PDB-6oe6: Structure of a Uncharacterized protein from Leptospira interrogan...

ID or keywords:

Entry

Database: PDB / ID: 6oe6

Title

Structure of a Uncharacterized protein from Leptospira interrogans serogroup Icterohaemorrhagiae serovar Copenhageni (strain Fiocruz L1-130)

Components

Uncharacterized protein

Keywords

UNKNOWN FUNCTION / SSGCID / Leptospirosis / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease

Function / homology

FORMIC ACID / Uncharacterized protein

Function and homology information

Biological species

Leptospira interrogans serogroup Icterohaemorrhagiae serovar copenhageni (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.7 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Citation

Journal: to be published
Title: Structure of an Uncharacterized protein from Leptospira interrogans serogroup Icterohaemorrhagiae serovar Copenhageni (strain Fiocruz L1-130)
Authors: Abendroth, J. / Mayclin, S.J. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.

History

Deposition	Mar 27, 2019	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 17, 2019	Provider: repository / Type: Initial release
Revision 1.1	Mar 13, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	6oe6.cif.gz	117.4 KB	Display	PDBx/mmCIF format
PDB format	pdb6oe6.ent.gz	90.1 KB	Display	PDB format
PDBx/mmJSON format	6oe6.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	6oe6_validation.pdf.gz	450.3 KB	Display	wwPDB validaton report
Full document	6oe6_full_validation.pdf.gz	452.9 KB	Display
Data in XML	6oe6_validation.xml.gz	12.9 KB	Display
Data in CIF	6oe6_validation.cif.gz	17.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/oe/6oe6 ftp://data.pdbj.org/pub/pdb/validation_reports/oe/6oe6	HTTPS FTP

-
Related structure data

Similar structure data	5aiw-d 2yz1-2 6v4b-2 6hm0-1 2hqt-10 6hm0-2 3zpv-7 2dww-d 6ee0-3 6y34-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: SSGCID-LpinA.19868.a

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Uncharacterized protein

B: Uncharacterized protein

hetero molecules

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

1

A: Uncharacterized protein

hetero molecules

defined by author&software
Evidence: gel filtration
17.6 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Uncharacterized protein

hetero molecules

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

Unit cell

Length a, b, c (Å)	50.630, 50.630, 99.480
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	144
Space group name H-M	P3₁

#1: Protein	Uncharacterized protein Mass: 17486.828 Da / Num. of mol.: 2 / Fragment: residues 29-171 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Leptospira interrogans serogroup Icterohaemorrhagiae serovar copenhageni (strain Fiocruz L1-130) (bacteria) Strain: Fiocruz L1-130 / Gene: LIC_12238 / Plasmid: LpinA.19858.a.B2 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) Strain (production host): BL21(DE3) / References: UniProt: Q72Q74
#2: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical	ChemComp-FMT / FORMIC ACID Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH₂O₂
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 164 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.11 Å³/Da / Density % sol: 42.7 %
Crystal grow	Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: Microlytic MCSG1 screen F8: 3500mM sodium formate: LpinA.19858.a.B2.PS38529 at 23.59mg/ml: cryo: direct: tray 306183 F8: puck lbo4-3. For experimental phasing, a crystal from the same well ...Details: Microlytic MCSG1 screen F8: 3500mM sodium formate: LpinA.19858.a.B2.PS38529 at 23.59mg/ml: cryo: direct: tray 306183 F8: puck lbo4-3. For experimental phasing, a crystal from the same well was incubated for 10sec in a solution of 90% reservoir and 10% 2.5M Sodium iodide in ethylene glycol and vitrified: tray: 306143 F8: puck: kzx0-14

Crystal

Density Matthews: 2.11 Å³/Da / Density % sol: 42.7 %

Crystal grow

Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Microlytic MCSG1 screen F8: 3500mM sodium formate: LpinA.19858.a.B2.PS38529 at 23.59mg/ml: cryo: direct: tray 306183 F8: puck lbo4-3. For experimental phasing, a crystal from the same well ...

