PDB-6o4n: Crystal Structure of Enolase from Chlamydia trachomatis

ID or keywords:

Entry

Database: PDB / ID: 6o4n

Title

Crystal Structure of Enolase from Chlamydia trachomatis

Components

Enolase

Keywords

HYDROLASE / SSGCID / enolase / 2-phospho-D-glycerate hydro-lyase / 2-phosphoglycerate dehydratase / strain D/UW-3/Cx / 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 / cell surface / magnesium ion binding / extracellular region
Similarity search - Function

Biological species

Chlamydia trachomatis serovar L2b

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.8 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Citation

Journal: to be published
Title: Crystal Structure of Enolase from Chlamydia trachomatis
Authors: Dranow, D.M. / Mayclin, S.J. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.

History

Deposition	Feb 28, 2019	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 13, 2019	Provider: repository / Type: Initial release
Revision 1.1	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

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Download

PDBx/mmCIF format	6o4n.cif.gz	355 KB	Display	PDBx/mmCIF format
PDB format	pdb6o4n.ent.gz	285.8 KB	Display	PDB format
PDBx/mmJSON format	6o4n.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6o4n_validation.pdf.gz	466.2 KB	Display	wwPDB validaton report
Full document	6o4n_full_validation.pdf.gz	467.8 KB	Display
Data in XML	6o4n_validation.xml.gz	40.2 KB	Display
Data in CIF	6o4n_validation.cif.gz	61.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/o4/6o4n ftp://data.pdbj.org/pub/pdb/validation_reports/o4/6o4n	HTTPS FTP

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Related structure data

Related structure data	4mksS S: Starting model for refinement
Similar structure data	2h6g-d 1d8c-d 3waz-d 3ksq-d 5h8u-2 2fym-2 6dlj-d 3pv8-2 5vfb-2 3qn3-3 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: ChtrB.00084.a

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#50 - Feb 2004 Glycolytic Enzymes similarity (12)

Deposited unit

A: Enolase

B: Enolase

hetero molecules

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

1

Idetical with deposited unit
defined by author
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	164.280, 164.280, 89.790
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	79
Space group name H-M	I4

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Protein , 1 types, 2 molecules AB

#1: Protein	Enolase / 2-phospho-D-glycerate hydro-lyase / 2-phosphoglycerate dehydratase Mass: 46503.457 Da / Num. of mol.: 2 / Fragment: ChtrB.00084.a.B1 / Mutation: M78V,T178K Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chlamydia trachomatis serovar L2b (strain UCH-1/proctitis) (bacteria) Strain: UCH-1/proctitis / Gene: eno, CTLon_0844 / Plasmid: CChtrB.00084.a.B1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B0BA40, phosphopyruvate hydratase

#1: Protein

Enolase / 2-phospho-D-glycerate hydro-lyase / 2-phosphoglycerate dehydratase

Mass: 46503.457 Da / Num. of mol.: 2 / Fragment: ChtrB.00084.a.B1 / Mutation: M78V,T178K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Chlamydia trachomatis serovar L2b (strain UCH-1/proctitis) (bacteria)
Strain: UCH-1/proctitis / Gene: eno, CTLon_0844 / Plasmid: CChtrB.00084.a.B1 / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B0BA40, phosphopyruvate hydratase

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Non-polymers , 6 types, 908 molecules

#2: Chemical	ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL Mass: 118.174 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₆H₁₄O₂ / Comment: precipitant*YM
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO₄
#5: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#6: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 888 / 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	Density Matthews: 3.26 Å³/Da / Density % sol: 62.23 %
Crystal grow	Temperature: 287 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: ChtrB.00084.a.B1.PW38531 at 13.38 mg/ml was incubated with 2 mM 2-Phosphoglyceric acid, then was mixed 1:1 with Morpheus(e12): 12.5% (w/v) PEG 1000, 12.5% (w/v) PEG 3350, 12.5% (v/v) MPD, 0. ...Details: ChtrB.00084.a.B1.PW38531 at 13.38 mg/ml was incubated with 2 mM 2-Phosphoglyceric acid, then was mixed 1:1 with Morpheus(e12): 12.5% (w/v) PEG 1000, 12.5% (w/v) PEG 3350, 12.5% (v/v) MPD, 0.1 M bicine/Trizma base, pH 8.5, and 0.03 M each diethyleneglycol, triethyleneglycol, tetraethyleneglycol, pentaethyleneglycol. Tray: 305547e12, puck: vvm7-8.

