PDB-4e5t: Crystal structure of a putative Mandelate racemase/Muconate lacto...

ID or keywords:

Entry

Database: PDB / ID: 4e5t

Title

Crystal structure of a putative Mandelate racemase/Muconate lactonizing enzyme (Target PSI-200750) from Labrenzia alexandrii DFL-11

Components

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

Keywords

ISOMERASE /

Racemase /

Mandelate racemase /

aldolase /

Structural genomics / PSI-Biology / New York Structural Genomics Research Consortium / NYSGRC

Function / homology

Enolase-like C-terminal domain / Enolase-like, N-terminal domain / Enolase-like; domain 1 /

TIM Barrel / Alpha-Beta Barrel / 2-Layer Sandwich / Alpha Beta / :

Function and homology information

Biological species

Labrenzia alexandrii (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.9 Å

Authors

Kumar, P.R. / Bonanno, J. / Chowdhury, S. / Foti, R. / Gizzi, A. / Glen, S. / Hammonds, J. / Hillerich, B. / Matikainen, B. / Seidel, R. ...

Citation

Journal: to be published
Title: Crystal structure of a putative MR/ML enzyme from Labrenzia alexandrii DFL-11
Authors: Kumar, P.R. / Bonanno, J. / Chowdhury, S. / Foti, R. / Gizzi, A. / Glen, S. / Hammonds, J. / Hillerich, B. / Matikainen, B. / Seidel, R. / Toro, R. / Zencheck, W. / Almo, S.C.

History

Deposition	Mar 14, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 28, 2012	Provider: repository / Type: Initial release
Revision 1.1	Feb 28, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_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_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_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_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_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	4e5t.cif.gz	1.1 MB	Display	PDBx/mmCIF format
PDB format	pdb4e5t.ent.gz	973.3 KB	Display	PDB format
PDBx/mmJSON format	4e5t.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/e5/4e5t ftp://data.pdbj.org/pub/pdb/validation_reports/e5/4e5t	HTTPS FTP

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Related structure data

Similar structure data	4h19-2 4ggb-1 3sjn-1 2qjj-3 4h19-3 4h19-1 4fi4-1 4jn8-1 3ssz-1 3tj4-1 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search
Other databases	TargetTrack: NYSGRC-200750

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

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

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

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

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

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

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

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

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

hetero molecules

355 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	98.900, 156.880, 218.240
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Details

The biological assembly is an octamer in the asymmetric unit

#1: Protein	Mandelate racemase / muconate lactonizing enzyme, C-terminal domain protein Mass: 44320.098 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Labrenzia alexandrii (bacteria) / Strain: DFL-11 / Gene: SADFL11_187 / Plasmid: PET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B9R417
#2: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 59 / 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: 2.39 Å³/Da / Density % sol: 48.48 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.5 Details: Protein (20 mM Hepes, pH 7.5, 150 mM NaCl, 10% glycerol; Reservoir (20% PEG1000, 0.1M Cacodylate 6.5, 0.2M MgCl2 Wizard II #44); Cryoprotection (Ethylene glycol), Sitting Drop Vapor ...Details: Protein (20 mM Hepes, pH 7.5, 150 mM NaCl, 10% glycerol; Reservoir (20% PEG1000, 0.1M Cacodylate 6.5, 0.2M MgCl2 Wizard II #44); Cryoprotection (Ethylene glycol), Sitting Drop Vapor Diffusion, temperature 298K, VAPOR DIFFUSION, SITTING DROP

Crystal

Density Matthews: 2.39 Å³/Da / Density % sol: 48.48 %

Crystal grow

Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: Protein (20 mM Hepes, pH 7.5, 150 mM NaCl, 10% glycerol; Reservoir (20% PEG1000, 0.1M Cacodylate 6.5, 0.2M MgCl2 Wizard II #44); Cryoprotection (Ethylene glycol), Sitting Drop Vapor ...

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

NSLS

/ Beamline: X29A / Wavelength: 1.075 Å

Detector

Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 23, 2011 / Details: MIRRORS

Radiation

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

Radiation wavelength

Wavelength: 1.075 Å / Relative weight: 1

Reflection

Highest resolution: 2.9 Å / Num. obs: 75923 / % possible obs: 100 % / Observed criterion σ(I): -3 / B_iso Wilson estimate: 49.935 Å² / R_merge(I) obs: 0.14 / Net I/σ(I): 18.73