-
Data collection

Diffraction

ID	Mean temperature (K)	Crystal-ID	Serial crystal experiment
1	100	1	N
2	100	1	N

Diffraction source

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

Detector

Type	ID	Detector	Date
RIGAKU SATURN 944+	1	CCD	Mar 7, 2019
RAYONIX MX-300	2	CCD	Mar 7, 2019

Radiation

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

Radiation wavelength

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

Reflection

Resolution: 1.7→40.122 Å / Num. obs: 31388 / % possible obs: 99.9 % / Redundancy: 4.789 % / B_iso Wilson estimate: 36.569 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.038 / R_rim(I) all: 0.043 / Χ²: 1.013 / Net I/σ(I): 22.21 / Num. measured all: 150310

Reflection shell

Diffraction-ID: 2

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique obs	CC_1/2	R_rim(I) all	% possible all
1.7-1.74	4.706	0.485	2.91	2372	0.842	0.547	99.9
1.74-1.79	4.771	0.356	3.99	2252	0.904	0.401	100
1.79-1.84	4.793	0.261	5.51	2176	0.958	0.293	100
1.84-1.9	4.753	0.184	7.88	2137	0.975	0.207	100
1.9-1.96	4.678	0.128	10.9	2077	0.988	0.144	100
1.96-2.03	4.809	0.095	14.53	2051	0.993	0.107	100
2.03-2.11	4.734	0.078	17.65	1905	0.995	0.088	99.9
2.11-2.19	4.826	0.064	20.95	1877	0.997	0.071	99.9
2.19-2.29	4.742	0.057	23.34	1750	0.997	0.064	99.9
2.29-2.4	4.842	0.051	25.68	1710	0.997	0.058	100
2.4-2.53	4.847	0.044	29.48	1638	0.998	0.05	99.9
2.53-2.69	4.834	0.04	33.21	1512	0.998	0.045	99.8
2.69-2.87	4.845	0.036	36.5	1421	0.998	0.04	100
2.87-3.1	4.863	0.034	39.97	1369	0.998	0.038	99.9
3.1-3.4	4.863	0.032	44	1237	0.999	0.036	99.4
3.4-3.8	4.85	0.03	46.29	1111	0.998	0.034	100
3.8-4.39	4.841	0.03	47.67	974	0.999	0.034	99.9
4.39-5.38	4.864	0.032	48.04	831	0.998	0.036	99.9
5.38-7.6	4.847	0.032	46.64	645	0.998	0.036	100
7.6-40.122	4.385	0.037	43.6	343	0.997	0.043	94.5

-
Processing

Software

Name	Version	Classification
XDS		data reduction
XSCALE		data scaling
PHENIX	(1.15rc1_3423)	refinement
PDB_EXTRACT	3.24	data extraction
PHASER		phasing
PARROT		phasing
Coot		model building

Refinement

Method to determine structure:

SAD / Resolution: 1.7→40.122 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 2.01 / Phase error: 21.76

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2079	1941	6.19 %	0
R_work	0.1756	-	-	-
obs	0.1775	31339	99.83 %	-

Solvent computation

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

Displacement parameters

B_iso max: 116.99 Å² / B_iso mean: 46.3919 Å² / B_iso min: 18.09 Å²

Refinement step

Cycle: final / Resolution: 1.7→40.122 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1849	0	8	168	2025
B_iso mean	-	-	37.97	46.25	-
Num. residues	-	-	-	-	237

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	1935
X-RAY DIFFRACTION	f_angle_d	0.872	2631
X-RAY DIFFRACTION	f_dihedral_angle_d	15.537	1165
X-RAY DIFFRACTION	f_chiral_restr	0.064	300
X-RAY DIFFRACTION	f_plane_restr	0.005	336