Crystal

Density Matthews: 3.26 Å³/Da / Density % sol: 62.23 %

Crystal grow

Temperature: 287 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: ChtrB.00084.a.B1.PW38531 at 13.38 mg/ml was incubated with 2 mM 2-Phosphoglyceric acid, then was mixed 1:1 with Morpheus(e12): 12.5% (w/v) PEG 1000, 12.5% (w/v) PEG 3350, 12.5% (v/v) MPD, 0. ...

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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: RAYONIX MX-300 / Detector: CCD / Date: Feb 7, 2019 / Details: Beryllium Lenses

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: 1.8→41.876 Å / Num. obs: 110319 / % possible obs: 99.9 % / Redundancy: 5.082 % / B_iso Wilson estimate: 32.418 Å² / CC_1/2: 0.997 / R_merge(I) obs: 0.072 / R_rim(I) all: 0.08 / Χ²: 0.984 / Net I/σ(I): 13.5 / Num. measured all: 560618 / Scaling rejects: 10

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. possible	Num. unique obs	CC_1/2	R_rim(I) all	% possible all
1.8-1.85	5.06	0.56	2.8	40882	8083	8079	0.821	0.624	100
1.85-1.9	5.073	0.414	3.74	40217	7932	7927	0.898	0.462	99.9
1.9-1.95	5.06	0.341	4.61	39221	7760	7751	0.929	0.381	99.9
1.95-2.01	5.084	0.25	6.02	37988	7474	7472	0.959	0.279	100
2.01-2.08	5.083	0.201	7.49	37042	7291	7288	0.97	0.224	100
2.08-2.15	5.098	0.16	9.09	35703	7004	7004	0.98	0.178	100
2.15-2.23	5.105	0.13	10.92	34662	6793	6790	0.987	0.145	100
2.23-2.32	5.025	0.116	12.18	32662	6507	6500	0.988	0.13	99.9
2.32-2.43	5.107	0.098	13.96	32112	6289	6288	0.992	0.109	100
2.43-2.55	5.111	0.086	15.67	30618	5994	5991	0.993	0.096	99.9
2.55-2.68	5.113	0.077	17.37	29122	5697	5696	0.994	0.085	100
2.68-2.85	5.116	0.069	19.15	27594	5395	5394	0.995	0.076	100
2.85-3.04	5.113	0.063	21.07	25972	5081	5080	0.995	0.07	100
3.04-3.29	5.11	0.059	23.02	24251	4749	4746	0.995	0.065	99.9
3.29-3.6	5.107	0.054	24.95	22155	4341	4338	0.995	0.06	99.9
3.6-4.02	5.075	0.053	26.19	20091	3959	3959	0.996	0.059	100
4.02-4.65	5.08	0.052	27.26	17699	3491	3484	0.996	0.058	99.8
4.65-5.69	5.057	0.053	27.05	14934	2959	2953	0.996	0.059	99.8
5.69-8.05	5.027	0.054	26.97	11531	2302	2294	0.995	0.06	99.7
8.05-41.876	4.795	0.054	27.6	6162	1307	1285	0.995	0.061	98.3

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
XDS		data reduction
XSCALE		data scaling
PHENIX		refinement
PDB_EXTRACT	3.24	data extraction
MoRDa		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4MKS

4mks

Resolution: 1.8→41.876 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 15.14

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.163	6502	6.1 %	RANDOM, 0
R_work	0.1374	-	-	-
obs	0.1389	106510	96.48 %	-

