PDB-4apa: Crystal structure of Mycobacterium tuberculosis fumarase (Rv1098c...

ID or keywords:

Entry

Database: PDB / ID: 4apa

Title

Crystal structure of Mycobacterium tuberculosis fumarase (Rv1098c) S318A in apo form

Components

FUMARATE HYDRATASE CLASS II

Keywords

HYDROLASE / METABOLISM

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: 2.04 Å

Authors

Bellinzoni, M. / Haouz, A. / Mechaly, A.E. / Alzari, P.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	Mar 31, 2012	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 / 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 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

Structure viewer	Molecule: MolmilJmol/JSmol

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ap/4apa ftp://data.pdbj.org/pub/pdb/validation_reports/ap/4apa	HTTPS FTP

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Related structure data

Related structure data	4adlSC 4admC 4apbC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6s7z-d 3no9-d 1fur-1 6nza-1 6s43-d 6s7u-d 1fup-1 6s7s-d 1kq7-1 5f91-d 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)

Deposited unit

A: FUMARATE HYDRATASE CLASS II

B: FUMARATE HYDRATASE CLASS II

C: FUMARATE HYDRATASE CLASS II

D: FUMARATE HYDRATASE CLASS II

200 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)	268.270, 97.142, 96.436
Angle α, β, γ (deg.)	90.00, 104.54, 90.00
Int Tables number	5
Space group name H-M	C121

Noncrystallographic symmetry (NCS)

NCS oper:

ID	Code	Matrix	Vector
1	given	(0.876, -0.0093, -0.4823), (-0.0099, -1, 0.0013), (-0.4823, 0.0037, -0.876)	11.4582, -97.5254, 46.377
2	given	(-0.9289, 0.2578, 0.2657), (0.2501, -0.0922, 0.9638), (0.273, 0.9618, 0.0212)	-89.5637, -76.6873, 95.9257
3	given	(-0.9427, -0.2515, 0.2192), (-0.2491, 0.0939, -0.9639), (0.2218, -0.9633, -0.1511)	-113.3202, -20.4331, 6.4166

#1: Protein	FUMARATE HYDRATASE CLASS II / FUMARASE C Mass: 50101.660 Da / Num. of mol.: 4 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Strain: H37RV / Plasmid: PDEST17 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS References: UniProt: O53446, UniProt: P9WN93*PLUS, fumarate hydratase
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 798 / Source method: isolated from a natural source / Formula: H₂O
Compound details	ENGINEERED RESIDUE IN CHAIN A, SER 318 TO ALA ENGINEERED RESIDUE IN CHAIN B, SER 318 TO ALA ...ENGINEERED RESIDUE IN CHAIN A, SER 318 TO ALA ENGINEERED RESIDUE IN CHAIN B, SER 318 TO ALA ENGINEERED RESIDUE IN CHAIN C, SER 318 TO ALA ENGINEERED RESIDUE IN CHAIN D, SER 318 TO ALA
Sequence details	N-TER GLY IS A PURIFICATION TAG LEFTOVER

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.04 Å³/Da / Density % sol: 59.5 % / Description: NONE
Crystal grow	pH: 8 / Details: 20% PEG 8000, 0.2 M CACL2, 0.1 M TRIS-HCL PH 8.0

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97895
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 18, 2012 / Details: KIRKPATRICK-BAEZ PAIR OF BI-MORPH MIRRORS
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97895 Å / Relative weight: 1
Reflection	Resolution: 2.04→43.41 Å / Num. obs: 148043 / % possible obs: 97.9 % / Observed criterion σ(I): 2 / Redundancy: 4.2 % / B_iso Wilson estimate: 29.34 Å² / R_merge(I) obs: 0.08 / Net I/σ(I): 13.1
Reflection shell	Resolution: 2.04→2.16 Å / Redundancy: 2.7 % / R_merge(I) obs: 0.48 / Mean I/σ(I) obs: 2.3 / % possible all: 86.8

