PDB-1w6t: Crystal Structure Of Octameric Enolase From Streptococcus pneumoniae

ID or keywords:

Entry

Database: PDB / ID: 1w6t

Title

Crystal Structure Of Octameric Enolase From Streptococcus pneumoniae

Components

ENOLASE

Keywords

LYASE /

BACTERIAL INFECTION /

SURFACE PROTEIN /

MOONLIGHTING PROTEIN /

GLYCOLYSIS /

PHOSPHOPYRUVATE HYDRATASE

Function / homology

Function and homology information

regulation of vacuole fusion, non-autophagic /

phosphopyruvate hydratase /

phosphopyruvate hydratase complex /

phosphopyruvate hydratase activity / : / glycolytic process / magnesium ion binding /

cell surface / extracellular region
Similarity search - Function

Biological species

STREPTOCOCCUS PNEUMONIAE (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.1 Å

Authors

Ehinger, S. / Schubert, W.-D. / Bergmann, S. / Hammerschmidt, S. / Heinz, D.W.

Citation

Journal: J.Mol.Biol. / Year: 2004
Title: Plasmin(Ogen)-Binding Alpha-Enolase from Streptococcus Pneumoniae: Crystal Structure and Evaluation of Plasmin(Ogen)-Binding Sites
Authors: Ehinger, S. / Schubert, W.-D. / Bergmann, S. / Hammerschmidt, S. / Heinz, D.W.

History

Deposition	Aug 24, 2004	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Aug 22, 2005	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Dec 13, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_sheet / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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 / _struct_conn.ptnr2_label_seq_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Remark 650

HELIX DETERMINATION METHOD: AUTHOR PROVIDED.

Remark 700

SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	1w6t.cif.gz	193.9 KB	Display	PDBx/mmCIF format
PDB format	pdb1w6t.ent.gz	154 KB	Display	PDB format
PDBx/mmJSON format	1w6t.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/w6/1w6t ftp://data.pdbj.org/pub/pdb/validation_reports/w6/1w6t	HTTPS FTP

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Related structure data

Related structure data	1e9iS S: Starting model for refinement
Similar structure data	5bof-1 4ewj-1 4a3r-2 5boe-1 4a3r-1 5j04-1 4rop-1 3uj2-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

hetero molecules

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

1

A: ENOLASE

B: ENOLASE

hetero molecules

A: ENOLASE

B: ENOLASE

hetero molecules

A: ENOLASE

B: ENOLASE

hetero molecules

A: ENOLASE

B: ENOLASE

hetero molecules

defined by author&software
391 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	143.702, 143.702, 100.579
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	79
Space group name H-M	I4

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Component-ID: 1

Dom-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Refine code	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	HIS	HIS	SER	SER	3	A	A	0 - 39	10 - 49
2	1	HIS	HIS	SER	SER	3	B	B	0 - 39	10 - 49
1	2	HIS	HIS	PHE	PHE	2	A	A	46 - 248	56 - 258
2	2	HIS	HIS	PHE	PHE	2	B	B	46 - 248	56 - 258
1	3	TYR	TYR	GLY	GLY	2	A	A	256 - 265	266 - 275
2	3	TYR	TYR	GLY	GLY	2	B	B	256 - 265	266 - 275
1	4	ALA	ALA	LEU	LEU	2	A	A	267 - 432	277 - 442
2	4	ALA	ALA	LEU	LEU	2	B	B	267 - 432	277 - 442
1	5	HIS	HIS	SER	SER	2	B	B	0 - 39	10 - 49
2	5	HIS	HIS	SER	SER	2	A	A	0 - 39	10 - 49
1	6	HIS	HIS	PHE	PHE	2	B	B	46 - 248	56 - 258
2	6	HIS	HIS	PHE	PHE	2	A	A	46 - 248	56 - 258
1	7	TYR	TYR	GLY	GLY	2	B	B	256 - 265	266 - 275
2	7	TYR	TYR	GLY	GLY	2	A	A	256 - 265	266 - 275
1	8	ALA	ALA	LEU	LEU	2	B	B	267 - 432	277 - 442
2	8	ALA	ALA	LEU	LEU	2	A	A	267 - 432	277 - 442