Solvent computation

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

Displacement parameters

B_iso max: 117.58 Å² / B_iso mean: 30.7026 Å² / B_iso min: 12.12 Å²

Refinement step

Cycle: final / Resolution: 1.8→41.876 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6313	0	88	893	7294
B_iso mean	-	-	52.85	41.98	-
Num. residues	-	-	-	-	844

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 30

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.8-1.8205	0.253	203	0.22	3009	3212	88
1.8205-1.8419	0.2259	197	0.2027	3090	3287	90
1.8419-1.8643	0.2433	203	0.1837	3120	3323	91
1.8643-1.8879	0.207	238	0.1764	3133	3371	91
1.8879-1.9128	0.218	199	0.1716	3130	3329	91
1.9128-1.939	0.2081	193	0.183	3158	3351	92
1.939-1.9667	0.1916	220	0.1648	3201	3421	94
1.9667-1.996	0.1832	209	0.152	3299	3508	94
1.996-2.0272	0.1761	207	0.144	3237	3444	95
2.0272-2.0605	0.1788	217	0.1447	3295	3512	96
2.0605-2.096	0.168	187	0.1393	3345	3532	96
2.096-2.1341	0.1591	202	0.1368	3331	3533	96
2.1341-2.1751	0.165	236	0.1322	3324	3560	97
2.1751-2.2195	0.1697	233	0.1315	3356	3589	97
2.2195-2.2678	0.1637	212	0.1367	3334	3546	97
2.2678-2.3205	0.1536	211	0.1279	3405	3616	98
2.3205-2.3786	0.1582	199	0.1293	3399	3598	98
2.3786-2.4429	0.1606	227	0.1367	3383	3610	98
2.4429-2.5148	0.1728	205	0.1342	3408	3613	99
2.5148-2.5959	0.1746	239	0.1376	3428	3667	99
2.5959-2.6887	0.1594	205	0.1351	3425	3630	99
2.6887-2.7963	0.1655	251	0.141	3424	3675	99
2.7963-2.9235	0.1706	237	0.1383	3418	3655	99
2.9235-3.0776	0.1728	226	0.1404	3449	3675	100
3.0776-3.2704	0.1619	230	0.1382	3447	3677	100
3.2704-3.5228	0.1517	217	0.1321	3454	3671	100
3.5228-3.8771	0.1564	224	0.1251	3493	3717	100
3.8771-4.4375	0.13	238	0.1133	3477	3715	100
4.4375-5.5887	0.147	204	0.1224	3499	3703	100
5.5887-41.8876	0.155	233	0.1521	3537	3770	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	8.1101	1.6919	1.3625	2.256	0.6918	2.141	0.0035	-0.2202	0.4259	0.1034	0.0565	-0.0444	-0.1702	0.0956	-0.05	0.2053	-0.0216	0.0231	0.1295	-0.015	0.173	-25.7224	-14.8464	-32.2433
2	1.6215	-0.1388	-0.5563	2.0048	-0.166	1.4293	0.0312	-0.2176	0.0583	0.2583	0.0809	0.0373	-0.0751	-0.0358	-0.1176	0.2047	-0.0127	0.0271	0.2117	-0.0226	0.1543	-31.2492	-20.4856	-27.2127
3	2.8197	-0.0727	-0.3629	2.8485	0.2736	3.7107	0.0752	-0.4799	0.0443	0.365	-0.0044	-0.152	0.0415	0.2091	-0.0617	0.186	-0.0228	-0.0473	0.2966	-0.0434	0.1757	-16.5722	-24.2613	-25.0239
4	0.6132	0.0559	0.2174	0.6294	0.1286	0.7873	-0.015	-0.0297	0.0392	-0.0406	0.0051	0.0384	0.0201	-0.0307	0.016	0.1669	-0.0157	0.0132	0.1674	-0.0024	0.1675	-31.6646	-28.6062	-48.475
5	0.5032	-0.0862	0.025	0.8146	-0.6673	1.4384	-0.0394	-0.0232	-0.0896	-0.0163	0.0074	0.1471	0.2426	-0.1945	0.019	0.2123	-0.0731	0.0112	0.2035	-0.0182	0.2152	-43.8862	-43.4549	-45.1814
6	1.7832	0.4289	-0.0538	2.3549	0.4852	2.3803	-0.0259	-0.106	-0.2022	0.1116	0.0054	-0.0952	0.3412	0.028	0.0211	0.1964	-0.0029	0.016	0.1676	0.0249	0.191	-28.067	-42.651	-37.3788