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Highest resolution (Å)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. unique obs	% possible all
2.9-2.98		0.953	2.89	61261	5501	100
2.98-3.06		0.711	3.88	60557	5413	100
3.06-3.15		0.634	4.34	59219	5281	100
3.15-3.24		0.489	5.6	57334	5114	100
3.24-3.35		0.423	6.42	55531	4947	100
3.35-3.47		0.321	8.27	53938	4813	100
3.47-3.6		0.236	11.25	51929	4640	100
3.6-3.74		0.189	13.97	50128	4484	100
3.74-3.91		0.146	17.72	47911	4298	100
3.91-4.1		0.114	22.05	45841	4111	100
4.1-4.32		0.094	25.98	43465	3933	100
4.32-4.59		0.082	28.94	41052	3708	100
4.59-4.9		0.073	31.91	38773	3514	100
4.9-5.29		0.073	31.81	35747	3268	100
5.29-5.8		0.081	29.1	32948	3045	100
5.8-6.48		0.084	28.04	28772	2725	100
6.48-7.49		0.055	39.91	27049	2447	100
7.49-9.17		0.033	58.41	22788	2090	100
9.17-12.97		0.027	66.51	17388	1641	100
	12.97	0.029	64.12	9227	950	97.5

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Processing

Software

Name	Version	Classification
XSCALE		data scaling
PHENIX	1.7.3_928	refinement
PDB_EXTRACT	3.1	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.9→49.45 Å / Occupancy max: 1 / Occupancy min: 0.45 / FOM work R set: 0.8177 / SU ML: 0.41 / σ(F): 1.34 / Phase error: 24.88 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2422	3817	5.03 %
R_work	0.1635	-	-
obs	0.1676	75910	99.97 %

Solvent computation

Shrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 29.83 Å² / k_sol: 0.326 e/Å³

Displacement parameters

B_iso max: 197.15 Å² / B_iso mean: 56.4834 Å² / B_iso min: 9.85 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	2.5152 Å²	-0 Å²	0 Å²
2-	-	-9.5236 Å²	-0 Å²
3-	-	-	7.0084 Å²

Refinement step

Cycle: LAST / Resolution: 2.9→49.45 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	23603	0	8	59	23670

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	24232
X-RAY DIFFRACTION	f_angle_d	1.188	32899
X-RAY DIFFRACTION	f_chiral_restr	0.077	3555
X-RAY DIFFRACTION	f_plane_restr	0.006	4310
X-RAY DIFFRACTION	f_dihedral_angle_d	15.246	8776

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 27 / % reflection obs: 100 %

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all
2.9-2.9368	0.4078	140	0.2908	2574	2714
2.9368-2.9754	0.3644	140	0.2324	2646	2786
2.9754-3.0161	0.3066	145	0.2115	2651	2796
3.0161-3.0592	0.343	129	0.2108	2624	2753
3.0592-3.1049	0.3595	146	0.2261	2667	2813
3.1049-3.1534	0.2868	121	0.2007	2644	2765
3.1534-3.2051	0.2992	137	0.1876	2665	2802
3.2051-3.2603	0.3006	131	0.1815	2627	2758
3.2603-3.3196	0.287	128	0.1809	2673	2801
3.3196-3.3834	0.2819	145	0.1779	2618	2763
3.3834-3.4525	0.283	121	0.1863	2672	2793
3.4525-3.5275	0.2777	136	0.1645	2664	2800
3.5275-3.6096	0.228	159	0.1567	2607	2766
3.6096-3.6998	0.2455	138	0.1433	2671	2809
3.6998-3.7998	0.2332	149	0.1535	2660	2809
3.7998-3.9116	0.2643	133	0.1472	2647	2780
3.9116-4.0378	0.2079	142	0.1378	2670	2812
4.0378-4.182	0.2097	144	0.1251	2652	2796
4.182-4.3494	0.1853	145	0.1255	2682	2827
4.3494-4.5472	0.1968	125	0.1291	2700	2825
4.5472-4.7867	0.2144	137	0.1193	2674	2811
4.7867-5.0864	0.2056	168	0.1424	2665	2833
5.0864-5.4786	0.2336	153	0.1551	2695	2848
5.4786-6.0291	0.2715	154	0.1865	2683	2837
6.0291-6.8995	0.2506	143	0.1771	2725	2868
6.8995-8.685	0.1928	149	0.1497	2771	2920
8.685-49.4572	0.2132	159	0.1998	2866	3025

