PDB-6nb2: CRYSTAL STRUCTURE OF ENOLASE FROM LEGIONELLA PNEUMOPHILA BOUND TO...

ID or keywords:

Entry

Database: PDB / ID: 6nb2

Title

CRYSTAL STRUCTURE OF ENOLASE FROM LEGIONELLA PNEUMOPHILA BOUND TO 2-PHOSPHOGLYCERIC ACID AND MAGNESIUM

Components

Enolase

Keywords

LYASE / SSGCID /

Structural Genomics / Seattle Structural Genomics Center for Infectious Disease

Function / homology

Function and homology information

phosphopyruvate hydratase /

phosphopyruvate hydratase complex /

phosphopyruvate hydratase activity / glycolytic process / magnesium ion binding /

cell surface / extracellular region
Similarity search - Function

Biological species

Legionella pneumophila subsp. pneumophila (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.85 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Funding support

United States, 1items

Citation

Journal: To Be Published
Title: CRYSTAL STRUCTURE OF ENOLASE FROM LEGIONELLA PNEUMOPHILA BOUND TO 2-PHOSPHOGLYCERIC ACID AND MAGNESIUM
Authors: Davies, D.R. / Abendroth, J. / Lorimer, D.D. / Edwards, T.E.

History

Deposition	Dec 6, 2018	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 23, 2019	Provider: repository / Type: Initial release
Revision 1.1	Dec 18, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2	Oct 11, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_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.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

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	6nb2.cif.gz	356.5 KB	Display	PDBx/mmCIF format
PDB format	pdb6nb2.ent.gz	288.5 KB	Display	PDB format
PDBx/mmJSON format	6nb2.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/nb/6nb2 ftp://data.pdbj.org/pub/pdb/validation_reports/nb/6nb2	HTTPS FTP

-
Related structure data

Related structure data	4z1yS S: Starting model for refinement
Similar structure data	3h8a-2 4ewj-d 1pdy-1 2fym-2 2zlf-d 3b97-1 3ksq-d 1b0k-d 1al6-1 8acn-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Other databases	TargetTrack: SSGCID-LepnA.01024.a.B1

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#50 - Feb 2004 Glycolytic Enzymes similarity (13)

Deposited unit

A: Enolase

B: Enolase

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	116.450, 116.450, 142.780
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	94
Space group name H-M	P4₂2₁2

#1: Protein	Enolase / / 2-phospho-D-glycerate hydro-lyase / 2-phosphoglycerate dehydratase Mass: 47298.504 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513) (bacteria) Strain: Philadelphia 1 / ATCC 33152 / DSM 7513 / Gene: eno, lpg2037 / Plasmid: LEPNA.01024.A.B1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q5ZTX1, phosphopyruvate hydratase
#2: Chemical	ChemComp-2PG / 2-PHOSPHOGLYCERIC ACID / 2-Phosphoglyceric acid Mass: 186.057 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₇O₇P
#3: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C₂H₆O₂
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 733 / 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: 2.56 Å³/Da / Density % sol: 51.92 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: MORPHEUS D6 (50 MM HEPES, 50 MM MOPS, PH 7.5, 20 MM 1,6 HEXANEDIOL, 20 MM 1-BUTANOL, 20 MM 1,2 PROPANEDIOL, 20 MM 2-PROPANOL, 20 MM 1,4-BUTANEDIOL; 20 MM 1,3- PROPANEDIOL, 20% GLYCEROL, 10% ...Details: MORPHEUS D6 (50 MM HEPES, 50 MM MOPS, PH 7.5, 20 MM 1,6 HEXANEDIOL, 20 MM 1-BUTANOL, 20 MM 1,2 PROPANEDIOL, 20 MM 2-PROPANOL, 20 MM 1,4-BUTANEDIOL; 20 MM 1,3- PROPANEDIOL, 20% GLYCEROL, 10% PEG 4000), TRAY 297441D6 PUCK VKP7- 5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 289K PH range: 7.5

Crystal

Density Matthews: 2.56 Å³/Da / Density % sol: 51.92 %

Crystal grow

Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: MORPHEUS D6 (50 MM HEPES, 50 MM MOPS, PH 7.5, 20 MM 1,6 HEXANEDIOL, 20 MM 1-BUTANOL, 20 MM 1,2 PROPANEDIOL, 20 MM 2-PROPANOL, 20 MM 1,4-BUTANEDIOL; 20 MM 1,3- PROPANEDIOL, 20% GLYCEROL, 10% ...
PH range: 7.5

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 12, 2018
Radiation	Monochromator: DIAMOND [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97872 Å / Relative weight: 1
Reflection	Resolution: 1.85→50 Å / Num. obs: 84112 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 10.27 % / B_iso Wilson estimate: 31.64 Å² / R_merge(I) obs: 0.059 / Net I/σ(I): 24.24
Reflection shell	Resolution: 1.85→1.9 Å / R_merge(I) obs: 0.502 / Mean I/σ(I) obs: 4.92 / Num. unique obs: 9340 / % possible all: 100

-
Processing

Software

Name	Version	Classification
PHENIX	DEV_3366	refinement
XSCALE		data scaling
XDS		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4Z1Y

4z1y

Resolution: 1.85→45.12 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 16.54 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.172	1969	2.34 %
R_work	0.146	-	-
obs	0.147	84018	100 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 31.48 Å²

Refinement step

Cycle: LAST / Resolution: 1.85→45.12 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6477	0	54	733	7264

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 (%)
1.85-1.8963	0.2469	130	0.1947	5757	X-RAY DIFFRACTION	100
1.8963-1.9475	0.1882	142	0.1726	5780	X-RAY DIFFRACTION	100
1.9475-2.0048	0.1943	134	0.1576	5802	X-RAY DIFFRACTION	100
2.0048-2.0696	0.1876	140	0.1546	5786	X-RAY DIFFRACTION	100
2.0696-2.1435	0.1988	145	0.1516	5774	X-RAY DIFFRACTION	100
2.1435-2.2293	0.1673	151	0.1509	5804	X-RAY DIFFRACTION	100
2.2293-2.3308	0.1819	144	0.1462	5824	X-RAY DIFFRACTION	100
2.3308-2.4537	0.2043	138	0.147	5812	X-RAY DIFFRACTION	100
2.4537-2.6074	0.1787	150	0.1468	5818	X-RAY DIFFRACTION	100
2.6074-2.8087	0.1786	127	0.1499	5860	X-RAY DIFFRACTION	100
2.8087-3.0913	0.1912	136	0.1516	5892	X-RAY DIFFRACTION	100
3.0913-3.5384	0.1932	123	0.1485	5937	X-RAY DIFFRACTION	100
3.5384-4.4574	0.1367	142	0.1272	5986	X-RAY DIFFRACTION	100
4.4574-45.1343	0.1501	167	0.1415	6217	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	7.7829	1.7194	-4.1816	2.4427	0.4416	3.1549	-0.017	-0.4227	-0.4642	0.4295	0.191	0.3139	0.2406	-0.708	-0.0457	0.2179	0.0324	0.0578	0.5162	0.0918	0.332	13.7701	10.0879	50.0778
2	2.3476	-1.2571	-0.3695	2.942	0.3873	1.9055	0.0987	0.0306	0.2307	0.0181	-0.0775	0.223	-0.5044	-0.4904	-0.0149	0.2714	0.1921	0.0381	0.3929	0.0396	0.2476	19.9182	28.165	45.8388
3	1.5116	0.1566	-0.1466	0.7743	-0.2984	1.8291	0.0137	-0.1281	0.0271	0.0365	-0.0076	-0.046	-0.2881	0.0511	0.0016	0.1803	0.0329	0.0269	0.159	0.006	0.1508	44.7875	22.8574	50.4142
4	0.8045	0.1284	-0.3419	0.9057	-0.6348	2.1571	-0.0278	-0.1761	-0.1064	0.0384	0.0002	-0.1026	0.1267	0.1545	0.0429	0.1565	0.0661	0.0126	0.2051	0.029	0.1913	46.4817	8.4444	58.1094
5	1.7602	-0.5359	-0.094	0.8996	0.0357	2.9614	-0.0902	-0.2639	-0.058	0.1632	0.103	0.1088	-0.1859	-0.3178	-0.0287	0.1885	0.1003	0.0549	0.2669	0.034	0.196	28.7277	18.0466	58.9994
6	2.1829	-0.2641	-1.0135	3.5051	0.7406	1.2885	0.0967	-0.1766	0.2436	0.1566	0.008	0.0146	-0.4679	-0.0581	-0.0685	0.2559	0.0647	0.0372	0.1707	-0	0.1861	38.6494	28.8167	50.627
7	1.5308	0.4061	-0.6449	1.0301	0.0747	1.9066	0.2822	0.1635	0.4995	-0.0821	-0.0275	0.0851	-0.8574	-0.2421	0.0198	0.5377	0.16	0.1347	0.1193	0.095	0.3286	40.7075	39.4444	28.4438
8	1.4356	0.055	-1.0961	0.6679	-0.1735	1.8325	-0.0473	0.1674	-0.1394	-0.0652	0.0094	-0.0658	0.0062	-0.0949	0.0488	0.2077	0.009	0.0104	0.1575	-0.0178	0.2027	47.8158	10.694	17.9443
9	1.8601	0.2092	0.1245	2.8663	0.2911	1.1882	0.0514	0.3862	0.2116	-0.2681	0.0307	-0.1572	-0.4194	-0.109	-0.0576	0.3373	0.0606	0.072	0.2278	0.0793	0.1957	47.0654	28.6641	10.7594
10	1.1356	-0.0161	-0.38	1.0987	-0.603	1.4169	0.0915	0.3319	0.1475	-0.126	0.0026	0.0862	-0.3826	-0.4444	-0.0551	0.289	0.127	0.0273	0.2783	0.061	0.2033	34.6173	25.8541	20.1422
11	9.9918	1.4724	-1.5951	2.0093	2.8888	6.136	-0.333	-0.4004	0.4787	0.3015	-0.3123	-0.3117	0.1729	0.5605	0.4414	0.6568	0.2366	0.0934	0.813	0.0332	0.5087	8.4111	39.0895	46.2395
12	3.6349	-2.9082	-1.4385	3.8975	1.5349	0.7006	0.0409	0.0963	-0.1809	-0.233	-0.0091	0.3483	-0.2239	-0.701	0.0438	0.1994	0.1518	0.0122	0.3969	0.062	0.2172	21.4367	21.0414	36.6726
13	2.2853	-0.5419	-0.3301	2.3313	0.2007	0.8568	-0.0622	-0.0896	-0.1116	-0.0605	0.0842	0.0786	-0.1181	-0.6959	-0.0134	0.1681	0.0566	0.0345	0.3461	0.0254	0.1927	23.1012	14.7563	42.746
14	3.6674	-1.7087	-2.7968	3.6408	1.6157	2.3333	-0.0459	0.2292	-0.2273	-0.0283	-0.0969	0.5783	-0.1588	-0.8784	0.1607	0.1691	0.06	-0.0292	0.472	0.0222	0.258	15.7149	13.6947	36.593
15	6.3854	-3.1433	0.2082	5.9447	0.1698	1.9333	0.1252	0.0291	0.162	0.2108	0.1208	0.5179	-0.1809	-0.3137	0.0348	0.368	0.3591	0.1139	0.5977	0.101	0.4272	9.9105	30.9337	48.1455
16	4.2156	-0.1105	-0.456	2.6386	0.9035	0.3699	-0.0921	-0.3038	-0.0635	0.2932	0.1668	0.2452	-0.0458	-0.4949	0.1521	0.064	0.2603	0.1494	0.816	0.1501	0.331	11.3807	21.5484	52.7272

