PDB-4adl: Crystal structures of Rv1098c in complex with malate

ID or keywords:

Entry

Database: PDB / ID: 4adl

Title

Crystal structures of Rv1098c in complex with malate

Components

FUMARATE HYDRATASE CLASS II

Keywords

LYASE / TRICARBOXYLIC ACID CYCLE

Function / homology

Function and homology information

tricarboxylic acid cycle heteromeric enzyme complex / fumarate hydratase activity / fumarate hydratase / fumarate metabolic process / tricarboxylic acid cycle / peptidoglycan-based cell wall / extracellular region / plasma membrane / cytosol
Similarity search - Function

Biological species

MYCOBACTERIUM TUBERCULOSIS (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.2 Å

Authors

Mechaly, A.E. / Haouz, A. / Miras, I. / Weber, P. / Shepard, W. / Cole, S. / Alzari, P.M. / Bellinzoni, M.

Citation

Journal: FEBS Lett. / Year: 2012
Title: Conformational Changes Upon Ligand Binding in the Essential Class II Fumarase Rv1098C from Mycobacterium Tuberculosis.
Authors: Mechaly, A.E. / Haouz, A. / Miras, I. / Barilone, N. / Weber, P. / Shepard, W. / Alzari, P.M. / Bellinzoni, M.

History

Deposition	Dec 26, 2011	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Apr 25, 2012	Provider: repository / Type: Initial release
Revision 1.1	Jun 6, 2012	Group: Other
Revision 1.2	Dec 20, 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 / 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 / _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	4adl.cif.gz	690.1 KB	Display	PDBx/mmCIF format
PDB format	pdb4adl.ent.gz	572.5 KB	Display	PDB format
PDBx/mmJSON format	4adl.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4adl_validation.pdf.gz	471.4 KB	Display	wwPDB validaton report
Full document	4adl_full_validation.pdf.gz	481.7 KB	Display
Data in XML	4adl_validation.xml.gz	72.4 KB	Display
Data in CIF	4adl_validation.cif.gz	107.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ad/4adl ftp://data.pdbj.org/pub/pdb/validation_reports/ad/4adl	HTTPS FTP

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Related structure data

Related structure data	4admC 4apaC 4apbC 3no9S C: citing same article (ref.) S: Starting model for refinement
Similar structure data	6s7k-d 6s43-d 6s7w-d 6s7z-d 6s7s-d 5f92-d 4adm-d 6s7u-d 4l1b-d 1fur-1 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	#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

Unit cell

Length a, b, c (Å)	271.530, 98.130, 90.000
Angle α, β, γ (deg.)	90.00, 101.34, 90.00
Int Tables number	5
Space group name H-M	C121

#1: Protein	FUMARATE HYDRATASE CLASS II / FUMARASE C Mass: 52719.566 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Strain: H37RV / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS References: UniProt: O53446, UniProt: P9WN93*PLUS, fumarate hydratase
#2: Chemical	ChemComp-LMR / (2S)-2-hydroxybutanedioic acid / L-Malate Mass: 134.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₄H₆O₅
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1271 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 2.8 Å³/Da / Density % sol: 56 % / Description: NONE

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Data collection

Diffraction	Mean temperature: 287 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.973
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.973 Å / Relative weight: 1
Reflection	Resolution: 2.2→46.84 Å / Num. obs: 116132 / % possible obs: 98.1 % / Observed criterion σ(I): 0 / Redundancy: 3.3 % / B_iso Wilson estimate: 26.09 Å² / R_merge(I) obs: 0.12 / Net I/σ(I): 7.6
Reflection shell	Resolution: 2.2→2.32 Å / Redundancy: 2.8 % / R_merge(I) obs: 0.43 / Mean I/σ(I) obs: 2.7 / % possible all: 93.3

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Processing

Software

Name	Version	Classification
BUSTER	2.11.2	refinement
MOSFLM		data reduction
SCALA		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3NO9

3no9

Resolution: 2.2→22.18 Å / Cor.coef. F_o:F_c: 0.9488 / Cor.coef. F_o:F_c free: 0.933 / SU R Cruickshank DPI: 0.173 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.178 / SU R_free Blow DPI: 0.141 / SU R_free Cruickshank DPI: 0.14
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1781	5827	5.02 %	RANDOM
R_work	0.1538	-	-	-
obs	0.155	116132	98.88 %	-

Displacement parameters

B_iso mean: 28.22 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	3.4112 Å²	0 Å²	-1.0237 Å²
2-	-	0.2035 Å²	0 Å²
3-	-	-	-3.6147 Å²

Refine analyze

Luzzati coordinate error obs: 0.208 Å

Refinement step

Cycle: LAST / Resolution: 2.2→22.18 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	13508	0	18	1271	14797

Refine LS restraints

Refine-ID	Type	Dev ideal	Number	Restraint function	Weight
X-RAY DIFFRACTION	t_bond_d	0.01	13719	HARMONIC	2
X-RAY DIFFRACTION	t_angle_deg	1.01	18664	HARMONIC	2
X-RAY DIFFRACTION	t_dihedral_angle_d		6400	SINUSOIDAL	2
X-RAY DIFFRACTION	t_incorr_chiral_ct
X-RAY DIFFRACTION	t_pseud_angle
X-RAY DIFFRACTION	t_trig_c_planes		349	HARMONIC	2
X-RAY DIFFRACTION	t_gen_planes		2045	HARMONIC	5
X-RAY DIFFRACTION	t_it		13719	HARMONIC	20
X-RAY DIFFRACTION	t_nbd
X-RAY DIFFRACTION	t_omega_torsion	2.89
X-RAY DIFFRACTION	t_other_torsion	2.52
X-RAY DIFFRACTION	t_improper_torsion
X-RAY DIFFRACTION	t_chiral_improper_torsion		1915	SEMIHARMONIC	5
X-RAY DIFFRACTION	t_sum_occupancies
X-RAY DIFFRACTION	t_utility_distance
X-RAY DIFFRACTION	t_utility_angle
X-RAY DIFFRACTION	t_utility_torsion
X-RAY DIFFRACTION	t_ideal_dist_contact		17510	SEMIHARMONIC	4

LS refinement shell

Resolution: 2.2→2.26 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.2237	388	5.07 %
R_work	0.1992	7261	-
all	0.2005	7649	-
obs	-	-	98.88 %

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	2.3872	0.6946	1.1931	2.3208	0.1735	1.404	-0.0985	0.5455	-0.2031	-0.4499	-0.1479	0.0913	0.1308	0.0751	0.2464	-0.0128	0.0142	-0.031	0.12	-0.1457	-0.0978	25.9244	-8.4395	-26.2975
2	7.8884	-1.2425	-0.5326	1.2133	-0.2353	0.9368	0.1665	1.0793	-0.8426	-0.1302	-0.159	0.2904	0.1317	-0.1592	-0.0076	-0.0868	-0.0304	-0.0595	0.0579	-0.1561	-0.0145	12.1637	-8.9411	-17.5932
3	0.7808	-0.1678	0.6311	0.3758	-0.1242	0.6765	0.032	-0.0397	-0.0224	0.0298	-0.0039	0.1679	0.0687	-0.0821	-0.0281	-0.0619	-0.0194	0.0271	-0.0372	-0.0265	0.02	20.0005	-10.748	15.7944
4	1.5221	1.9986	-1.2458	0.3034	-0.9345	2.7347	-0.0593	-0.0381	0.1302	-0.053	0.0413	-0.0502	-0.0516	-0.2607	0.018	-0.0794	0.0334	-0.0196	0.0749	-0.0045	0.0539	3.7518	-0.6479	-6.1086
5	0.5168	-0.0222	-0.0818	0.7173	-0.04	0.3657	0.0322	0.0069	-0.0886	0.0023	-0.0172	0.0987	0.0786	-0.0021	-0.015	-0.0855	-0.0176	0.0088	-0.0659	-0.0383	-0.0262	29.2711	-12.5645	10.4212
6	-0.0183	1.6545	1.9644	0.1658	-1.46	2.4082	-0.0003	0.1341	-0.1748	0.2399	-0.0471	-0.1961	-0.1057	0.1257	0.0474	-0.0219	0.0194	0.0124	0.0666	0.0269	0.0099	39.0965	-14.947	48.1202
7	0.77	1.311	1.4086	1.4216	-1.7371	4.2286	-0.0348	-0.1537	-0.0004	0.3454	-0.1115	0.024	-0.0138	-0.222	0.1463	0.0382	0.0579	0.0473	-0.0473	-0.0178	-0.1109	32.8233	-16.3774	55.4582
8	4.3284	-2.8475	1.2326	1.4693	1.6834	1.7934	-0.0438	-0.1082	0.2258	0.1578	-0.0152	-0.1312	0.0959	0.2256	0.059	0.0991	0.0329	-0.0807	0.0359	-0.0515	-0.1613	49.3818	7.6558	49.2419
9	1.6268	-0.2956	-0.411	1.871	0.1316	2.9739	0.0581	-0.2721	0.1982	0.1979	0.0438	-0.1056	-0.0328	0.1689	-0.1018	-0.0361	-0.0551	-0.0182	-0.0248	-0.0283	-0.0507	46.9096	11.1696	39.2855
10	2.4702	0.4761	-1.5925	0.4685	-0.1772	2.4745	0.1272	-0.1668	0.097	0.1341	-0.0587	0.0341	-0.2337	0.0642	-0.0685	-0.0022	0.0086	0.0218	-0.0803	-0.0335	-0.1035	31.4054	10.8371	43.0612
11	0.0836	0.0631	0.0855	0.515	-0.3364	1.1154	0.0098	-0.0612	0.0674	0.0926	0.0017	0.1404	-0.0484	-0.0946	-0.0115	-0.0678	0.005	0.026	-0.0343	-0.0313	0.0322	18.6927	12.6993	11.206
12	2.7563	-1.4252	0.747	0.0279	0.3549	3.3613	0.0606	-0.0894	-0.0596	0.0903	-0.062	0.2158	0.0377	-0.2058	0.0014	-0.0511	-0.0383	0.0706	0.0061	-0.0108	-0.0013	17.7966	2.7015	38.537
13	0.4787	0.0366	-0.0265	0.6894	-0.025	0.3625	0.0396	-0.0131	0.0868	0.0493	-0.0282	0.0884	-0.0791	0.016	-0.0114	-0.0557	-0.0063	0.0228	-0.0447	-0.0425	-0.0189	29.2954	14.3064	10.3219
14	-0.3348	-1.7056	0.9975	0.0625	0.8145	5.4989	0.1045	0.138	0.0703	-0.3183	0.0764	0.0611	-0.0477	0.0892	-0.181	-0.0983	-0.0077	-0.0392	0.044	0.0352	-0.0106	15.8371	17.1444	-26.4552
15	-0.3557	-1.3699	0.6315	0.0301	-0.287	2.5467	-0.0054	0.017	0.19	-0.1956	-0.0493	0.2352	0.0211	-0.0992	0.0547	-0.017	-0.003	-0.1475	-0.0193	0.0515	-0.022	6.2149	18.0172	-28.8712
16	3.3762	-1.8129	-0.2901	4.3419	1.4324	2.6775	-0.0225	0.1427	-0.799	0.1856	0.0234	0.3425	0.4389	-0.1147	-0.0009	-0.0709	-0.0724	-0.0178	-0.1088	-0.0346	0.1526	33.3173	-35.6306	1.9524
17	2.9271	-1.3188	-0.5972	1.7284	0.5574	1.0918	0.0597	0.2287	-0.3061	-0.0987	-0.0989	0.1408	0.0282	-0.0327	0.0392	-0.0641	-0.0082	-0.0031	-0.1201	-0.0472	-0.032	48.1068	-31.6358	-3.637
18	0.3187	-0.172	0.1052	1.2259	-0.2259	0.4201	0.0247	0.086	-0.0078	-0.1207	-0.0041	-0.0483	0.0063	0.1017	-0.0206	-0.045	-0.0072	0.0086	-0.0019	-0.0392	-0.0385	48.8694	4.5862	-10.0933
19	2.0605	0.2945	-1.5036	1.4883	-0.5321	2.2463	0.0232	-0.0325	-0.004	0.0212	0.0034	-0.0569	-0.0822	0.1025	-0.0266	-0.0531	0.0045	-0.0133	-0.0586	-0.0331	-0.0058	60.2398	-22.6952	1.9762
20	0.3695	-0.1113	0.0886	0.75	-0.288	0.5929	0.0254	0.0603	-0.0465	-0.0889	0.0171	0.0777	0.016	0.001	-0.0425	-0.0625	-0.0128	0.0061	-0.0451	-0.0459	-0.0302	39.2035	-0.2971	-6.7028
21	1.6737	0.0763	-0.7397	7.1802	1.0846	1.8764	0.0527	-0.1388	0.4197	0.116	0.0107	0.4908	0.0007	-0.1192	-0.0634	-0.0011	0.0135	-0.0024	-0.0455	0.0132	0.0926	38.4466	39.3328	-16.656
22	2.8678	-2.075	0.5648	4.3918	-1.2122	2.377	-0.0935	0.2555	0.4681	-0.39	0.0209	0.0012	-0.3368	-0.0197	0.0726	-0.0181	-0.0214	-0.0136	-0.152	0.0295	0.003	44.6699	42.0907	-22.2475
23	3.5929	1.2138	0.8668	2.0912	-0.6543	2.4114	-0.0119	-0.2984	0.7417	0.0901	0.0317	0.3714	-0.4245	-0.0406	-0.0198	-0.0167	0.0347	0.0716	-0.1116	-0.102	0.0601	37.6793	37.2527	14.7891
24	2.4522	1.4387	-0.9376	2.8707	-0.7307	1.5691	0.1675	-0.2629	0.1252	0.2475	-0.1796	-0.2064	-0.1245	0.2579	0.0121	-0.0529	-0.0211	-0.0358	-0.0448	-0.038	-0.004	58.137	32.1247	10.7211
25	2.3378	1.4247	-0.6853	1.9239	-0.4246	0.7602	0.1166	-0.1312	0.3565	0.2251	-0.053	0.1815	-0.1577	0.0407	-0.0637	-0.0388	-0.0074	0.0142	-0.103	-0.0509	-0.0096	48.0266	34.4179	11.2838
26	0.1463	0.0895	0.037	1.3568	-0.558	0.5685	0.0292	0.0081	-0.0102	0.1053	-0.0542	-0.0806	-0.041	0.1201	0.025	-0.0721	-0.0103	0.0005	-0.0358	-0.0361	-0.0388	56.4431	0.5083	13.386
27	4.0284	-1.4281	1.2255	3.0794	-1.5146	1.9605	-0.0322	0.1009	-0.0755	-0.1082	-0.0722	-0.0859	0.0785	-0.0103	0.1044	-0.0238	-0.0172	0.0441	-0.0342	-0.0042	0.0212	62.8574	23.9666	1.4036
28	0.4781	-0.0626	0.1035	0.6557	-0.2216	0.7489	0.0426	-0.0536	0.0022	0.1046	0.0057	0.0435	-0.0448	0.0659	-0.0482	-0.0518	-0.014	0.0036	-0.05	-0.0455	-0.0459	47.1622	1.992	18.6101
29	1.8594	0.0542	0.6312	6.331	-0.037	0.6044	-0.0351	0.1948	-0.2111	0.0857	-0.0631	0.0985	-0.017	-0.1428	0.0981	0.0051	0.0045	-0.0563	-0.0401	0.0174	0.0218	54.5714	-35.3341	25.9738
30	1.147	0.2501	0.5982	9.2002	-1.5417	3.1154	-0.0653	-0.2314	-0.376	0.5944	-0.0605	-0.1102	0.3986	-0.0489	0.1258	-0.0206	0.0192	-0.0133	-0.132	0.0184	0.0093	56.5586	-41.2273	28.0209

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN A AND RESSEQ 9:44
2	X-RAY DIFFRACTION	2	CHAIN A AND RESSEQ 45:137
3	X-RAY DIFFRACTION	3	CHAIN A AND RESSEQ 138:232
4	X-RAY DIFFRACTION	4	CHAIN A AND RESSEQ 233:260
5	X-RAY DIFFRACTION	5	CHAIN A AND RESSEQ 261:395
6	X-RAY DIFFRACTION	6	CHAIN A AND RESSEQ 396:433
7	X-RAY DIFFRACTION	7	CHAIN A AND RESSEQ 434:467
8	X-RAY DIFFRACTION	8	CHAIN B AND RESSEQ 9:19
9	X-RAY DIFFRACTION	9	CHAIN B AND RESSEQ 20:44
10	X-RAY DIFFRACTION	10	CHAIN B AND RESSEQ 45:137
11	X-RAY DIFFRACTION	11	CHAIN B AND RESSEQ 138:232
12	X-RAY DIFFRACTION	12	CHAIN B AND RESSEQ 233:260
13	X-RAY DIFFRACTION	13	CHAIN B AND RESSEQ 261:395
14	X-RAY DIFFRACTION	14	CHAIN B AND RESSEQ 396:435
15	X-RAY DIFFRACTION	15	CHAIN B AND RESSEQ 436:466
16	X-RAY DIFFRACTION	16	CHAIN C AND RESSEQ 9:44
17	X-RAY DIFFRACTION	17	CHAIN C AND RESSEQ 45:137
18	X-RAY DIFFRACTION	18	CHAIN C AND RESSEQ 138:222
19	X-RAY DIFFRACTION	19	CHAIN C AND RESSEQ 223:259
20	X-RAY DIFFRACTION	20	CHAIN C AND RESSEQ 260:395
21	X-RAY DIFFRACTION	21	CHAIN C AND RESSEQ 396:432
22	X-RAY DIFFRACTION	22	CHAIN C AND RESSEQ 433:467
23	X-RAY DIFFRACTION	23	CHAIN D AND RESSEQ 9:44
24	X-RAY DIFFRACTION	24	CHAIN D AND RESSEQ 45:90
25	X-RAY DIFFRACTION	25	CHAIN D AND RESSEQ 91:136
26	X-RAY DIFFRACTION	26	CHAIN D AND RESSEQ 137:235
27	X-RAY DIFFRACTION	27	CHAIN D AND RESSEQ 236:259
28	X-RAY DIFFRACTION	28	CHAIN D AND RESSEQ 260:395
29	X-RAY DIFFRACTION	29	CHAIN D AND RESSEQ 396:418
30	X-RAY DIFFRACTION	30	CHAIN D AND RESSEQ 419:467

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The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

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