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	1.5155	-0.1353	-0.0113	1.5389	0.0917	2.1791	0.0223	-0.2029	0.1064	0.1946	0.1005	0.0816	0.0092	0.1061	-0.0779	0.2273	-0.0073	0.0093	0.1099	-0.0513	0.0926	-25.4436	36.3854	-4.3
2	0.4914	0.4137	-0.0528	1.4314	-0.4953	1.0801	0.0751	0.1683	0.0467	-0.0502	-0.076	0.3644	-0.1331	-0.0998	-0.0213	0.1818	0.0606	-0.1117	0.2535	0.0284	0.3454	-45.7201	21.7628	-23.3494
3	0.6934	-0.1404	0.2409	1.519	0.34	1.0768	-0.0385	-0.101	0.0251	0.222	0.0019	0.3141	-0.1344	-0.1707	0.0039	0.2098	0.0188	0.0219	0.0883	0.02	0.0893	-33.7424	33.1446	-15.6386
4	0.6907	-0.1188	0.2919	1.3589	0.076	1.9004	0.0533	0.5536	0.2165	-0.4327	0.0387	-0.1677	-0.063	0.3145	-0.0372	0.3675	-0.0466	0.0327	0.4809	0.1597	0.1815	-4.9455	37.928	-33.4876
5	0.4112	0.0414	0.1027	1.7612	0.5934	1.3263	-0.021	0.2272	-0.1165	-0.2239	0.0346	-0.326	-0.056	0.3395	-0.0573	0.1693	-0.0099	0.0161	0.3071	-0.0843	0.2039	8.3305	12.3467	-21.1738
6	0.9731	-0.0724	0.4717	1.7228	-0.3537	0.9138	0.0201	0.4405	-0.0038	-0.3081	-0.0015	-0.4828	-0.2256	0.273	-0.0001	0.2907	-0.0612	0.0816	0.3424	0.0066	0.1634	0.8412	29.4584	-23.7974
7	2.0917	-0.1625	-0.321	2.1242	-0.2003	0.852	0.1215	0.0239	-0.4672	0.236	-0.1214	0.2304	0.0889	-0.0493	0.0018	0.2313	0.0092	0.0905	0.1497	0.0903	0.5231	-44.2236	-18.8172	4.0806
8	0.4374	0.1842	0.1052	0.4412	0.6212	1.1617	0.0052	0.2159	-0.3024	-0.0319	-0.0187	0.3134	0.1143	-0.1038	-0.0165	0.163	-0.0003	-0.1771	0.2748	-0.1235	0.5775	-52.8194	-6.3806	-23.5572
9	1.1176	0.4906	-0.3982	0.7271	-0.6058	1.2537	-0.06	0.2099	-0.4225	0.1239	0.0521	0.3704	0.2972	-0.3135	-0.015	0.1644	-0.0136	0.0214	0.1093	-0.0127	0.4963	-50.2478	-9.7581	-4.9998
10	0.2967	-0.1247	0.0126	1.6862	0.0744	0.3363	-0.0149	0.0762	-0.3842	-0.0009	0.0349	0.3861	0.1454	-0.0616	0.029	0.2165	-0.0185	-0.0545	0.1134	-0.1758	0.8111	-34.5683	-37.9077	-14.8753
11	0.922	-0.4194	-0.6548	0.7556	0.5977	0.6442	-0.0385	-0.0506	-0.3499	0.0928	0.0117	-0.0764	0.1478	0.1595	0.0123	0.1305	0.0794	-0.1712	0.0793	0.0159	0.4376	-8.545	-22.5485	-6.2875
12	0.8175	-0.5676	-0.0331	2.3818	-0.3013	0.5001	-0.0797	-0.0576	-0.4095	0.3213	0.0225	0.0606	0.137	-0.0057	-0.002	0.2206	0.0571	-0.0478	0.0221	-0.2543	0.5474	-20.8901	-34.5563	-14.3551
13	0.7278	-0.4409	0.4188	2.5376	-0.6756	3.374	0.018	-0.1096	0.0016	0.3001	-0.167	0.01	-0.2302	0.0461	0.1201	0.254	0.0054	0.1258	0.1701	0.0233	0.1798	-34.7826	14.8312	11.8356
14	0.9887	0.3288	-0.7339	0.9213	-0.6812	0.8836	0.1352	-0.128	-0.1017	0.322	-0.0972	-0.159	-0.0858	0.1657	-0.0477	0.2556	-0.0405	-0.115	0.2282	0.033	0.199	-6.1293	4.8893	2.6501
15	1.5914	-0.2765	0.1687	0.6561	0.2433	2.0203	0.0091	-0.2879	0.0361	0.3887	-0.0587	0.0568	-0.2519	0.1512	0.0035	0.3097	-0.0464	0.0539	0.1808	0.0513	0.0844	-24.4985	4.9432	10.7826
16	0.3446	-0.0568	0.0855	0.3012	0.3064	0.3567	0.1104	0.363	-0.3047	-0.3824	-0.0553	-0.0107	0.097	0.0433	0.1086	0.5606	0.0916	0.0382	0.8231	-0.5006	0.4235	-4.59	-14.7903	-60.1658
17	0.9576	0.0951	-0.422	0.6687	-0.2223	1.2684	0.12	0.2081	-0.3652	-0.2701	-0.0303	-0.2183	0.1022	0.1904	-0.0037	0.2387	0.1016	0.0123	0.3978	-0.2473	0.5371	6.1185	-15.6895	-30.6119
18	0.5804	-0.0774	-0.3392	0.6928	-0.0166	0.8238	-0.0281	0.2765	-0.2846	-0.3508	-0.0018	-0.2169	0.1867	0.2819	-0.0121	0.2484	0.0867	0.133	0.4241	-0.3969	0.1825	3.31	-11.5974	-48.8632
19	0.4281	0.1345	-0.1342	1.6858	-0.0162	2.1591	0.0243	0.3487	0.0008	-0.5535	-0.1513	-0.0849	-0.2904	-0.1158	0.0027	0.5499	-0.0586	0.0958	0.8536	0.0417	0.1427	-2.116	20.8026	-56.1988
20	0.2309	0.2048	-0.31	0.5386	0.1113	1.0245	0.0133	0.4584	0.0142	-0.3939	0.077	0.1533	-0.1316	0.0122	0.0033	0.446	0.0901	-0.1787	0.5389	-0.0616	0.1003	-32.7962	18.3243	-49.2917
21	0.6151	0.1407	0.1537	1.3531	-1.0335	1.2364	-0.0107	0.5422	0.0393	-0.4367	0.026	0.0482	-0.3787	-0.0636	0.0106	0.6141	0.0785	-0.0061	0.7481	-0.1258	0.1341	-15.0758	14.7882	-57.8378
22	0.88	-0.0331	-0.3026	1.4106	0.811	0.8616	-0.0175	0.5447	-0.2959	-0.2803	0.0022	0.0432	0.0168	-0.0266	0.0476	0.3948	0.0765	-0.0633	0.5616	-0.5486	0.6418	-21.1324	-34.771	-47.8564
23	0.3957	0.3062	-0.2901	0.6096	-0.4089	0.3917	-0.0923	0.3876	-0.2704	-0.3554	0.1621	0.1445	0.0089	-0.1189	-0.0494	0.5137	0.0278	-0.2968	0.6465	-0.2975	0.4104	-40.1226	-9.6175	-49.2843
24	0.5136	0.0793	-0.0825	1.1464	-0.0645	0.6307	-0.1478	0.4655	-0.3275	-0.641	0.0779	0.219	0.1456	-0.0992	0.007	0.4515	0.0128	-0.1797	0.449	-0.4292	0.5106	-33.1887	-27.8447	-44.8657

