PDB-3tji: CRYSTAL STRUCTURE OF AN ENOLASE FROM ENTEROBACTER sp. 638 (EFI TA...

ID or keywords:

Entry

Database: PDB / ID: 3tji

Title

CRYSTAL STRUCTURE OF AN ENOLASE FROM ENTEROBACTER sp. 638 (EFI TARGET EFI-501662) with BOUND MG

Components

Mandelate racemase/muconate lactonizing enzyme, N-terminal domain protein

Keywords

LYASE /

Enolase /

dehydratase /

enzyme function initiative / EFI /

Structural Genomics

Function / homology

Function and homology information

amino acid catabolic process / magnesium ion binding
Similarity search - Function

Biological species

Enterobacter sp. 638 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MIR / Resolution: 1.8 Å

Authors

Vetting, M.W. / Toro, R. / Bhosle, R. / Wasserman, S.R. / Morisco, L.L. / Hillerich, B. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. ...

Citation

Journal: to be published
Title: Crystal structure of an enolase from enterobacter sp. 638 (efi target efi-501662) with boung mg
Authors: Vetting, M.W. / Toro, R. / Bhosle, R. / Wasserman, S.R. / Morisco, L.L. / Hillerich, B. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. / Zencheck, W.D. / ...

History

Deposition	Aug 24, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 14, 2011	Provider: repository / Type: Initial release
Revision 1.1	Feb 22, 2012	Group: Structure summary
Revision 1.2	Jan 24, 2018	Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.3	Sep 13, 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 / struct_ref_seq_dif / struct_site 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_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3tji.cif.gz	642 KB	Display	PDBx/mmCIF format
PDB format	pdb3tji.ent.gz	528.3 KB	Display	PDB format
PDBx/mmJSON format	3tji.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/tj/3tji ftp://data.pdbj.org/pub/pdb/validation_reports/tj/3tji	HTTPS FTP

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Related structure data

Related structure data	3gy1S S: Starting model for refinement
Similar structure data	4ggh-1 4hnl-1 3sbf-7 3twb-4 3twa-5 3twa-6 4k8g-1 3twb-5 4kpl-d 4il2-1 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
Other databases	TargetTrack: EFI-501662

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#50 - Feb 2004 Glycolytic Enzymes similarity (2)

Deposited unit

A: Mandelate racemase/muconate lactonizing enzyme, N-terminal domain protein

B: Mandelate racemase/muconate lactonizing enzyme, N-terminal domain protein

C: Mandelate racemase/muconate lactonizing enzyme, N-terminal domain protein

D: Mandelate racemase/muconate lactonizing enzyme, N-terminal domain protein

hetero molecules

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

1

A: Mandelate racemase/muconate lactonizing enzyme, N-terminal domain protein

B: Mandelate racemase/muconate lactonizing enzyme, N-terminal domain protein

C: Mandelate racemase/muconate lactonizing enzyme, N-terminal domain protein

D: Mandelate racemase/muconate lactonizing enzyme, N-terminal domain protein

hetero molecules

A: Mandelate racemase/muconate lactonizing enzyme, N-terminal domain protein

B: Mandelate racemase/muconate lactonizing enzyme, N-terminal domain protein

C: Mandelate racemase/muconate lactonizing enzyme, N-terminal domain protein

D: Mandelate racemase/muconate lactonizing enzyme, N-terminal domain protein

hetero molecules

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

Unit cell

Length a, b, c (Å)	182.150, 182.150, 104.800
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	94
Space group name H-M	P4₂2₁2

Components on special symmetry positions

ID	Model	Components
1	1	B-482- HOH
2	1	B-519- HOH
3	1	B-944- HOH
4	1	C-460- HOH
5	1	C-692- HOH

