PDB-7t93: Crystal Structure of Fumarate hydratase class II from Mycobacteri...

ID or keywords:

Entry

Database: PDB / ID: 7t93

Title

Crystal Structure of Fumarate hydratase class II from Mycobacterium ulcerans in complex with L-Malate

Components

Fumarate hydratase class II

Keywords

LYASE / SSGCID / Tricarboxylic acid cycle / fumarate metabolic process / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease

Function / homology

Function and homology information

fumarate hydratase activity / fumarate hydratase / fumarate metabolic process / tricarboxylic acid cycle / cytoplasm
Similarity search - Function

Biological species

Mycobacterium ulcerans Agy99 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.65 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Funding support

1items

Citation

Journal: to be published
Title: Crystal Structure of Fumarate hydratase class II from Mycobacterium ulcerans in complex with L-Malate
Authors: DeBouver, N.D. / Abendroth, J. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.

History

Deposition	Dec 17, 2021	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 13, 2022	Provider: repository / Type: Initial release
Revision 1.1	Oct 18, 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	7t93.cif.gz	718.1 KB	Display	PDBx/mmCIF format
PDB format	pdb7t93.ent.gz	585.8 KB	Display	PDB format
PDBx/mmJSON format	7t93.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7t93_validation.pdf.gz	2 MB	Display	wwPDB validaton report
Full document	7t93_full_validation.pdf.gz	2 MB	Display
Data in XML	7t93_validation.xml.gz	83.7 KB	Display
Data in CIF	7t93_validation.cif.gz	129.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/t9/7t93 ftp://data.pdbj.org/pub/pdb/validation_reports/t9/7t93	HTTPS FTP

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Related structure data

Related structure data	3qbpS S: Starting model for refinement
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Other databases	TargetTrack: MyulA.01507.a.A1

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#154 - Oct 2012 Citric Acid Cycle similarity (11) #127 - Jul 2010 Crystallins similarity (7) #190 - Oct 2015 Two-component Systems similarity (1)

Deposited unit

A: Fumarate hydratase class II

B: Fumarate hydratase class II

C: Fumarate hydratase class II

D: Fumarate hydratase class II

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	98.040, 120.820, 158.780
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Fumarate hydratase class II / Fumarase C / Aerobic fumarase / Iron-independent fumarase Mass: 52471.172 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium ulcerans Agy99 (bacteria) Strain: Agy99 / Gene: fum, fumC, MUL_0181 / Plasmid: MyulA.01507.a.A1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0PKR5, fumarate hydratase
#2: Chemical	ChemComp-LMR / (2S)-2-hydroxybutanedioic acid / L-Malate Mass: 134.087 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₄H₆O₅ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₁₄O₂ / Comment: precipitant*YM
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 2165 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.24 Å³/Da / Density % sol: 45.1 %
Crystal grow	Temperature: 287 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: [Protein: MyulA.01507.a.A1.PW29760 25mg/mL] [Barcode: 321232f4] [Collection: aps21idf 9/23/21] [Crystallization conditions: Molecular Dimensions Morpheus sparse matrix screen, condition F4: ...Details: [Protein: MyulA.01507.a.A1.PW29760 25mg/mL] [Barcode: 321232f4] [Collection: aps21idf 9/23/21] [Crystallization conditions: Molecular Dimensions Morpheus sparse matrix screen, condition F4: 0.1M MES/Imidazole pH 6.5, 12.5%(w/v) PEG 1000, 12.5%(w/v) PEG 3350, 12.5%(v/v) MPD, 0.02M each of (D-glucose, D-mannose, D-galactose, L-fucose, D-xylose, N-acetyl-D-glusosamine)] [Cryo: Direct]

Crystal

Density Matthews: 2.24 Å³/Da / Density % sol: 45.1 %

Crystal grow

Temperature: 287 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: [Protein: MyulA.01507.a.A1.PW29760 25mg/mL] [Barcode: 321232f4] [Collection: aps21idf 9/23/21] [Crystallization conditions: Molecular Dimensions Morpheus sparse matrix screen, condition F4: ...

