PDB-7e2q: Crystal structure of Mycoplasma pneumoniae Enolase

ID or keywords:

Entry

Database: PDB / ID: 7e2q

Title

Crystal structure of Mycoplasma pneumoniae Enolase

Components

Enolase

Keywords

LYASE / phosphopyruvate hydratase / moon light protein / CELL ADHESION

Function / homology

:

Function and homology information

Biological species

Mycoplasma pneumoniae (Filterable agent of primary atypical pneumonia)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.8 Å

Authors

Chen, R. / Zhang, S. / Gan, R. / Wang, W. / Ran, T. / Xiong, Q. / Shao, G. / Feng, Z.

Funding support

China, 2items

Citation

Journal: Front Mol Biosci / Year: 2022
Title: Evidence for the Rapid and Divergent Evolution of Mycoplasmas: Structural and Phylogenetic Analysis of Enolases.
Authors: Chen, R. / Zhao, L. / Gan, R. / Feng, Z. / Cui, C. / Xie, X. / Hao, F. / Zhang, Z. / Wang, L. / Ran, T. / Wang, W. / Zhang, S. / Li, Y. / Zhang, W. / Pang, M. / Xiong, Q. / Shao, G.

History

Deposition	Feb 7, 2021	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Feb 2, 2022	Provider: repository / Type: Initial release
Revision 1.1	Nov 29, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7e2q.cif.gz	829.2 KB	Display	PDBx/mmCIF format
PDB format	pdb7e2q.ent.gz	571.1 KB	Display	PDB format
PDBx/mmJSON format	7e2q.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/e2/7e2q ftp://data.pdbj.org/pub/pdb/validation_reports/e2/7e2q	HTTPS FTP

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Related structure data

Related structure data	7e2pC 6j36S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	7e2q-2 3qtp-d 5enl-1 7e2p-d 2xh2-2 6j36-d 3otr-3 2y08-d 5bof-d 2al2-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

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Enolase

B: Enolase

C: Enolase

D: Enolase

hetero molecules

202 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Enolase

B: Enolase

hetero molecules

defined by author&software
Evidence: native gel electrophoresis, gel filtration
101 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Enolase

hetero molecules

D: Enolase

hetero molecules

defined by author&software
101 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	76.074, 106.548, 128.589
Angle α, β, γ (deg.)	90.000, 103.146, 90.000
Int Tables number	4
Space group name H-M	P12₁1
Space group name Hall	P2yb
Symmetry operation	#1: x,y,z #2: -x,y+1/2,-z

#1: Protein	Enolase / 2-phospho-D-glycerate hydro-lyase / 2-phosphoglycerate dehydratase Mass: 50353.332 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycoplasma pneumoniae (Filterable agent of primary atypical pneumonia) Gene: eno, NCTC10119_00092 Production host: Escherichia coli O104:H4 str. 2009EL-2050 (bacteria) References: UniProt: A0A449A037, phosphopyruvate hydratase
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO₄
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 872 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.52 Å³/Da / Density % sol: 51.18 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 0.2M Sodium citrate tribasic dihydrate, 0.1M TRIS hydrochloride pH 8.5, 30% v/v Polyethylene glycol 400

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
Detector	Type: AGILENT ATLAS CCD / Detector: CCD / Date: Dec 19, 2018
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97853 Å / Relative weight: 1
Reflection	Resolution: 1.8→19.84 Å / Num. obs: 183711 / % possible obs: 99.6 % / Redundancy: 6.4 % / B_iso Wilson estimate: 24.35 Å² / CC_1/2: 0.997 / Net I/σ(I): 6.4
Reflection shell	Resolution: 1.8→1.9 Å / Num. unique obs: 26642 / CC_1/2: 0.76

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Processing

Software

Name	Version	Classification
PHENIX	1.16_3549	refinement
HKL-3000		data reduction
HKL-3000		data scaling
HKL-3000		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6J36

6j36

Resolution: 1.8→19.84 Å / SU ML: 0.2216 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 22.305
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2226	9135	5.03 %
R_work	0.1892	172488	-
obs	0.1909	181623	98.46 %

Solvent computation

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

Displacement parameters

B_iso mean: 30.87 Å²

Refinement step

Cycle: LAST / Resolution: 1.8→19.84 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	13707	0	20	873	14600

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0059	13932
X-RAY DIFFRACTION	f_angle_d	0.7871	18830
X-RAY DIFFRACTION	f_chiral_restr	0.0497	2188
X-RAY DIFFRACTION	f_plane_restr	0.0042	2417
X-RAY DIFFRACTION	f_dihedral_angle_d	11.9665	8450