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Processing

Software

Name	Version	Classification
BUSTER	2.11.2	refinement
XDS		data reduction
SCALA		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4ADL

4adl

Resolution: 2.04→43.41 Å / Cor.coef. F_o:F_c: 0.944 / Cor.coef. F_o:F_c free: 0.9376 / SU R Cruickshank DPI: 0.13 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.129 / SU R_free Blow DPI: 0.111 / SU R_free Cruickshank DPI: 0.112
Details: NCS REPRESENTATION: RESTRAINT LSSR SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY. NUMBER OF LIBRARIES USED: 8

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1791	7424	5.01 %	RANDOM
R_work	0.1654	-	-	-
obs	0.1661	148043	97.15 %	-

Displacement parameters

B_iso mean: 34.21 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	5.6417 Å²	0 Å²	3.8676 Å²
2-	-	1.056 Å²	0 Å²
3-	-	-	-6.6977 Å²

Refine analyze

Luzzati coordinate error obs: 0.215 Å

Refinement step

Cycle: LAST / Resolution: 2.04→43.41 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	12898	0	0	798	13696

Refine LS restraints

Refine-ID	Type	Dev ideal	Number	Restraint function	Weight
X-RAY DIFFRACTION	t_bond_d	0.01	13078	HARMONIC	2
X-RAY DIFFRACTION	t_angle_deg	0.97	17823	HARMONIC	2
X-RAY DIFFRACTION	t_dihedral_angle_d		6044	SINUSOIDAL	2
X-RAY DIFFRACTION	t_incorr_chiral_ct
X-RAY DIFFRACTION	t_pseud_angle
X-RAY DIFFRACTION	t_trig_c_planes		330	HARMONIC	2
X-RAY DIFFRACTION	t_gen_planes		1959	HARMONIC	5
X-RAY DIFFRACTION	t_it		13078	HARMONIC	20
X-RAY DIFFRACTION	t_nbd
X-RAY DIFFRACTION	t_omega_torsion	3.03
X-RAY DIFFRACTION	t_other_torsion	2.37
X-RAY DIFFRACTION	t_improper_torsion
X-RAY DIFFRACTION	t_chiral_improper_torsion		1856	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		16745	SEMIHARMONIC	4

LS refinement shell

Resolution: 2.04→2.09 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.237	405	5 %
R_work	0.2064	7693	-
all	0.2079	8098	-
obs	-	-	97.15 %

