PDB-4gqo: 2.1 Angstrom resolution crystal structure of uncharacterized prot...

ID or keywords:

Entry

Database: PDB / ID: 4gqo

Title

2.1 Angstrom resolution crystal structure of uncharacterized protein lmo0859 from Listeria monocytogenes EGD-e

Components

Lmo0859 protein

Keywords

UNKNOWN FUNCTION / virulence / pathogenesis / vaccine candidate / Center for Structural Genomics of Infectious Diseases / CSGID / NIAID / National Institute of Allergy and Infectious Diseases

Function / homology

Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta / TRIETHYLENE GLYCOL / Lmo0859 protein

Function and homology information

Biological species

Listeria monocytogenes (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.1 Å

Authors

Halavaty, A.S. / Filippova, E.V. / Minasov, G. / Dubrovska, I. / Winsor, J. / Shuvalova, L. / Peterson, S.N. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)

Citation

Journal: To be Published
Title: 2.1 Angstrom resolution crystal structure of uncharacterized protein lmo0859 from Listeria monocytogenes EGD-e
Authors: Halavaty, A.S. / Filippova, E.V. / Minasov, G. / Dubrovska, I. / Winsor, J. / Shuvalova, L. / Peterson, S.N. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)

History

Deposition	Aug 23, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 19, 2012	Provider: repository / Type: Initial release
Revision 1.1	Nov 15, 2017	Group: Refinement description / Category: software / Item: _software.name

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	4gqo.cif.gz	521.6 KB	Display	PDBx/mmCIF format
PDB format	pdb4gqo.ent.gz	448.5 KB	Display	PDB format
PDBx/mmJSON format	4gqo.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	4gqo_validation.pdf.gz	461.8 KB	Display	wwPDB validaton report
Full document	4gqo_full_validation.pdf.gz	477.4 KB	Display
Data in XML	4gqo_validation.xml.gz	50.6 KB	Display
Data in CIF	4gqo_validation.cif.gz	72.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/gq/4gqo ftp://data.pdbj.org/pub/pdb/validation_reports/gq/4gqo	HTTPS FTP

-
Related structure data

Similar structure data	1miq-2 2hma-d 1zmg-d 4eae-d 1pfz-3 4njg-d 1fqa-d 1zkb-d 1pfz-4 4wua-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
Other databases	TargetTrack: CSGID-IDP05674

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#205 - Jan 2017 Nuclear Pore Complex similarity (1) #221 - May 2018 Human Papillomavirus and Vaccines similarity (1) #243 - Mar 2020 Voltage-gated Sodium Channels similarity (1)

Deposited unit

A: Lmo0859 protein

B: Lmo0859 protein

C: Lmo0859 protein

hetero molecules

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

1

A: Lmo0859 protein

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

2

B: Lmo0859 protein

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

3

C: Lmo0859 protein

hetero molecules

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

Unit cell

Length a, b, c (Å)	44.865, 120.033, 221.448
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Lmo0859 protein / uncharacterized protein lmo0859 Mass: 49498.824 Da / Num. of mol.: 3 / Fragment: UNP residues 31-439 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Listeria monocytogenes (bacteria) / Strain: ATCC BAA-679 / EGD-e / Gene: lmo0859 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21/Magic / References: UniProt: Q8Y8N7
#2: Chemical	ChemComp-PGE / TRIETHYLENE GLYCOL Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₁₄O₄
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 585 / 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: 2.01 Å³/Da / Density % sol: 38.74 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 4 Details: protein: 7.1 mg/mL in 10 mM Tris-HCl, pH 8.3, 250 mM sodium chloride, 5 mM BME, crystallized with the PACT Suite (B1: 0.1 M MIB buffer, pH 4, 25% w/v PEG1500), VAPOR DIFFUSION, SITTING DROP, temperature 295K

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
Detector	Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 13, 2012 / Details: Be Lenses
Radiation	Monochromator: Diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97856 Å / Relative weight: 1
Reflection	Resolution: 2.1→30 Å / Num. all: 71083 / Num. obs: 70880 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 3.9 % / B_iso Wilson estimate: 27 Å² / R_merge(I) obs: 0.098 / Net I/σ(I): 19.72
Reflection shell	Resolution: 2.1→2.14 Å / Redundancy: 3.9 % / R_merge(I) obs: 0.54 / Mean I/σ(I) obs: 2.76 / Num. unique all: 6838 / % possible all: 100

