PDB-5ueb: Novel crystal structure of a hypothetical protein from Neisseria ...

ID or keywords:

Entry

Database: PDB / ID: 5ueb

Title

Novel crystal structure of a hypothetical protein from Neisseria gonorrhoeae

Components

NegoA.19184.a

Keywords

UNKNOWN FUNCTION / SSGCID / Neisseria gonorrhoeae / hypothetical protein / iodide phasing / PEGASIS / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease

Function / homology

Protein of unknown function DUF4265 / Domain of unknown function (DUF4265) / Uncharacterized protein

Function and homology information

Biological species

Neisseria gonorrhoeae (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.5 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Citation

Journal: to be published
Title: Novel crystal structure of a hypothetical protein from Neisseria gonorrhoeae
Authors: Mayclin, S.J. / Dranow, D.M. / Lorimer, D.D. / Edwards, T.E.

History

Deposition	Dec 30, 2016	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 18, 2017	Provider: repository / Type: Initial release
Revision 1.1	Mar 6, 2024	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine_hist Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_low

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5ueb.cif.gz	146.3 KB	Display	PDBx/mmCIF format
PDB format	pdb5ueb.ent.gz	115 KB	Display	PDB format
PDBx/mmJSON format	5ueb.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5ueb_validation.pdf.gz	442.1 KB	Display	wwPDB validaton report
Full document	5ueb_full_validation.pdf.gz	442.4 KB	Display
Data in XML	5ueb_validation.xml.gz	18.7 KB	Display
Data in CIF	5ueb_validation.cif.gz	28.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ue/5ueb ftp://data.pdbj.org/pub/pdb/validation_reports/ue/5ueb	HTTPS FTP

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Related structure data

Similar structure data	6k6a-d 3ipl-1 2hka-d 6cph-d 3r6s-3 5i47-d 3r6s-4 5c7m-1 3a9u-d 5aqq-1 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: NegoA.19184.a

B: NegoA.19184.a

hetero molecules

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

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	50.220, 74.520, 86.160
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	NegoA.19184.a Mass: 16783.152 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Neisseria gonorrhoeae (strain NCCP11945) (bacteria) Strain: NCCP11945 / Gene: NGK_1626, NGK_1893 / Plasmid: NegoA.00101.b.B1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B4RJ46
#2: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 489 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal

ID	Density Matthews (Å³/Da)	Density % sol (%)
1	2.41	49
2	2.71	55

Crystal grow

Temperature (K)	Crystal-ID	Method	pH	Details
290	1	vapor diffusion, sitting drop	5.5	MCSG1 C1 (284216c1): 100mM Ammonium acetate, 100mM Bis-tris:HCl pH5.5, 17% (w/v) PEG 10000: protein conc. 20.9mg/mL, 20eg: puck pdx4-1: aps21idg 20161216
290	2	vapor diffusion, sitting drop	4.5	JCSG+ A1 (284217a1): 200mM Lithium sulfate, 100mM Sodium acetate pH4.5, 50% (w/v) PEG 400: protein conc. 20.9mg/mL, 10% pegasis: handmount, sat3 20161020

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Data collection

Diffraction

ID	Mean temperature (K)	Crystal-ID
1	290	1
2	100	2

Diffraction source

Source	Site	Beamline	Type	ID	Wavelength (Å)
SYNCHROTRON	APS	21-ID-G		1	0.97857
ROTATING ANODE			RIGAKU FR-E+ SUPERBRIGHT	2	1.5418

Detector

Type	ID	Detector	Date
RAYONIX MX-300	1	CCD	Dec 16, 2016
RIGAKU SATURN 944+	2	CCD	Nov 24, 2016

Radiation

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

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.97857	1
2	1.5418	1

Reflection

Resolution: 1.5→50 Å / Num. obs: 52482 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 6.036 % / B_iso Wilson estimate: 15.47 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.045 / Net I/σ(I): 22.58

