PDB-7e2p: The Crystal Structure of Mycoplasma bovis enolase

ID or keywords:

Entry

Database: PDB / ID: 7e2p

Title

The Crystal Structure of Mycoplasma bovis enolase

Components

Enolase

Keywords

LYASE / moon light protein / phosphopyruvate hydratase / CELL ADHESION

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

Mycoplasma bovis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.7 Å

Authors

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

Funding support

China, 1items

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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PDBx/mmCIF format	7e2p.cif.gz	420.9 KB	Display	PDBx/mmCIF format
PDB format	pdb7e2p.ent.gz	285.4 KB	Display	PDB format
PDBx/mmJSON format	7e2p.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	7e2p_validation.pdf.gz	441.8 KB	Display	wwPDB validaton report
Full document	7e2p_full_validation.pdf.gz	447.6 KB	Display
Data in XML	7e2p_validation.xml.gz	34.8 KB	Display
Data in CIF	7e2p_validation.cif.gz	50.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/e2/7e2p ftp://data.pdbj.org/pub/pdb/validation_reports/e2/7e2p	HTTPS FTP

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Related structure data

Related structure data	7e2qC 6j36S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6j36-1 4ewj-1 5bof-1 4xgu-d 4a3r-1 4a3r-2 4yvs-d 6mgq-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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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

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

1

A: Enolase

B: Enolase

A: Enolase

B: Enolase

A: Enolase

B: Enolase

A: Enolase

B: Enolase

defined by author&software
Evidence: native gel electrophoresis, gel filtration
404 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	142.221, 142.221, 107.422
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	79
Space group name H-M	I4
Space group name Hall	I4
Symmetry operation	#1: x,y,z #2: -y,x,z #3: y,-x,z #4: -x,-y,z #5: x+1/2,y+1/2,z+1/2 #6: -y+1/2,x+1/2,z+1/2 #7: y+1/2,-x+1/2,z+1/2 #8: -x+1/2,-y+1/2,z+1/2

#1: Protein	Enolase / 2-phospho-D-glycerate hydro-lyase / 2-phosphoglycerate dehydratase Mass: 50512.305 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycoplasma bovis (bacteria) / Gene: eno, H0I36_02020 Production host: Escherichia coli O104:H4 str. 2009EL-2050 (bacteria) References: UniProt: A0A7D5V839, phosphopyruvate hydratase
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 391 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

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

Mass: 50512.305 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Mycoplasma bovis (bacteria) / Gene: eno, H0I36_02020
Production host:

Escherichia coli O104:H4 str. 2009EL-2050 (bacteria)
References: UniProt: A0A7D5V839, phosphopyruvate hydratase

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 391 / 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: 2.69 Å³/Da / Density % sol: 54.25 %
Crystal grow	Temperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 0.14M Calcium chloride dihydrate, 0.07M Sodium acetate trihydrate pH 4.6, 14% v/v 2-Propanol, 30% v/v Glycerol

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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: 1.7→19.96 Å / Num. obs: 115149 / % possible obs: 98.3 % / Redundancy: 12.6 % / B_iso Wilson estimate: 28.51 Å² / R_rim(I) all: 0.071 / Net I/σ(I): 18.6
Reflection shell	Resolution: 1.7→1.79 Å / Num. unique obs: 15087 / R_rim(I) all: 0.775

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Processing

Software

Name	Version	Classification
PHENIX	1.16_3549	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6j36

6j36

Resolution: 1.7→19.72 Å / SU ML: 0.1589 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.7033
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.1821	5819	5.07 %
R_work	0.1581	109010	-
obs	0.1593	114829	98.08 %

Solvent computation

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

Displacement parameters

B_iso mean: 34.74 Å²

Refinement step

Cycle: LAST / Resolution: 1.7→19.72 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6851	0	0	391	7242

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0142	6947
X-RAY DIFFRACTION	f_angle_d	1.2848	9364
X-RAY DIFFRACTION	f_chiral_restr	0.1156	1074
X-RAY DIFFRACTION	f_plane_restr	0.0081	1211
X-RAY DIFFRACTION	f_dihedral_angle_d	13.1267	4240