Details

biological unit is an octamer

#1: Protein	Mandelate racemase/muconate lactonizing enzyme, N-terminal domain protein Mass: 47420.836 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacter sp. 638 (bacteria) / Strain: strain C58 / Gene: Ent638_0932 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A4W7D6
#2: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Chemical	ChemComp-CL / CHLORIDE ION / Chloride Mass: 35.453 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Cl
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 1329 / 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: 2.29 Å³/Da / Density % sol: 46.32 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8 Details: Protein (10 mM Hepes, pH 7.8, 150 mM NaCl, 10% glycerol, 5 mM DTT, 5 mM MgCl2; Reservoir (2.5M NaCl, 100 mM Tris pH 7.5, 200 mM MgCl2); Cryoprotection (Reservoir + 20% glycerol), sitting ...Details: Protein (10 mM Hepes, pH 7.8, 150 mM NaCl, 10% glycerol, 5 mM DTT, 5 mM MgCl2; Reservoir (2.5M NaCl, 100 mM Tris pH 7.5, 200 mM MgCl2); Cryoprotection (Reservoir + 20% glycerol), sitting drop vapor diffuction, temperature 298K, VAPOR DIFFUSION, SITTING DROP

Crystal

Density Matthews: 2.29 Å³/Da / Density % sol: 46.32 %

Crystal grow

Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8
Details: Protein (10 mM Hepes, pH 7.8, 150 mM NaCl, 10% glycerol, 5 mM DTT, 5 mM MgCl2; Reservoir (2.5M NaCl, 100 mM Tris pH 7.5, 200 mM MgCl2); Cryoprotection (Reservoir + 20% glycerol), sitting ...

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 31-ID / Wavelength: 0.9793 Å

Detector

Type: RAYONIX MX225HE / Detector: CCD / Date: Aug 1, 2011 / Details: MIRRORS

Radiation

Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.9793 Å / Relative weight: 1

Reflection

Resolution: 1.799→182.149 Å / Num. all: 162263 / Num. obs: 162263 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.4 % / B_iso Wilson estimate: 21 Å² / R_sym value: 0.129 / Net I/σ(I): 8.1

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured all	Num. unique all	R_sym value	% possible all
1.8-1.9	6	0.497	1.5	140503	23392	0.497	99.8
1.9-2.01	6.7	0.358	2.1	148620	22164	0.358	99.8
2.01-2.15	7.5	0.274	2.6	156469	20907	0.274	99.9
2.15-2.32	8.5	0.225	3.1	166142	19497	0.225	99.9
2.32-2.54	9.8	0.186	3.4	176609	17993	0.186	100
2.54-2.84	11.2	0.15	3.9	183311	16346	0.15	100
2.84-3.28	12.2	0.122	4.3	176246	14477	0.122	100
3.28-4.02	13.6	0.095	5.1	167506	12301	0.095	100
4.02-5.69	13.7	0.078	5.8	132236	9643	0.078	100
5.69-182.149	13.1	0.068	6.7	72800	5543	0.068	99.8

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Processing

Software

Name	Version	Classification
SCALA	3.3.9	data scaling
REFMAC	5.5.0109	refinement
PDB_EXTRACT	3.1	data extraction
MAR345dtb		data collection
MOSFLM		data reduction
PHASES		phasing

Refinement

Method to determine structure:

MIR
Starting model: PDB entry 3GY1

3gy1

Resolution: 1.8→128.8 Å / Cor.coef. F_o:F_c: 0.956 / Cor.coef. F_o:F_c free: 0.948 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 7.401 / SU ML: 0.103 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.154 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2819	1966	1.2 %	RANDOM
R_work	0.2519	-	-	-
all	0.2523	159493	-	-
obs	0.2523	159493	98.22 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso max: 38.23 Å² / B_iso mean: 12.595 Å² / B_iso min: 2 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.52 Å²	0 Å²	0 Å²
2-	-	-0.52 Å²	0 Å²
3-	-	-	1.05 Å²

Refinement step

Cycle: LAST / Resolution: 1.8→128.8 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	12620	0	46	1329	13995