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 21-ID-F / Wavelength: 0.97872 Å

Detector

Type: RAYONIX MX-300 / Detector: CCD / Date: Sep 23, 2021 / Details: Beryllium Lenses

Radiation

Monochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97872 Å / Relative weight: 1

Reflection

Resolution: 1.65→48.48 Å / Num. obs: 225586 / % possible obs: 99.9 % / Redundancy: 6.219 % / B_iso Wilson estimate: 11.63 Å² / CC_1/2: 0.998 / R_merge(I) obs: 0.109 / R_rim(I) all: 0.118 / Χ²: 0.904 / Net I/σ(I): 11.91 / Num. measured all: 1402855 / Scaling rejects: 14

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. possible	Num. unique obs	CC_1/2	R_rim(I) all	% possible all
1.65-1.69	6.203	0.553	3.25	102604	16603	16540	0.898	0.602	99.6
1.69-1.74	6.207	0.481	3.73	99626	16084	16051	0.92	0.524	99.8
1.74-1.79	6.213	0.406	4.35	97551	15743	15700	0.943	0.441	99.7
1.79-1.84	6.222	0.359	4.95	94645	15235	15212	0.955	0.391	99.8
1.84-1.91	6.226	0.297	5.87	92300	14849	14824	0.967	0.323	99.8
1.91-1.97	6.234	0.254	6.9	89248	14334	14317	0.976	0.277	99.9
1.97-2.05	6.231	0.2	8.56	86247	13851	13842	0.985	0.218	99.9
2.05-2.13	6.244	0.175	9.68	83156	13327	13318	0.988	0.191	99.9
2.13-2.22	6.244	0.143	11.57	80030	12821	12817	0.991	0.155	100
2.22-2.33	6.243	0.119	13.31	76378	12239	12234	0.993	0.13	100
2.33-2.46	6.243	0.11	14.42	72715	11653	11647	0.994	0.12	99.9
2.46-2.61	6.246	0.1	15.64	68904	11038	11031	0.995	0.109	99.9
2.61-2.79	6.25	0.087	17.52	64930	10396	10388	0.996	0.095	99.9
2.79-3.01	6.247	0.076	19.83	60629	9714	9706	0.996	0.083	99.9
3.01-3.3	6.24	0.067	22.06	55782	8944	8940	0.997	0.072	100
3.3-3.69	6.222	0.058	24.94	50579	8133	8129	0.997	0.063	100
3.69-4.26	6.212	0.053	27.37	44796	7218	7211	0.998	0.057	99.9
4.26-5.22	6.166	0.049	28.07	37816	6136	6133	0.998	0.053	100
5.22-7.38	6.089	0.052	25.8	29283	4812	4809	0.998	0.057	99.9
7.38-48.48	5.713	0.045	28.24	15636	2771	2737	0.998	0.05	98.8

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Processing

Software

Name	Version	Classification
XDS		data reduction
XSCALE		data scaling
PHENIX	1.20-4438	refinement
PDB_EXTRACT	3.27	data extraction
MoRDa		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3QBP

3qbp

Resolution: 1.65→48.48 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 14.94 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1607	2020	0.9 %
R_work	0.1376	223498	-
obs	0.1378	225518	99.84 %

Solvent computation

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

Displacement parameters

B_iso max: 91.86 Å² / B_iso mean: 15.9495 Å² / B_iso min: 4.4 Å²

Refinement step

Cycle: final / Resolution: 1.65→48.48 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	13511	0	62	2207	15780
B_iso mean	-	-	19.8	26.83	-
Num. residues	-	-	-	-	1841

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 14 / % reflection obs: 100 %

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all
1.65-1.69	0.2235	134	0.1833	15804	15938
1.69-1.74	0.2155	154	0.1712	15750	15904
1.74-1.79	0.1859	162	0.1588	15823	15985
1.79-1.85	0.1846	147	0.1539	15796	15943
1.85-1.91	0.1931	165	0.1493	15863	16028
1.91-1.99	0.2051	131	0.1497	15906	16037
1.99-2.08	0.1696	119	0.1429	15931	16050
2.08-2.19	0.1747	141	0.1341	15880	16021
2.19-2.33	0.1501	139	0.1277	15962	16101
2.33-2.51	0.1642	125	0.1297	15983	16108
2.51-2.76	0.1466	146	0.1355	15983	16129
2.76-3.16	0.143	166	0.1318	16069	16235
3.16-3.98	0.1273	141	0.1198	16185	16326
3.98-48.48	0.1494	150	0.1349	16563	16713