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN 'B' AND (RESID 98 THROUGH 106 )
2	X-RAY DIFFRACTION	2	CHAIN 'B' AND (RESID 107 THROUGH 126 )
3	X-RAY DIFFRACTION	3	CHAIN 'B' AND (RESID 127 THROUGH 195 )
4	X-RAY DIFFRACTION	4	CHAIN 'B' AND (RESID 196 THROUGH 317 )
5	X-RAY DIFFRACTION	5	CHAIN 'B' AND (RESID 318 THROUGH 372 )
6	X-RAY DIFFRACTION	6	CHAIN 'B' AND (RESID 373 THROUGH 420 )
7	X-RAY DIFFRACTION	7	CHAIN 'A' AND (RESID -1 THROUGH 150 )
8	X-RAY DIFFRACTION	8	CHAIN 'A' AND (RESID 151 THROUGH 302 )
9	X-RAY DIFFRACTION	9	CHAIN 'A' AND (RESID 303 THROUGH 342 )
10	X-RAY DIFFRACTION	10	CHAIN 'A' AND (RESID 343 THROUGH 421 )
11	X-RAY DIFFRACTION	11	CHAIN 'B' AND (RESID -3 THROUGH 2 )
12	X-RAY DIFFRACTION	12	CHAIN 'B' AND (RESID 3 THROUGH 26 )
13	X-RAY DIFFRACTION	13	CHAIN 'B' AND (RESID 27 THROUGH 55 )
14	X-RAY DIFFRACTION	14	CHAIN 'B' AND (RESID 56 THROUGH 78 )
15	X-RAY DIFFRACTION	15	CHAIN 'B' AND (RESID 79 THROUGH 85 )
16	X-RAY DIFFRACTION	16	CHAIN 'B' AND (RESID 86 THROUGH 97 )

-
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://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