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.022	13281
X-RAY DIFFRACTION	r_angle_refined_deg	1.274	1.941	18175
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.766	5	1651
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.503	23.975	644
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.933	15	2050
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.879	15	81
X-RAY DIFFRACTION	r_chiral_restr	0.089	0.2	1955
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.021	10482
X-RAY DIFFRACTION	r_mcbond_it	0.519	1.5	8125
X-RAY DIFFRACTION	r_mcangle_it	0.904	2	13191
X-RAY DIFFRACTION	r_scbond_it	1.605	3	5156
X-RAY DIFFRACTION	r_scangle_it	2.508	4.5	4971

LS refinement shell

Resolution: 1.799→1.845 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.296	146	-
R_work	0.319	11667	-
all	-	11813	-
obs	-	-	99.4 %

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	1.8471	0.6246	0.4281	1.461	0.8673	2.4931	-0.0635	-0.0955	0.3967	0.02	-0.0803	0.15	-0.1342	0.0503	0.1438	0.07	0.0244	0.0119	0.0052	-0.0218	0.1922	33.054	95.601	56.453
2	0.3077	0.003	-0.0627	0.3118	-0.0408	0.3609	0.0059	-0.0363	0.0823	0.0344	-0.001	0.0149	-0.0609	0.0152	-0.0048	0.0447	0.0061	0.0002	0.0146	-0.0175	0.0935	36.211	83.464	61.755
3	1.0462	0.022	-0.1722	0.5503	0.0382	0.4341	-0.0049	-0.0655	0.0188	0.0887	-0.0166	-0.0262	0.002	0.0229	0.0215	0.0444	0.0089	-0.0086	0.0375	-0.012	0.0369	49.638	66.74	75.893
4	0.6137	0.0497	-0.0544	0.6901	-0.1438	0.3141	0.0047	-0.055	0.0988	0.0496	0.0015	0.0395	-0.0531	-0.0095	-0.0062	0.0352	0.0046	0.0021	0.0209	-0.0113	0.0589	33.432	78.568	64.201
5	2.8594	-0.6893	0.5793	1.1423	-0.4754	0.8697	-0.0067	-0.0732	0.1927	0.0674	-0.0143	0.0354	-0.1304	-0.1473	0.021	0.0531	-0.0014	-0.0119	0.0516	-0.0275	0.081	58.021	81.789	70.053
6	1.3492	-0.1127	-0.4257	2.0205	1.3281	3.6523	0.0061	-0.0897	-0.117	0.0929	-0.0152	0.2343	-0.0569	-0.1431	0.0091	0.002	-0.007	0.0129	0.0468	0.0089	0.1784	1.255	33.848	57.429
7	0.2456	-0.0851	0.051	0.411	-0.054	0.4128	-0.0017	0.0067	-0.0476	-0.0128	-0.0006	0.0956	0.0206	-0.0635	0.0023	0.0113	-0.014	0.0034	0.0352	-0.002	0.089	11.103	33.115	53.713
8	2.7463	0.2917	0.2791	5.4975	0.5312	2.9611	0.0571	-0.2352	0.0781	0.1274	-0.0552	0.188	-0.0357	-0.1157	-0.002	0.0405	-0.0045	0.0446	0.0996	0.021	0.0508	19.57	38.344	87.573
9	0.8532	-0.709	0.53	2.4795	-0.9798	0.6167	-0.0362	-0.1594	0.1009	0.2315	0.0296	0.1207	-0.1393	-0.0516	0.0066	0.107	0.0102	0.038	0.1075	-0.0221	0.0679	22.729	54.797	81.106
10	0.3512	0.0073	0.0808	0.4374	0.0398	0.2578	0.0121	-0.0434	-0.0261	0.0597	-0.0073	0.0653	0.0107	-0.029	-0.0048	0.0248	-0.004	0.0151	0.0376	0.0059	0.049	22.18	39.705	67.748