NCS ensembles :

ID
1
2
3
4
5
6
7
8

NCS oper: (Code: given
Matrix: (0.147, -0.989, -0.002), (-0.989, -0.146, -0.006), (0.006, 0.003, -1)
Vector: 142.16521, 164.56519, 5.3543)

#1: Protein	ENOLASE / / 2-PHOSPHOGLYCERATE DEHYDRATASE / PHOSPHOPYRUVATE HYDRATASE / 2-PHOSPHO-D-GLYCERATE HYDRO-LYASE Mass: 48412.113 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) STREPTOCOCCUS PNEUMONIAE (bacteria) / Strain: TIGR4 / Plasmid: PQE30 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 References: UniProt: Q8DPS0, UniProt: Q97QS2*PLUS, phosphopyruvate hydratase
#2: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical	ChemComp-2PE / NONAETHYLENE GLYCOL / Polyethylene glycol Mass: 414.488 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₈H₃₈O₁₀ / Comment: precipitant*YM
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 535 / Source method: isolated from a natural source / Formula: H₂O
Compound details	CATALYTIC ACTIVITY: 2-PHOSPHO-D-GLYCERATE = PHOSPHOENOLPYRUVATE + H(2)O. MAGNESIUM IS REQUIRED FOR ...CATALYTIC ACTIVITY: 2-PHOSPHO-D-GLYCERATE = PHOSPHOENOLPYRUVATE + H(2)O. MAGNESIUM IS REQUIRED FOR CATALYSIS AND FOR STABILIZING THE DIMER. THE PROTEIN FUNCTIONS AS A HOMODIMER.
Sequence details	CLONING INTRODUCES THE RESIDUES MRGSHHHHHHL TO REPLACE THE N-TERMINAL M.

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.76 Å³/Da / Density % sol: 55.12 %
Crystal grow	pH: 7.5 Details: 20% (W/V) PEG 1000, 0.3 M MGCL2, AND 0.1 M MES PH 7.5

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.05
Detector	Type: MARRESEARCH / Detector: CCD / Date: Feb 20, 2002
Radiation	Monochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.05 Å / Relative weight: 1
Reflection	Resolution: 2→20 Å / Num. obs: 68907 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 3.3 % / R_merge(I) obs: 0.08 / Net I/σ(I): 14.5
Reflection shell	Resolution: 2→2.03 Å / Redundancy: 3.4 % / R_merge(I) obs: 0.4 / Mean I/σ(I) obs: 2.6 / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0005	refinement
DENZO		data reduction
SCALEPACK		data scaling
EPMR		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1E9I

1e9i

Resolution: 2.1→100 Å / Cor.coef. F_o:F_c: 0.969 / Cor.coef. F_o:F_c free: 0.952 / SU B: 6.592 / SU ML: 0.094 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.166 / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.187	3008	5.1 %	RANDOM
R_work	0.148	-	-	-
obs	0.15	56519	99.8 %	-

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: 22.68 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.08 Å²	0 Å²	0 Å²
2-	-	1.08 Å²	0 Å²
3-	-	-	-2.16 Å²

Refinement step

Cycle: LAST / Resolution: 2.1→100 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6566	0	28	535	7129