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	CC_1/2	Diffraction-ID	% possible all
1.5-1.54	6.065	0.504	3.52	0.911	1	100
1.54-1.58	6.09	0.394	4.52	0.941	1	100
1.58-1.63	6.094	0.307	5.76	0.962	1	100
1.63-1.68	6.102	0.243	7.21	0.975	1	99.9
1.68-1.73	6.123	0.201	8.69	0.982	1	100
1.73-1.79	6.11	0.154	11.31	0.989	1	100
1.79-1.86	6.11	0.121	14.44	0.992	1	100
1.86-1.94	6.082	0.095	18.05	0.995	1	100
1.94-2.02	6.104	0.075	22.46	0.997	1	100
2.02-2.12	6.064	0.062	26.15	0.997	1	100
2.12-2.24	6.07	0.052	30.35	0.998	1	99.9
2.24-2.37	6.042	0.048	33.42	0.998	1	99.9
2.37-2.54	6.043	0.043	36.52	0.998	1	100
2.54-2.74	6.004	0.038	40.24	0.999	1	100
2.74-3	5.99	0.033	44.86	0.999	1	100
3-3.35	5.934	0.029	48.84	0.999	1	100
3.35-3.87	5.882	0.025	52.92	0.999	1	99.9
3.87-4.74	5.785	0.023	54.71	0.999	1	99.9
4.74-6.71	5.681	0.024	53.6	0.999	1	99.7
6.71-50	4.986	0.025	51.36	0.999	1	95.9

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Phasing

Phasing	Method: SAD

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Processing

Software

Name	Version	Classification
XSCALE		data scaling
PHASER	2.6.1	phasing
PHENIX		refinement
PDB_EXTRACT	3.22	data extraction
XDS		data reduction

Refinement

Method to determine structure:

SAD / Resolution: 1.5→50 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 16.74

	R_factor	Num. reflection	% reflection
R_free	0.1768	2081	3.97 %
R_work	0.1548	-	-
obs	0.1557	52477	99.9 %

Solvent computation

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

Displacement parameters

B_iso max: 70.09 Å² / B_iso mean: 21.7541 Å² / B_iso min: 6.91 Å²

Refinement step

Cycle: final / Resolution: 1.5→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2280	0	59	498	2837
B_iso mean	-	-	37.23	35.22	-
Num. residues	-	-	-	-	286

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.005	2494
X-RAY DIFFRACTION	f_angle_d	0.814	3369
X-RAY DIFFRACTION	f_chiral_restr	0.097	372
X-RAY DIFFRACTION	f_plane_restr	0.005	439
X-RAY DIFFRACTION	f_dihedral_angle_d	21.41	951