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	2.2875	0.9257	-0.061	0.8129	-0.4939	1.6703	-0.0069	-0.3016	-0.2295	0.2489	-0.052	-0.197	0.075	0.0863	0.0383	0.1766	0.01	-0.0431	0.1777	0.0421	0.1383	14.1299	5.712	63.265
2	0.6555	0.2775	-0.0665	2.4015	0.3242	0.541	-0.0253	-0.0405	0.0247	0.0897	0.0537	-0.1429	-0.0647	0.0892	-0.0377	0.0778	-0.0026	-0.0162	0.0788	0.0049	0.059	12.5389	18.8117	52.2243
3	0.1389	0.0088	-0.0205	0.1647	0.0383	0.3248	0.0033	0.0016	0.0338	0.0163	0.0093	-0.0179	-0.0521	0.0358	-0.0223	0.0798	-0.0042	-0.0027	0.0547	0.005	0.0864	10.4483	19.8545	29.0526
4	2.4164	0.0778	1.3918	0.2901	-0.0585	2.9339	0.0269	0.4955	-0.0277	-0.1066	0.0072	-0.0095	0.0678	0.163	-0.0278	0.1536	-0.0082	0.0322	0.1639	0.0245	0.1234	13.4532	17.1445	-11.8547
5	1.8406	0.3887	1.0288	1.9564	0.3969	4.7479	-0.0691	0.5793	0.2402	-0.4722	0.0521	-0.176	-0.52	0.0517	0.0456	0.2565	-0.0027	0.055	0.3635	0.0863	0.2087	12.0976	23.7116	-20.5003
6	2.1844	-0.4782	0.1045	1.1047	0.3983	1.5362	-0.067	0.2845	-0.2228	-0.081	-0.0086	0.1942	0.0677	-0.1527	0.0132	0.1054	-0.0195	-0.0155	0.1744	-0.0157	0.1287	-15.1907	6.6647	-15.7555
7	0.4855	-0.1162	-0.0303	0.5929	0.0908	0.3148	0.0053	0.1255	0.0498	-0.0489	-0.0128	0.0566	-0.0638	-0.0649	0.0049	0.0889	0.018	-0.0055	0.1078	0.0219	0.0849	-12.3556	19.8713	-4.4072
8	0.1287	0.0357	-0.1004	0.0865	-0.1055	0.645	0.0048	0.0275	0.0529	0.0044	0.0067	0.017	-0.1278	-0.067	-0.037	0.1031	0.0203	0.0026	0.066	0.0102	0.1024	-9.3686	26.5063	22.7626
9	0.261	0.0435	-0.1727	0.1898	-0.0418	0.5089	-0.0029	0.0156	0.0131	0.0058	0.0047	0.0349	-0.0131	-0.08	-0.0071	0.0692	0.01	-0.0017	0.0627	0.0082	0.0833	-14.9262	12.4278	26.3785
10	2.724	-0.1064	0.5593	2.2041	-0.1254	2.6	0.0214	-0.739	-0.1143	0.6678	0.0075	-0.267	-0.0728	-0.0127	-0.0235	0.3158	-0.0009	-0.0228	0.2408	0.0189	0.2121	-14.651	16.521	59.8728
11	3.1807	-0.1142	0.5419	2.0659	0.2055	3.1351	-0.2303	-1.0161	0.0652	1.3608	-0.0488	-0.1252	-0.3662	0.06	0.0636	0.6866	0.031	0.0126	0.4867	-0.043	0.2871	-13.7556	23.0114	68.7856
12	0.994	-0.2039	0.0838	0.2182	-0.3834	3.6372	0.1125	-0.1702	0.142	0.044	0.0641	-0.0842	-0.1214	0.3326	-0.1131	0.088	-0.0103	-0.0001	0.2366	-0.0365	0.1318	41.1044	6.4437	26.146
13	0.8147	-0.4813	-0.0349	2.0098	-0.0949	0.68	-0.0469	-0.1105	-0.1039	0.1135	0.0434	-0.0245	0.1015	0.2236	-0.0176	0.0752	0.0353	0.0042	0.1419	0.0159	0.0832	30.1652	-5.5144	28.6686
14	0.7435	-0.0146	-0.3622	0.0447	-0.0181	0.4639	-0.0575	-0.0795	-0.089	0.0036	0.0128	-0.0099	0.0936	0.0825	0.0555	0.0816	0.0143	0.0046	0.0408	0.007	0.089	9.4781	-10.4923	31.9406
15	0.8759	-0.1078	-0.7106	0.0238	0.1583	0.9454	0.0028	0.0272	-0.0154	-0.0033	0.0067	-0.0284	0.0308	-0	-0.007	0.0754	-0.0041	-0.0012	0.0366	0.0023	0.0851	8.151	-10.5479	27.8882
16	2.061	0.3613	0.1634	0.8727	-0.5281	0.6783	0.0187	-0.2068	0.2231	0.2262	-0.0252	0.0573	-0.1915	-0.0189	0.0081	0.1292	0.0062	0.0176	0.0998	-0.0139	0.0816	-7.7917	6.3793	56.1025
17	0.716	-0.0264	-0.8543	0.017	-0.0327	1.9468	0.011	-0.0111	0.0024	-0.0062	0.0118	-0.0014	0.0214	0.0323	-0.016	0.063	0.001	0.0001	0.0352	-0.001	0.0781	7.4877	-0.2724	31.6138
18	4.3299	-0.182	0.8549	0.1002	0.1936	1.6327	-0.084	-0.1251	0.0729	-0.007	-0.0105	0.0099	-0.0914	-0.3339	0.0871	0.1119	-0.0039	0.0222	0.09	0.0204	0.1041	-31.1374	-3.4963	47.5668
19	4.9552	-0.5384	0.5252	2.02	-0.4691	2.1651	-0.0701	0.0566	-0.4306	0.1356	-0.0521	0.1806	0.1163	-0.5811	0.0811	0.1386	-0.0469	0.0136	0.2456	-0.0056	0.1105	-40.1471	-10.1701	49.0081
20	0.8119	0.1429	-0.1506	0.7141	0.0969	0.4932	-0.0299	0.1643	-0.0541	-0.0649	0.0158	0.0425	0.0337	-0.22	0.0128	0.0729	-0.0138	-0.0043	0.1723	-0.0108	0.0783	-34.0077	-2.9019	19.9605
21	0.3056	0.0199	-0.1316	0.1102	0.0172	0.3567	-0.0265	0.0589	-0.0417	-0.0138	0.0078	0.0084	0.0412	-0.0455	0.0258	0.0639	-0.0011	0.0003	0.0458	-0.0056	0.0696	-4.934	-6.4799	12.8754
22	2.7857	0.1272	-0.1379	1.3983	0.1884	1.898	-0.0232	0.0346	-0.1374	-0.1029	0.0664	-0.1124	0.0236	0.2947	-0.0367	0.0978	0.0228	0.0199	0.1598	-0.0319	0.0928	39.2573	-6.1031	0.9367