-
Processing

Software

Name	Version	Classification
Blu-Ice	Max	data collection
HKL-3000		phasing
REFMAC	5.5.0102	refinement
HKL-3000		data reduction
HKL-3000		data scaling

Refinement

Method to determine structure:

SAD / Resolution: 2.1→29.86 Å / Cor.coef. F_o:F_c: 0.963 / Cor.coef. F_o:F_c free: 0.94 / SU B: 9.798 / SU ML: 0.118 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / ESU R: 0.231 / ESU R Free: 0.18 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.21144	3581	5.1 %	RANDOM
R_work	0.16511	-	-	-
obs	0.16744	67299	99.72 %	-
all	-	67299	-	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 26.306 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.48 Å²	-0 Å²	-0 Å²
2-	-	1.09 Å²	0 Å²
3-	-	-	-1.56 Å²

Refinement step

Cycle: LAST / Resolution: 2.1→29.86 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9624	0	10	585	10219

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.022	10304
X-RAY DIFFRACTION	r_bond_other_d	0	0.02	6918
X-RAY DIFFRACTION	r_angle_refined_deg	1.554	1.959	14058
X-RAY DIFFRACTION	r_angle_other_deg	0.895	3	17067
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	1.794	5	1298
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	28.876	26.341	481
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	8.335	15	1784
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	13.132	15	19
X-RAY DIFFRACTION	r_chiral_restr	0.101	0.2	1498
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.021	11669
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1937
X-RAY DIFFRACTION	r_mcbond_it	0.908	1.5	6367
X-RAY DIFFRACTION	r_mcbond_other	0.279	1.5	2482
X-RAY DIFFRACTION	r_mcangle_it	1.643	2	10357
X-RAY DIFFRACTION	r_scbond_it	3.089	3	3937
X-RAY DIFFRACTION	r_scangle_it	4.819	4.5	3701

LS refinement shell

Resolution: 2.1→2.154 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.254	247	-
R_work	0.191	4790	-
obs	-	4790	97.37 %