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 (%)
1.8-1.82	0.3305	316	0.299	5869	X-RAY DIFFRACTION	99.69
1.82-1.84	0.3059	314	0.266	5780	X-RAY DIFFRACTION	99.64
1.84-1.86	0.3103	302	0.2778	5720	X-RAY DIFFRACTION	98.64
1.86-1.89	0.3857	322	0.3445	5606	X-RAY DIFFRACTION	97.32
1.89-1.91	0.541	274	0.5173	5001	X-RAY DIFFRACTION	85.86
1.91-1.94	0.3595	312	0.3505	5098	X-RAY DIFFRACTION	88.64
1.94-1.97	0.2612	298	0.2373	5790	X-RAY DIFFRACTION	98.83
1.97-2	0.2268	343	0.1834	5767	X-RAY DIFFRACTION	99.87
2-2.03	0.2451	292	0.1865	5824	X-RAY DIFFRACTION	99.92
2.03-2.06	0.3306	292	0.3066	5710	X-RAY DIFFRACTION	97.39
2.06-2.1	0.313	303	0.2651	5647	X-RAY DIFFRACTION	97.51
2.1-2.13	0.2234	315	0.1819	5801	X-RAY DIFFRACTION	99.93
2.13-2.17	0.2353	328	0.174	5826	X-RAY DIFFRACTION	99.97
2.17-2.22	0.2071	312	0.1849	5799	X-RAY DIFFRACTION	99.27
2.22-2.27	0.374	305	0.312	5360	X-RAY DIFFRACTION	92.81
2.27-2.32	0.2392	277	0.2076	5808	X-RAY DIFFRACTION	99.48
2.32-2.38	0.2092	298	0.167	5895	X-RAY DIFFRACTION	99.94
2.38-2.44	0.2247	295	0.1667	5832	X-RAY DIFFRACTION	99.93
2.44-2.51	0.219	285	0.1886	5830	X-RAY DIFFRACTION	99.85
2.51-2.59	0.2241	312	0.178	5790	X-RAY DIFFRACTION	99.87
2.59-2.69	0.2459	270	0.1956	5873	X-RAY DIFFRACTION	99.81
2.69-2.79	0.1957	297	0.1782	5856	X-RAY DIFFRACTION	99.97
2.79-2.92	0.2046	297	0.1758	5855	X-RAY DIFFRACTION	99.95
2.92-3.07	0.2079	332	0.1771	5800	X-RAY DIFFRACTION	100
3.07-3.27	0.2204	303	0.1845	5887	X-RAY DIFFRACTION	99.97
3.27-3.52	0.2042	326	0.1792	5802	X-RAY DIFFRACTION	99.92
3.52-3.87	0.179	321	0.1581	5865	X-RAY DIFFRACTION	99.95
3.87-4.42	0.177	296	0.1406	5901	X-RAY DIFFRACTION	99.97
4.42-5.55	0.1703	313	0.1418	5890	X-RAY DIFFRACTION	100
5.55-19.84	0.1543	285	0.1489	6006	X-RAY DIFFRACTION	99.92