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 (%)
1.7-1.72	0.2612	154	0.2145	2944	X-RAY DIFFRACTION	80.11
1.72-1.74	0.2817	161	0.2083	3131	X-RAY DIFFRACTION	84.17
1.74-1.76	0.2439	136	0.1951	3290	X-RAY DIFFRACTION	88.21
1.76-1.78	0.2192	181	0.1845	3466	X-RAY DIFFRACTION	93.68
1.78-1.81	0.2269	203	0.1754	3659	X-RAY DIFFRACTION	99.2
1.81-1.83	0.2148	179	0.1824	3647	X-RAY DIFFRACTION	99.2
1.83-1.86	0.2167	201	0.1721	3676	X-RAY DIFFRACTION	99.56
1.86-1.89	0.2096	202	0.1659	3665	X-RAY DIFFRACTION	99.59
1.89-1.91	0.195	215	0.1666	3664	X-RAY DIFFRACTION	99.59
1.91-1.95	0.2093	203	0.1618	3681	X-RAY DIFFRACTION	99.77
1.95-1.98	0.2046	211	0.1563	3682	X-RAY DIFFRACTION	99.72
1.98-2.02	0.1971	166	0.1581	3711	X-RAY DIFFRACTION	99.82
2.02-2.05	0.2078	187	0.1594	3663	X-RAY DIFFRACTION	99.84
2.05-2.1	0.1825	201	0.1614	3760	X-RAY DIFFRACTION	99.97
2.1-2.14	0.1925	204	0.1639	3670	X-RAY DIFFRACTION	100
2.14-2.19	0.2058	195	0.1562	3720	X-RAY DIFFRACTION	99.92
2.19-2.25	0.1763	188	0.1505	3680	X-RAY DIFFRACTION	99.97
2.25-2.31	0.1749	197	0.1508	3695	X-RAY DIFFRACTION	99.97
2.31-2.37	0.182	209	0.1573	3743	X-RAY DIFFRACTION	100
2.37-2.45	0.2062	198	0.1699	3656	X-RAY DIFFRACTION	100
2.45-2.54	0.2059	226	0.1717	3709	X-RAY DIFFRACTION	100
2.54-2.64	0.2055	182	0.1711	3681	X-RAY DIFFRACTION	100
2.64-2.76	0.1934	165	0.1716	3754	X-RAY DIFFRACTION	100
2.76-2.9	0.1892	209	0.1765	3697	X-RAY DIFFRACTION	99.97
2.9-3.09	0.1978	197	0.1778	3730	X-RAY DIFFRACTION	100
3.09-3.32	0.195	230	0.1805	3653	X-RAY DIFFRACTION	100
3.32-3.66	0.1908	186	0.1655	3750	X-RAY DIFFRACTION	100
3.66-4.18	0.1421	223	0.1373	3709	X-RAY DIFFRACTION	100
4.18-5.25	0.1459	192	0.121	3750	X-RAY DIFFRACTION	99.97
5.25-19.72	0.1605	218	0.1459	3774	X-RAY DIFFRACTION	99.95

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	1.04851316247	0.131958310611	-0.207760354101	0.628118182399	0.0175460604867	0.840368443318	0.00277216220599	0.180014588592	0.0136290019561	-0.119274490889	-0.00766796738468	0.0352601508655	-0.0336625790147	-0.0768212496545	-2.94307868107E-5	0.251903888965	0.015633036945	0.0164076804192	0.232231855858	-0.000460946925086	0.195862944766	13.047285352	-28.4391391567	-8.81483629939
2	1.28195354686	0.146869203556	0.186124569257	0.968405615638	0.101732973663	0.579323194185	-0.0204007605031	0.0169601553583	-0.253860363789	0.0628877675681	-0.00623615321785	-0.146308772202	0.214603916659	0.108299660171	1.43113369073E-5	0.316755653815	0.0341061289396	0.0362897254598	0.215595650607	0.0404845988222	0.313294425641	25.7103213457	-56.2308558962	7.12194127001
3	0.658305404477	-0.0435870670729	-0.0589559819608	0.689584174057	0.090206853546	0.467024437318	-0.0117570547583	0.0250430397533	-0.115336827676	-0.0415227615477	-0.0272057748558	0.0302656527177	0.100847436804	-0.045553917282	-2.66968014515E-5	0.268492742099	-0.000317201680832	0.019941707554	0.21736831555	-0.00135475272191	0.25502574331	9.55168624765	-45.3427710258	2.71995825959
4	0.409787403561	0.302924423609	-0.0582379090284	0.994749788375	-0.228999815791	0.81169610225	0.0591366402879	-0.0950425322814	0.051244059039	0.163554809018	-0.0350076526008	0.00311458430711	-0.0953664445516	-0.0291630228882	-7.82516231892E-6	0.229444925974	0.0152482983992	0.0129458863382	0.245255971685	0.0121625807776	0.215517629274	26.1303077955	-17.8290239691	17.3253254957
5	0.962432729877	0.463990937189	-0.147021784402	1.30660619195	0.421305274076	0.446404252799	0.0212908930716	-0.0358994570998	-0.28806113862	0.0717709429526	-0.0054716563325	-0.336826465838	0.194011236268	0.119779766354	0.000285638514974	0.265423846769	0.0504848516194	0.0489707941293	0.29482481771	0.0318443344255	0.382760066827	51.0800134811	-35.0092047453	1.13341812569
6	0.573915214869	0.0604023238594	0.127370736395	0.73725952483	0.103785809272	0.36136308352	-0.0196630805637	-0.0182788740727	-0.0145424946781	0.0138336145355	0.00170945258397	-0.14708133951	-0.00721930804829	0.0837216172934	-6.42869724026E-6	0.225817482276	0.0104736738004	0.0223826824296	0.269088769261	0.0143300798782	0.264547517025	43.0431704843	-17.219457562	5.68869920683

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 2 through 155 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 156 through 305 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 306 through 454 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 2 through 155 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 156 through 305 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 306 through 454 )

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