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 (%)
1.7002-1.7427	0.3265	126	0.2664	2153	2279	100
1.7427-1.7898	0.2747	158	0.2374	2067	2225	100
1.7898-1.8425	0.2357	157	0.2153	2078	2235	100
1.8425-1.9019	0.2293	148	0.1978	2092	2240	100
1.9019-1.9699	0.2367	141	0.1957	2095	2236	100
1.9699-2.0488	0.2283	168	0.1881	2065	2233	100
2.0488-2.142	0.2171	130	0.1888	2125	2255	100
2.142-2.255	0.244	96	0.1824	2143	2239	100
2.255-2.3962	0.2348	173	0.1867	2066	2239	100
2.3962-2.5812	0.2262	138	0.1929	2100	2238	100
2.5812-2.8409	0.2359	136	0.1826	2116	2252	100
2.8409-3.2518	0.205	126	0.1774	2094	2220	100
3.2518-4.0963	0.144	109	0.1532	2120	2229	100
4.0963-40.1336	0.1997	135	0.1583	2084	2219	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	3.5165	2.8622	-0.6806	2.6412	-2.0598	9.2485	-0.0898	-0.0887	-0.3522	-0.4312	-0.4367	-1.0704	0.8923	1.1441	0.5511	0.2907	0.0985	0.0347	0.4334	0.0636	0.3694	67.0803	18.7916	14.5901
2	8.5894	2.1453	2.9347	0.537	0.6476	8.1756	0.61	1.0133	0.2446	-0.468	0.4088	-0.3082	-0.9535	2.0156	-0.2285	0.6039	-0.0109	0.2819	0.7467	0.1296	0.6578	71.7301	25.3969	6.222
3	3.6837	-0.8226	0.3886	6.4494	1.6464	2.4566	-0.0317	-0.6375	-0.0463	0.5006	0.1964	-0.2436	0.3431	0.767	-0.0559	0.3049	0.0734	-0.0288	0.5386	0.1279	0.2868	68.3599	18.945	19.084
4	4.5905	2.0857	0.154	3.2659	3.215	7.1102	-0.068	-0.0146	0.0461	-0.3399	-0.0881	-0.5944	-0.1978	0.8772	0.1012	0.2155	-0.0209	0.008	0.374	0.076	0.2488	65.3555	25.2692	13.3244
5	4.1518	-0.3441	2.1257	7.1982	2.8005	3.6295	0.0911	1.1539	-0.7346	0.1184	-0.3435	0.2037	1.4432	0.1839	-0.161	0.6857	0.1177	0.0936	0.478	-0.1266	0.5893	59.7885	5.6069	5.3468
6	4.69	-4.4933	-4.4132	5.8226	4.1151	4.3115	0.221	0.3263	-0.206	-0.2763	-0.2328	0.3056	-0.0527	-0.4337	0.0315	0.2707	-0.0308	0.0244	0.2522	-0.0449	0.2963	50.8983	21.9547	15.5049
7	7.6987	-4.8813	-4.2341	8.9516	4.8464	3.2444	0.0293	0.9285	-0.4912	-0.5109	-0.5412	0.6693	0.0129	-0.3901	0.6828	0.2294	-0.0216	-0.0263	0.2925	-0.0532	0.2386	50.3593	20.8468	11.0371
8	4.8257	-3.8762	-5.879	3.9205	5.4255	8.5172	-0.0292	0.097	-0.369	-0.0264	-0.0748	0.0915	0.4337	-0.5123	0.0484	0.5371	0.09	0.1401	0.2574	-0.0284	0.3712	65.1053	8.7027	2.6838
9	4.9524	-1.4948	-1.1071	7.4764	-0.5141	5.8868	-0.1252	-0.0967	-0.3714	0.1365	-0.1848	0.3467	0.4731	0.3084	0.1717	0.2075	-0.0134	0.0325	0.1963	0.0013	0.1829	57.5949	19.6963	14.5561
10	8.3572	2.1115	-1.7127	3.2291	1.8779	4.7576	-1.2921	-0.1024	-1.0246	-0.1283	0.1479	0.3102	0.7275	0.1821	0.8445	1.5348	0.0596	-0.0936	0.8212	-0.0549	1.0012	61.442	35.646	29.344
11	8.7221	0.1616	0.8953	3.8747	-2.1428	5.4547	0.1993	-0.1622	-0.5626	-0.3211	0.1392	0.4116	1.2326	-1.165	-0.2043	0.3945	-0.1589	-0.0502	0.4467	0.0783	0.3274	32.997	17.5978	30.5888
12	5.5983	1.2995	1.334	2.966	-0.9305	4.4855	-0.1949	0.1281	0.3165	-0.2511	0.2678	0.3287	0.1395	-0.6119	0.0042	0.1658	-0.0169	-0.0052	0.2641	0.0342	0.2049	36.6772	26.6091	28.8766
13	8.324	2.5672	3.4017	1.8926	0.6891	3.6219	-0.4624	0.5889	0.567	-0.3422	0.3031	0.3838	-0.2774	-0.3002	0.1808	0.2256	-0.0096	-0.055	0.372	0.0501	0.3048	36.0203	31.0288	25.4567
14	7.1299	0.6261	1.0787	3.8869	-0.771	7.135	-0.1162	-0.1698	0.0588	0.0713	0.144	0.0507	0.1184	-0.4924	-0.0306	0.1295	-0.0187	0.0141	0.1777	0.0036	0.156	39.0252	26.5082	31.6184

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 33 through 41 )	A	33 - 41
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 42 through 58 )	A	42 - 58
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 59 through 66 )	A	59 - 66
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 67 through 79 )	A	67 - 79
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 80 through 89 )	A	80 - 89
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 90 through 99 )	A	90 - 99
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 100 through 109 )	A	100 - 109
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 110 through 116 )	A	110 - 116
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 117 through 149 )	A	117 - 149
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 150 through 168 )	A	150 - 168
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 33 through 66 )	B	33 - 66
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 67 through 99 )	B	67 - 99
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 100 through 116 )	B	100 - 116
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 117 through 152 )	B	117 - 152

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi