55
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 56 through 71 )	A	56 - 71
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 72 through 80 )	A	72 - 80
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 81 through 95 )	A	81 - 95
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 96 through 105 )	A	96 - 105
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 0 through 8 )	B	0 - 8
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 9 through 29 )	B	9 - 29
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 30 through 42 )	B	30 - 42
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 43 through 55 )	B	43 - 55
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 56 through 71 )	B	56 - 71
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 72 through 80 )	B	72 - 80

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