11	2.3426	-0.2211	1.5466	1.2222	-1.0425	3.755	-0.057	0.2177	0.2257	-0.045	-0.0368	-0.0506	-0.0922	0.086	0.0938	0.0698	-0.0174	0.0112	0.0275	0.007	0.154	62.899	95.964	47.352
12	0.2385	0.036	-0.0062	0.3327	0.0595	0.3864	-0.0075	0.0227	0.082	-0.0177	0.0028	-0.0212	-0.0654	0.0296	0.0047	0.0346	-0.0109	-0.0013	0.0096	0.0116	0.0962	63.042	84.62	45.553
13	6.1276	-1.2337	0.0877	1.7856	-0.1667	1.355	0.0044	0.2034	0.3485	-0.1162	0.0342	0.1451	-0.0889	-0.2137	-0.0385	0.1157	-0.0069	0.0022	0.0862	0.056	0.1179	46.528	76.548	23.57
14	0.3649	0.0405	0.0768	0.3983	0.0392	0.3039	-0.0095	0.054	0.0632	-0.0537	0.0096	-0.0112	-0.0388	-0.01	-0.0001	0.0409	-0.0017	0.0095	0.0241	0.0181	0.0595	56.352	73.397	35.339
15	3.8733	-0.3329	1.241	0.905	1.0559	0.7898	-0.023	0.1564	0.2706	-0.143	0.0587	-0.0894	-0.1417	0.1084	-0.0357	0.0592	-0.0008	-0.0084	0.054	0.0392	0.1007	38.856	81.628	34.578
16	0.5642	0.011	-0.0059	0.907	-0.0753	0.5187	0.0049	-0.0019	0.0349	-0.0117	-0.0195	0.1136	-0.0325	-0.0811	0.0147	0.0042	0.0136	0.0004	0.0351	-0.0041	0.0823	8.402	63.494	52.073
17	0.57	-0.2983	-0.2803	2.2793	1.8638	2.209	0.0316	0.1553	-0.0039	-0.1298	-0.0532	0.0594	-0.0681	-0.1312	0.0215	0.0308	0.0064	-0.0221	0.0691	0.0267	0.0645	21.149	60.467	22.258
18	1.2517	1.4846	-0.9314	3.474	-1.6215	0.8688	-0.0595	0.1618	-0.0789	-0.3435	0.0662	0.1829	0.2079	-0.0445	-0.0067	0.1182	-0.0022	-0.0413	0.1165	-0.0259	0.0802	22.91	40.673	22.996
19	0.4404	-0.0169	-0.1014	0.384	0.1139	0.3841	0.0143	0.0439	0.0228	-0.0527	-0.0056	0.0513	-0.0092	-0.0381	-0.0087	0.0218	0.0016	-0.012	0.0291	0.0085	0.0541	22.947	59.043	37.48
20	1.3681	-1.3016	-1.2049	5.3549	1.3087	1.6411	0.0267	0.2242	0.0584	-0.156	-0.0188	0.2986	-0.1092	-0.0722	-0.008	0.0344	-0.0029	-0.0376	0.0517	-0.0098	0.0942	15.24	38.773	34.559

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	2 - 18
2	X-RAY DIFFRACTION	2	A	19 - 165
3	X-RAY DIFFRACTION	3	A	166 - 253
4	X-RAY DIFFRACTION	4	A	254 - 381
5	X-RAY DIFFRACTION	5	A	382 - 399
6	X-RAY DIFFRACTION	6	B	3 - 18
7	X-RAY DIFFRACTION	7	B	19 - 126
8	X-RAY DIFFRACTION	8	B	127 - 148
9	X-RAY DIFFRACTION	9	B	149 - 194
10	X-RAY DIFFRACTION	10	B	195 - 399
11	X-RAY DIFFRACTION	11	C	3 - 18
12	X-RAY DIFFRACTION	12	C	19 - 147
13	X-RAY DIFFRACTION	13	C	148 - 165
14	X-RAY DIFFRACTION	14	C	166 - 381
15	X-RAY DIFFRACTION	15	C	382 - 399
16	X-RAY DIFFRACTION	16	D	3 - 116
17	X-RAY DIFFRACTION	17	D	117 - 154
18	X-RAY DIFFRACTION	18	D	155 - 196
19	X-RAY DIFFRACTION	19	D	197 - 381
20	X-RAY DIFFRACTION	20	D	382 - 399

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Yorodumi