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	% reflection obs (%)
1.5-1.5348	0.2167	142	0.2042	3318	100
1.5348-1.5732	0.1992	138	0.1868	3306	100
1.5732-1.6158	0.2172	129	0.1764	3322	100
1.6158-1.6633	0.196	129	0.1674	3338	100
1.6633-1.717	0.2071	156	0.1621	3294	100
1.717-1.7784	0.2095	141	0.168	3322	100
1.7784-1.8496	0.1773	135	0.1588	3339	100
1.8496-1.9338	0.1753	155	0.1593	3300	100
1.9338-2.0357	0.2072	114	0.1507	3381	100
2.0357-2.1632	0.1656	137	0.1541	3355	100
2.1632-2.3303	0.1569	153	0.1507	3350	100
2.3303-2.5647	0.1976	128	0.1605	3378	100
2.5647-2.9358	0.1898	130	0.1569	3418	100
2.9358-3.6985	0.1578	142	0.1399	3427	100
3.6985-50	0.1613	152	0.1491	3548	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	2.0069	0.1891	1.4516	0.7349	0.7543	1.8824	-0.0059	-0.2388	-0.0294	0.0885	-0.0621	-0.1144	-0.0472	-0.1487	0.0679	0.1107	-0.0128	-0.0229	0.1156	0.0187	0.1071	-5.0151	-16.3134	-11.7034
2	1.4428	-1.3216	1.8803	1.4702	-1.938	2.637	0.0683	0.0743	0.0289	-0.0132	-0.0758	-0.046	0.0269	0.2611	0.0398	0.1002	-0.01	0.0091	0.1358	0.0155	0.0999	-5.8919	-17.2064	-19.3189
3	1.3607	0.7585	-0.644	2.9938	-2.5427	4.4405	0.0375	0.0029	0.0329	-0.0008	-0.0517	-0.0435	-0.0832	-0.0832	-0.0049	0.0965	0.0023	0.0127	0.1094	-0.0076	0.0889	-13.4467	-15.4543	-20.8892
4	5.838	2.1068	-2.4434	4.3545	-0.8369	5.1989	0.0636	-0.3295	0.2523	0.1108	-0.0628	-0.3395	-0.1287	0.7327	-0.0103	0.1572	-0.0258	-0.0042	0.1685	-0.0001	0.1174	-2.3577	-8.6827	-21.2943
5	4.3973	4.4438	-0.2028	4.522	-0.3835	2.8825	-0.0853	-0.0106	-0.0364	-0.0384	0.1267	0.0063	-0.2476	-0.3063	-0.0137	0.1454	0.0287	0.0198	0.1368	0.0096	0.1487	-17.2538	-9.2475	-18.6948
6	7.1154	0.2929	1.6368	0.2992	0.8629	4.9728	0.1167	-0.0861	-0.7179	0.2604	-0.0333	-0.2878	0.5975	0.0131	-0.0809	0.1704	-0.0237	0.0243	0.1642	0.0173	0.1287	-17.1288	-31.6887	-7.1004
7	4.2199	1.8407	-2.1064	2.5524	-2.329	2.8386	-0.0091	0.1902	-0.166	-0.2862	0.0325	0.1143	0.4118	-0.3025	0.0101	0.2107	-0.0534	-0.0031	0.1934	-0.0599	0.1535	-23.0963	-31.7669	-14.809
8	3.8588	1.0301	-0.0904	3.4984	-0.3876	4.5295	-0.1048	0.0274	-0.136	-0.0595	0.0403	0.0829	0.3288	-0.2235	0.0598	0.1268	-0.0253	0.0213	0.1156	0.0026	0.0797	-20.2277	-26.3997	-12.6689
9	4.7544	-6.2221	3.9144	9.155	-4.1373	7.0032	0.0823	0.0123	-0.3624	0.1182	0.0194	0.4061	0.1829	-0.3727	-0.1017	0.1651	-0.059	0.0612	0.2057	-0.0237	0.1825	-26.6765	-30.1119	-1.5379
10	2.9881	-0.4735	0.3443	4.4013	-4.6252	5.7448	0.1222	-0.1214	-0.152	0.3048	0.0347	0.3728	-0.1454	-0.2468	-0.0597	0.1582	-0.0207	0.0408	0.1659	-0.0041	0.1118	-20.0382	-23.9229	-4.6855
11	1.0364	0.2776	-0.297	1.9011	0.3538	2.1872	-0.0114	-0.0066	-0.2628	-0.0818	0.1109	-0.1748	0.2446	0.135	-0.1447	0.0949	0.0201	-0.0055	0.0833	-0.0118	0.158	-0.8773	5.7298	-2.4607
12	2.775	0.3206	-0.3843	2.1722	-0.0956	3.7293	-0.0919	0.1995	-0.047	-0.2391	0.0311	-0.0751	-0.0444	0.045	0.0613	0.0871	-0.0126	-0.0035	0.0583	-0.0141	0.1099	-6.7142	8.5824	-9.9287
13	2.4319	0.9278	0.9514	1.2697	-0.4511	2.3181	-0.1347	0.382	0.2055	0.0176	0.0168	-0.3438	-0.0358	0.4049	0.0607	0.1083	-0.0015	0.0033	0.1438	-0.0389	0.1557	2.2678	11.0398	-10.1928
14	2.5807	-1.2198	1.1177	2.2589	1.0709	2.8821	0.1089	-0.2758	-0.232	0.254	0.0096	0.2633	0.357	-0.1499	-0.0681	0.1041	-0.0268	-0.0165	0.0907	0.0124	0.1077	-21.6816	6.1818	5.3504
15	4.2629	-0.0218	-2.2073	5.4384	0.0853	2.3418	0.1593	-0.05	-0.2599	0.0665	-0.0653	0.0458	0.3004	-0.531	-0.0911	0.1077	-0.041	-0.0429	0.1288	0.0142	0.1916	-29.6317	3.1894	-2.3177
16	6.0541	-4.9755	5.9337	4.7504	-4.4553	6.6369	0.3064	-0.0017	-0.5781	-0.2493	-0.0278	0.2288	0.464	-0.0617	-0.3082	0.1355	-0.017	-0.0213	0.0897	-0.0299	0.1585	-19.6545	2.6466	-5.3625
17	2.2026	0.1659	-0.6131	1.9144	0.7699	0.8077	-0.0137	0.0803	-0.1995	0.0292	0.0196	0.0645	0.1319	-0.08	0.0285	0.0921	-0.0092	-0.0006	0.0809	-0.0148	0.1079	-19.6345	7.4009	-2.7924
18	0.9868	0.113	1.8221	2.1227	-2.0114	8.9694	0.0587	-0.2164	-0.0443	0.0548	0.0227	0.1274	0.0389	-0.5233	-0.0464	0.0671	-0.0002	-0.0065	0.1437	-0.0009	0.1368	-29.3543	13.0389	3.5449
19	3.8648	-0.6867	0.2323	1.9468	1.9774	2.9642	0.0793	0.1942	0.1996	-0.1906	-0.0245	-0.0201	-0.1683	-0.1446	-0.1327	0.0762	0.0278	-0.0243	0.0657	-0.0045	0.0928	-19.2193	14.3391	1.2626
20	4.8484	-0.9928	-1.1755	8.8617	3.2638	2.336	-0.0745	0.3563	-0.6246	-0.4417	-0.0449	0.3932	-0.0532	-0.208	0.1832	0.1323	-0.0191	-0.0031	0.1258	-0.0088	0.1727	-8.4148	-21.06	-41.362