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 resseq 1:117	A	1 - 117
2	X-RAY DIFFRACTION	2	chain 'A' and resseq 118:263	A	118 - 263
3	X-RAY DIFFRACTION	3	chain 'A' and resseq 264:402	A	264 - 402
4	X-RAY DIFFRACTION	4	chain 'B' and resseq 1:117	B	1 - 117
5	X-RAY DIFFRACTION	5	chain 'B' and resseq 118:263	B	118 - 263
6	X-RAY DIFFRACTION	6	chain 'B' and resseq 264:402	B	264 - 402
7	X-RAY DIFFRACTION	7	chain 'C' and resseq 1:117	C	1 - 117
8	X-RAY DIFFRACTION	8	chain 'C' and resseq 118:263	C	118 - 263
9	X-RAY DIFFRACTION	9	chain 'C' and resseq 264:402	C	264 - 402
10	X-RAY DIFFRACTION	10	chain 'D' and resseq 1:117	D	1 - 117
11	X-RAY DIFFRACTION	11	chain 'D' and resseq 118:263	D	118 - 263
12	X-RAY DIFFRACTION	12	chain 'D' and resseq 264:402	D	264 - 402
13	X-RAY DIFFRACTION	13	chain 'E' and resseq 1:117	E	1 - 117
14	X-RAY DIFFRACTION	14	chain 'E' and resseq 118:263	E	118 - 263
15	X-RAY DIFFRACTION	15	chain 'E' and resseq 264:402	E	264 - 402
16	X-RAY DIFFRACTION	16	chain 'F' and resseq 1:117	F	1 - 117
17	X-RAY DIFFRACTION	17	chain 'F' and resseq 118:263	F	118 - 263
18	X-RAY DIFFRACTION	18	chain 'F' and resseq 264:402	F	264 - 402
19	X-RAY DIFFRACTION	19	chain 'G' and resseq 1:117	G	1 - 117
20	X-RAY DIFFRACTION	20	chain 'G' and resseq 118:263	G	118 - 263
21	X-RAY DIFFRACTION	21	chain 'G' and resseq 264:402	G	264 - 402
22	X-RAY DIFFRACTION	22	chain 'H' and resseq 1:117	H	1 - 117
23	X-RAY DIFFRACTION	23	chain 'H' and resseq 118:263	H	118 - 263
24	X-RAY DIFFRACTION	24	chain 'H' and resseq 264:402	H	264 - 402

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