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	2.4188	-0.2779	-0.1435	3.5996	0.2879	2.9146	0.0264	-0.074	0.1863	-0.0591	0.0913	-0.2794	-0.1112	0.151	-0.1176	0.0762	-0.0458	0.02	0.1087	-0.007	0.186	-6.0878	-13.1888	33.7739
2	2.0099	0.0665	-0.7099	2.7891	0.4476	1.7365	0.1266	0.078	0.1246	-0.1	-0.0909	0.2033	-0.373	-0.239	-0.0357	0.1028	0.0214	-0.0222	0.0943	0.0046	0.1219	-22.0679	-11.2036	38.3112
3	0.9576	-0.1582	0.0053	1.7864	-0.523	3.0465	-0.0194	-0.0882	-0.018	0.228	0.0969	0.0988	0.0402	-0.1107	-0.0775	0.0573	-0.01	-0.0051	0.1028	-0.0092	0.0916	-22.6112	-25.719	64.8323
4	2.2867	-0.5103	-0.9855	1.6449	0.6553	3.2999	0.0078	-0.0918	0.0261	0.2077	0.0632	-0.1593	0.0731	0.3174	-0.0711	0.1369	0.003	-0.0338	0.1338	0.0079	0.1259	-13.0989	-29.9893	64.0041
5	0.7621	0.0237	-0.2777	1.2929	0.2329	1.939	0.0193	0.0269	0.0054	-0.0057	-0.0289	0.0039	-0.0868	-0.0762	0.0096	0.0074	-0.0056	-0.0156	0.0891	-0.0119	0.1128	-18.2709	-23.4507	41.5341
6	2.9977	-0.3757	1.2939	4.4768	-2.6371	7.9013	-0.0391	-0.2038	0.2412	0.6485	0.0348	0.2427	-1.0291	-0.5307	0.0043	0.3498	0.074	0.0749	0.1336	-0.0583	0.143	-27.8215	-9.7602	69.5479
7	1.8456	0.8352	0.9334	4.1154	1.0286	3.0606	0.0444	-0.0804	-0.1657	0.0785	0.1493	-0.2321	0.2651	0.2774	-0.1937	0.0691	0.0587	-0.0456	0.1573	0.0081	0.215	16.1417	-51.9346	41.7017
8	0.8897	-0.1951	0.3402	0.7424	-0.1845	2.1209	0.027	0.0358	-0.0867	-0.0913	0.0475	0.0528	-0.0022	0.0203	-0.0746	0.0332	-0.0248	-0.0061	0.0803	-0.0564	0.1239	0.5688	-39.8727	24.7462
9	2.0306	0.0079	0.5447	2.8148	-1.5875	5.8084	0.1389	0.0358	-0.1941	-0.3591	0.0411	0.1979	0.4998	0.2208	-0.18	0.1631	0.0012	-0.064	0.0614	-0.0728	0.153	-3.6052	-44.3553	12.8687
10	2.2461	-0.6684	-0.038	1.4431	-0.5868	4.0949	0.0477	0.1891	-0.1304	-0.1046	-0.0857	-0.3111	-0.1569	0.8611	0.0381	0.1857	-0.0912	0.0225	0.2922	-0.0208	0.1651	10.0637	-31.435	14.0259
11	1.2249	-0.5335	0.5001	1.5094	0.1399	2.0858	0.0015	-0.0861	-0.0364	0.0494	0.0232	-0.0557	0.0078	-0.0119	-0.0248	0.0035	-0.0124	-0.0042	0.1115	-0.0231	0.1012	5.4525	-38.6158	38.2001
12	0.8309	0.0556	0.6772	1.7608	-0.2671	3.6768	0.1184	0.0961	-0.1664	-0.5281	0.0079	0.2142	0.7273	0.0757	-0.1263	0.2803	0.0333	-0.0838	0.0926	-0.0617	0.1666	-3.361	-48.865	14.2163
13	4.0146	-1.5586	-0.1017	6.2474	-1.4991	2.4309	0.2041	0.0998	-0.4514	-0.4163	-0.0363	0.6017	0.1614	-0.1135	-0.1678	0.1228	-0.0256	-0.1118	0.1318	-0.0459	0.2419	-16.2498	14.9107	-11.8924
14	0.812	-0.1241	0.3182	1.5403	0.1976	1.2368	0.0458	0.1705	-0.1157	-0.1877	-0.0054	-0.0278	0.2107	0.1555	-0.0404	0.0798	0.0137	-0.0055	0.0558	-0.0115	0.1462	-1.4001	13.5013	-3.0213
15	1.4693	-0.069	-0.2309	1.8065	0.451	3.6523	0.0258	-0.1334	-0.0517	0.166	0.0406	0.0304	0.1215	0.0914	-0.0664	0.1416	-0.0107	-0.0099	0.037	0.0269	0.1013	1.9957	12.2142	23.3837
16	2.3166	-0.4415	0.641	1.663	-0.3535	3.2939	-0.0129	-0.0296	-0.0223	0.1516	0.1508	0.3722	-0.0805	-0.508	-0.1379	0.173	-0.0128	0.0484	0.1445	0.0257	0.1593	-10.3855	20.1267	21.5772
17	0.9579	-0.1496	0.4672	1.7375	-0.3877	1.8795	0.0493	0.0962	0.0103	-0.0827	-0.0499	0.0513	0.0491	0.0196	0.0006	0.0344	-0.0078	0.0159	0.0592	-0.0036	0.0913	-4.2819	22.9408	-0.9404
18	2.2246	0.1156	-0.9783	2.149	1.8468	11.1447	-0.0784	-0.083	-0.3353	0.1393	0.0157	-0.0015	0.9297	0.4484	0.0627	0.3073	0.0448	-0.0122	0.028	0.0394	0.188	5.1544	-2.2303	17.5694

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	35 - 84
2	X-RAY DIFFRACTION	2	A	85 - 150
3	X-RAY DIFFRACTION	3	A	151 - 245
4	X-RAY DIFFRACTION	4	A	246 - 305
5	X-RAY DIFFRACTION	5	A	306 - 404
6	X-RAY DIFFRACTION	6	A	405 - 438
7	X-RAY DIFFRACTION	7	B	35 - 93
8	X-RAY DIFFRACTION	8	B	94 - 194
9	X-RAY DIFFRACTION	9	B	195 - 252
10	X-RAY DIFFRACTION	10	B	253 - 305
11	X-RAY DIFFRACTION	11	B	306 - 379
12	X-RAY DIFFRACTION	12	B	380 - 438
13	X-RAY DIFFRACTION	13	C	35 - 84
14	X-RAY DIFFRACTION	14	C	85 - 164
15	X-RAY DIFFRACTION	15	C	165 - 253
16	X-RAY DIFFRACTION	16	C	254 - 305
17	X-RAY DIFFRACTION	17	C	306 - 398
18	X-RAY DIFFRACTION	18	C	399 - 438

-
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