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 2 through 15 )	B	2 - 15
2	X-RAY DIFFRACTION	2	chain 'B' and (resid 16 through 25 )	B	16 - 25
3	X-RAY DIFFRACTION	3	chain 'B' and (resid 26 through 47 )	B	26 - 47
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 48 through 60 )	B	48 - 60
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 61 through 69 )	B	61 - 69
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 70 through 81 )	B	70 - 81
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 82 through 97 )	B	82 - 97
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 98 through 113 )	B	98 - 113
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 114 through 125 )	B	114 - 125
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 126 through 138 )	B	126 - 138
11	X-RAY DIFFRACTION	11	chain 'A' and (resid -2 through 25 )	A	-2 - 25
12	X-RAY DIFFRACTION	12	chain 'A' and (resid 26 through 47 )	A	26 - 47
13	X-RAY DIFFRACTION	13	chain 'A' and (resid 48 through 69 )	A	48 - 69
14	X-RAY DIFFRACTION	14	chain 'A' and (resid 70 through 81 )	A	70 - 81
15	X-RAY DIFFRACTION	15	chain 'A' and (resid 82 through 90 )	A	82 - 90
16	X-RAY DIFFRACTION	16	chain 'A' and (resid 91 through 97 )	A	91 - 97
17	X-RAY DIFFRACTION	17	chain 'A' and (resid 98 through 113 )	A	98 - 113
18	X-RAY DIFFRACTION	18	chain 'A' and (resid 114 through 125 )	A	114 - 125
19	X-RAY DIFFRACTION	19	chain 'A' and (resid 126 through 139 )	A	126 - 139
20	X-RAY DIFFRACTION	20	chain 'B' and (resid -5 through 1 )	B	-5 - 1

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