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	0.57984352722	0.0903240741829	-0.0144496906208	1.27061843512	-0.16309203904	0.503638485383	0.0307176902236	-0.021790847107	0.16387637652	0.040049964367	-0.0156380299245	0.178902133458	-0.0594390561602	-0.0797752214666	0.00032869564285	0.18797492428	0.000509109747987	0.00467149011411	0.0954542258146	-0.0170439915141	0.225509780228	3.74200931598	0.053085841411	-67.1517180427
2	0.797881352738	0.283535243319	-0.212560892311	0.741405059098	-0.00129143337002	0.968352945933	0.108858174629	-0.189209726933	-0.020805797611	0.118326096281	-0.128387937989	-0.00567654809072	-0.00949791660889	0.0431178765678	-0.0012287034477	0.145253079431	-0.0382751801489	-0.0135249169251	0.135566912109	0.00864729130218	0.158858335783	16.1812846461	-22.9909458783	-47.0959832055
3	0.689362413363	0.195582902887	0.134314095311	1.15555854939	-0.0494676045006	0.75767221489	0.0737222076491	-0.0948408585151	0.0640943814668	0.138213026861	-0.104113846803	-0.0407356944192	-0.13750996513	0.0121739520493	-0.00955423077912	0.157137412038	-0.0398922094992	-0.00680224644691	0.107355187533	0.00451041331017	0.153310630082	19.5714869215	-9.31358329534	-59.0781387464
4	0.651154065662	-0.564031711633	-0.103738271159	0.52790234935	0.31138327944	0.967504153606	0.0358922073116	0.189019034328	-0.00245804900382	-0.0806918592682	-0.0348703150434	-0.10505899347	0.0192410132627	0.0630743890872	0.00051716131218	0.220418106357	0.00671048929766	0.0213460288131	0.1836241966	-0.0021218029796	0.158896986695	12.3804529959	-25.6908449873	-86.5476986565
5	0.684978693868	-0.00851600075103	-0.274229759898	0.37819776288	0.160658043592	0.173450245335	0.012499552069	0.122100248366	-0.0600020424452	-0.116495910294	-0.0160819198077	0.0642757198924	0.0106802012179	-0.0984071916319	0.000135710356916	0.20009859691	0.00536081333693	-0.0257277551254	0.199816250701	-0.00294578695074	0.200244397895	-8.77158166702	-23.548552979	-77.3931224982
6	1.13963972343	-0.247439125796	0.0871973136812	0.534512869527	0.123848112639	0.919602347135	0.0681531226501	-0.0213897649143	-0.151668061504	0.117797452896	-0.0303712649914	0.0977084516667	0.081876405936	-0.0101774091935	0.010547257973	0.102639155956	-0.000120052666134	-0.00902012862228	0.114659505244	0.00128374109138	0.200990922458	-13.1954054275	-36.7113635084	-62.9895019845
7	0.864618348259	0.0434328353159	-0.0109575831425	0.707028561485	-0.351593066837	0.649523199691	-0.00380415979283	0.236307777191	-0.0662370832006	-0.187972916326	0.00519627989606	0.105430668965	0.0513117272399	-0.089931227515	0.000266443182377	0.183854310984	-0.000956622179086	-0.0362037350181	0.210220718355	-0.0345681503775	0.180779927331	-11.4354290202	-29.3527097595	-80.5662455363
8	0.303403656701	0.189987549608	0.18428312366	0.973806552173	-0.282742205604	1.22097280026	0.0476539310585	-0.18362074014	-0.0321955788214	0.177008885098	0.0311939711868	0.0136636000921	-0.00866468130489	-0.0101598026147	0.00105491963745	0.214917044362	0.00811498142681	0.017941753964	0.291419654753	0.00180666207091	0.140215040353	9.50851965893	-26.6347547336	-116.705992571
9	0.937500596339	-0.0375574743398	0.0944351947146	0.468691736414	0.134868162435	1.02835500368	0.028725721667	-0.101921782302	-0.0924044776622	-0.0163013173701	0.00416394869162	-0.074754247182	0.0979840729967	0.220909411128	2.46443107147E-5	0.180646078069	-0.0631901075844	0.0202825508012	0.300261922005	-0.00271388912722	0.182698508134	35.382304545	-23.2780620473	-136.654657356
10	0.926071691496	0.223715555682	-0.280306322318	0.492085273682	-0.184456439384	1.10218661303	0.0584925469295	-0.271523152808	0.0538157379944	0.134817584654	0.0229196934668	-0.0791190050436	-0.154103077375	0.288748696803	0.00392560886003	0.233295827576	-0.0541819006464	-0.00260378520778	0.354968261472	-0.0678195939204	0.202985025778	24.9520225866	-15.8888941022	-123.216938543
11	1.07368912	-0.053246918998	0.319306503205	0.76735679956	-0.0786105685527	1.32670906907	-0.00143573032256	0.0264239667157	0.280777557817	0.0022523550379	-0.020403500148	-0.127562622552	-0.305506923889	0.181729994601	-0.000757585964562	0.257274842122	-0.0631343148494	0.00589473412985	0.248564438242	0.00495591930546	0.287074843102	-14.4715554778	42.3338459185	-109.413288997
12	0.837451296007	-0.0229100632778	0.0125800394754	0.344681391284	-0.157274782289	1.31245012823	0.00385636744444	-0.0569911049606	-0.0157783564215	0.0174823750645	0.0229953259525	0.0471206647266	0.203261800423	-0.029775632065	1.63726548028E-5	0.201479700609	0.0211024462074	-0.0105949507945	0.152330487046	-0.000530706405228	0.194294917248	-24.7169068921	14.6060881718	-95.165190718
13	0.732340385415	0.141686533036	0.206337611198	0.471237042304	0.0770504962558	1.24889816578	0.00221027028265	0.0194811822367	-0.00428642097598	0.0082513711216	0.0246834711531	-0.0893715384645	0.0703114022425	0.2795270717	5.04317000575E-5	0.158870518572	0.0272028097352	-0.000226375497098	0.281289160893	-0.0256442270044	0.191428490088	-11.430207234	22.8154002078	-104.553708662

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 8 through 157 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 158 through 328 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 329 through 459 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 8 through 133 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 134 through 188 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 189 through 303 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 304 through 459 )
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 8 through 159 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 160 through 328 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 329 through 459 )
11	X-RAY DIFFRACTION	11	chain 'D' and (resid 7 through 157 )
12	X-RAY DIFFRACTION	12	chain 'D' and (resid 158 through 328 )
13	X-RAY DIFFRACTION	13	chain 'D' and (resid 329 through 460 )

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