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 (resid 12 through 34 )	A	12 - 34
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 35 through 110 )	A	35 - 110
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 111 through 391 )	A	111 - 391
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 392 through 436 )	A	392 - 436
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 437 through 472 )	A	437 - 472
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 12 through 34 )	B	12 - 34
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 35 through 162 )	B	35 - 162
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 163 through 276 )	B	163 - 276
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 277 through 391 )	B	277 - 391
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 392 through 436 )	B	392 - 436
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 437 through 472 )	B	437 - 472
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 14 through 34 )	C	14 - 34
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 35 through 110 )	C	35 - 110
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 111 through 245 )	C	111 - 245
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 246 through 303 )	C	246 - 303
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 304 through 332 )	C	304 - 332
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 333 through 391 )	C	333 - 391
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 392 through 436 )	C	392 - 436
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 437 through 472 )	C	437 - 472
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 14 through 110 )	D	14 - 110
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 111 through 422 )	D	111 - 422
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 423 through 473 )	D	423 - 473

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-Yorodumi

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Movie

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Structure viewers

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Viewer log

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This page

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This web site

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Options

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Open data

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Basic information

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Structure visualization

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Downloads & links

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Download

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Validation report

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Related structure data

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Links

-
Assembly

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Components

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Experimental details

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Experiment

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Sample preparation

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Data collection

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Processing

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About Yorodumi

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News

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Feb 9, 2022. New format data for meta-information of EMDB entries

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Aug 12, 2020. Covid-19 info

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Mar 5, 2020. Novel coronavirus structure data

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Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

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Jul 12, 2017. Major update of PDB

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Yorodumi