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.02	0.022	6993
X-RAY DIFFRACTION	r_bond_other_d	0.003	0.02	6294
X-RAY DIFFRACTION	r_angle_refined_deg	1.752	1.962	9487
X-RAY DIFFRACTION	r_angle_other_deg	1.095	3	14662
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.11	5	912
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.834	24.836	335
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.494	15	1178
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.511	15	43
X-RAY DIFFRACTION	r_chiral_restr	0.097	0.2	1037
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	8099
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	1420
X-RAY DIFFRACTION	r_nbd_refined	0.204	0.2	1597
X-RAY DIFFRACTION	r_nbd_other	0.17	0.2	6797
X-RAY DIFFRACTION	r_nbtor_refined	0.176	0.2	3576
X-RAY DIFFRACTION	r_nbtor_other	0.083	0.2	4082
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.153	0.2	594
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined	0.003	0.2	2
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.138	0.2	7
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.179	0.2	46
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.2	0.2	23
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	2.679	2.5	4513
X-RAY DIFFRACTION	r_mcbond_other	0.577	2.5	1850
X-RAY DIFFRACTION	r_mcangle_it	3.379	3	7065
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	3.183	2.5	2795
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	4.236	3	2422
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	A	210	tight positional	0.02	0.05
2	A	1113	tight positional	0.03	0.05
3	A	52	tight positional	0.01	0.05
4	A	976	tight positional	0.02	0.05
5	B	210	tight positional	0.02	0.05
6	B	1113	tight positional	0.03	0.05
7	B	52	tight positional	0.01	0.05
8	B	976	tight positional	0.02	0.05
2	A	1624	medium positional	0.24	0.5
3	A	81	medium positional	0.86	0.5
4	A	1502	medium positional	0.27	0.5
5	B	316	medium positional	0.12	0.5
6	B	1624	medium positional	0.24	0.5
7	B	81	medium positional	0.86	0.5
8	B	1502	medium positional	0.27	0.5
1	A	316	loose positional	0.12	5
1	A	210	tight thermal	0.12	0.5
2	A	1113	tight thermal	0.12	0.5
3	A	52	tight thermal	0.06	0.5
4	A	976	tight thermal	0.11	0.5
5	B	210	tight thermal	0.12	0.5
6	B	1113	tight thermal	0.12	0.5
7	B	52	tight thermal	0.06	0.5
8	B	976	tight thermal	0.11	0.5
2	A	1624	medium thermal	0.46	2
3	A	81	medium thermal	0.36	2
4	A	1502	medium thermal	0.46	2
5	B	316	medium thermal	0.51	2
6	B	1624	medium thermal	0.46	2
7	B	81	medium thermal	0.36	2
8	B	1502	medium thermal	0.46	2
1	A	316	loose thermal	0.51	10

LS refinement shell

Resolution: 2.1→2.15 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.212	199	-
R_work	0.148	4174	-
obs	-	-	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	1.1372	0.3063	-0.4653	0.7858	-0.0241	0.5112	-0.0361	0.1626	0.0103	-0.114	0.0859	0.0315	0.0505	-0.0183	-0.0499	0.0383	0.0195	0.0025	0.0625	-0.0033	0.0519	17.249	119.071	-12.953
2	1.2443	-0.0569	0.7607	0.6132	-0.2352	1.1476	0.1531	0.1476	-0.2094	-0.0488	-0.0358	-0.048	0.2974	0.1579	-0.1173	0.0772	0.0733	-0.0244	0.0066	-0.0118	0.0923	23.128	98.509	4.33
3	0.5437	0.2448	0.1125	1.6342	-0.264	0.8149	0.0549	-0.0846	-0.0093	0.3316	-0.0258	-0.0264	-0.0348	0.0339	-0.029	0.0781	0.0111	-0.0157	0.0478	0.0088	0.0632	26.863	130.114	18.806
4	0.4708	0.2054	0.0047	1.4586	0.2042	0.7082	-0.0015	-0.0046	-0.1024	0.0947	0.0295	-0.3999	0.0649	0.236	-0.0281	-0.0118	0.0482	-0.0153	0.0952	-0.0018	0.1779	48.059	127.223	1.56

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	0 - 126
2	X-RAY DIFFRACTION	2	A	127 - 433
3	X-RAY DIFFRACTION	3	B	0 - 126
4	X-RAY DIFFRACTION	4	B	127 - 433

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