7	1.002	0.0304	-0.0779	0.4084	0.0173	1.2972	-0.0308	-0.087	-0.0135	0.0517	0.0092	0.0097	0.0286	0.121	0.013	0.1756	-0.0321	0.0126	0.2012	0.0011	0.1791	-25.8926	-32.0178	-42.7085
8	3.0858	-0.262	-1.5916	2.6474	-0.6624	2.2738	0.0495	0.0121	0.0069	-0.2436	-0.0829	-0.1306	0.0139	0.1116	0.0135	0.1337	-0.0281	-0.0352	0.1626	-0.0018	0.0866	-26.5212	-29.5181	-54.0617
9	8.8114	6.4458	-1.3935	4.8068	-0.7822	0.9356	-0.0947	0.0843	-0.0277	-0.318	0.1892	-0.1956	-0.0626	0.0548	-0.036	0.21	0.0023	0.0284	0.1379	-0.0205	0.2471	-28.0708	-10.5941	-57.9083
10	0.4517	0.1076	0.0656	2.0637	0.6652	1.3914	0.0449	0.1382	0.0732	-0.3884	0.0189	0.1002	-0.0781	-0.1522	-0.0516	0.3109	-0.0135	-0.0045	0.2112	0.0007	0.238	-35.6212	-11.4376	-63.1727
11	0.6976	0.1576	-0.0242	1.2871	0.4667	1.2341	-0.0418	0.0502	0.014	-0.1887	0.0386	0.0813	-0.0941	-0.1456	-0.0149	0.2583	0.0155	-0.0025	0.1672	0.0027	0.2241	-36.4292	-1.2285	-51.7375
12	6.4134	6.8009	2.2741	8.787	2.6216	3.7035	0.2321	-0.5335	-0.1318	0.4142	-0.2585	0.1715	0.1477	-0.3403	0.0132	0.2764	0.001	0.0733	0.3319	0.0052	0.2877	-49.1159	-14.9695	-31.3981
13	1.4876	-0.1679	0.1531	2.3821	-0.5907	1.8378	-0.0022	0.0737	0.1046	-0.1208	-0.0364	0.7909	-0.139	-0.5919	-0.0017	0.2593	0.0207	-0.0157	0.5016	-0.0386	0.5427	-61.4105	-6.1205	-45.1742
14	0.6791	0.1413	-0.1345	2.3117	0.2614	1.7108	-0.0204	0.0356	0.0705	-0.1962	-0.038	0.3827	-0.2927	-0.2476	0.0469	0.2612	0.026	-0.0228	0.2281	-0.014	0.2551	-45.1319	2.7641	-49.9922
15	1.9946	-0.0435	1.8701	3.5497	0.0757	2.5153	-0.2236	-0.1615	0.1638	0.3634	0.0704	0.1828	-0.2054	-0.2144	0.1108	0.2283	0.0043	0.0454	0.1988	0.0034	0.1809	-39.714	-1.4429	-36.1403

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 3 through 29 )	A	3 - 29
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 30 through 75 )	A	30 - 75
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 76 through 109 )	A	76 - 109
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 110 through 197 )	A	110 - 197
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 198 through 301 )	A	198 - 301
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 302 through 341 )	A	302 - 341
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 342 through 392 )	A	342 - 392
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 393 through 424 )	A	393 - 424
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 3 through 29 )	B	3 - 29
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 30 through 75 )	B	30 - 75
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 76 through 176 )	B	76 - 176
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 177 through 197 )	B	177 - 197
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 198 through 301 )	B	198 - 301
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 302 through 392 )	B	302 - 392
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 393 through 424 )	B	393 - 424

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