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	-0.2525	0.3232	0.3835	0	-0.7887	0.7965	-0.0048	0.0012	-0.0597	0.0427	-0.0124	0.0256	0.045	-0.0464	0.0172	-0.0409	-0.004	0.0052	0.1016	0.2485	-0.1113	-37.8626	-65.015	77.6373
2	5.4833	0.3256	0.4692	0.7632	-1.3795	3.0425	0.015	-0.6908	-0.3515	0.1975	-0.0605	-0.0483	0.0201	-0.0003	0.0455	-0.027	0.0286	-0.0151	0.0127	0.0525	-0.0367	-40.2061	-59.9327	67.7819
3	2.4252	-0.2108	-0.1371	0.1929	0.1867	1.0342	-0.0579	-0.3788	-0.2795	0.0843	0.0422	-0.0462	0.1883	0.1976	0.0157	-0.0956	0.0559	-0.0506	-0.0271	0.0478	-0.0372	-25.7901	-59.7861	61.8357
4	0.6663	-0.0136	0.2608	0.3456	0.0515	0.6166	0.006	0.0079	-0.0473	-0.0311	0.0506	-0.1596	-0.0039	0.1407	-0.0566	-0.0922	0.0129	-0.0014	-0.0282	0.017	0.0083	-29.0459	-58.2836	37.688
5	0.4132	-0.03	0.0823	0.1075	-0.1694	0.487	0.0186	0.0124	-0.0553	-0.0414	0.0003	-0.1291	0.0381	0.069	-0.019	-0.0789	0.0136	-0.0098	-0.0166	0.0168	0.005	-33.8094	-59.0977	35.473
6	0.586	-0.0424	0.1732	0.476	0.0602	0.5042	0.0292	-0.0596	0.0386	0.0451	-0.0272	-0.1079	-0.0163	0.0262	-0.0019	-0.1609	0.0079	-0.0163	-0.1077	0.0292	-0.1069	-40.5854	-56.4508	42.093
7	1.8531	-0.0583	2.1237	2.0084	-0.7611	8.4815	-0.0849	0.4259	-0.0773	-0.6738	0.0606	0.1246	0.0053	-0.272	0.0244	-0.0021	0.0143	-0.0231	0.0057	-0.0774	-0.1513	-46.3803	-70.9852	0.4002
8	1.7154	1.8917	-3.3133	0.1489	-0.2859	0.0487	-0.0143	0.342	-0.0225	-0.3216	0.0124	-0.0198	0.0582	0.0276	0.0019	0.0588	0.0974	0.0458	0.0688	-0.0422	-0.2091	-37.0223	-69.3756	-5.929
9	5.3988	3.7331	2.713	2.4537	-0.6041	6.0385	0.061	-0.1272	0.0437	0.01	0.0367	0.0775	-0.0727	0.0647	-0.0977	0.043	0.0055	-0.0287	-0.0369	0.0822	-0.0337	-59.9971	-35.6251	-3.1986
10	0.8862	-0.0249	0.5624	0.4191	-0.2355	2.4299	0.0615	0.1262	0.2588	-0.2938	-0.0257	-0.0088	-0.0302	0.0297	-0.0358	0.018	-0.0218	-0.0492	-0.0858	0.075	-0.0785	-54.7115	-36.2692	7.8034
11	1.9902	0.5244	-0.4477	0.7488	-0.4351	1.0979	-0.1192	0.3542	0.2832	-0.325	0.0557	-0.0866	-0.0728	0.0765	0.0635	0.0509	-0.0643	0.0112	0.0121	0.0908	-0.0814	-40.1556	-37.4579	4.0215
12	0.4234	0.0306	0.0114	0.604	0.3553	1.2256	-0.0035	0.1156	0.0604	-0.1454	0.0715	-0.1953	-0.0772	0.182	-0.0679	-0.0859	-0.0316	0.0172	-0.0417	0.0383	-0.0014	-31.7395	-38.8562	27.0417
13	0.411	0.0184	0.0596	0.2831	0.2119	0.8399	0.0181	0.0662	0.0814	-0.1268	0.0069	-0.1127	-0.1148	0.0563	-0.025	-0.0814	-0.018	0.0025	-0.0544	0.0424	-0.023	-38.8692	-39.4073	30.3642
14	0.8734	-0.3773	1.1525	1.0425	0.1323	3.6571	-0.0345	-0.0583	0.3132	0.0615	0.024	-0.0818	-0.2679	-0.0119	0.0105	-0.1032	-0.0685	-0.0176	-0.0962	0.0023	0.0674	-32.3761	-23.0884	49.9971
15	3.5715	0.0609	-2.6343	3.2477	-0.1599	12.3526	-0.0208	-0.4701	-0.1032	0.7044	0.0259	0.0095	0.2542	0.3941	-0.005	0.0408	-0.0095	-0.1294	0.0272	-0.1077	-0.1638	-25.2938	-27.7331	78.4383
16	-0.6536	-2.0102	1.3526	1.1277	-0.815	0.7456	-0.1176	-0.0951	0.1631	0.1334	0.1793	-0.0636	0.096	0.0878	-0.0617	-0.1298	-0.0642	-0.1267	0.0206	-0.0767	0.0317	-18.4614	-29.5444	65.8499
17	0.0136	-0.2238	-0.0245	0.7753	-0.336	-0.0136	-0.0047	0.0542	0.0238	0.0106	-0.0018	-0.0021	-0.0226	0.0173	0.0066	0.0781	0.0622	0.1018	-0.1908	0.2817	0.1063	-50.0943	-5.2251	25.8479
18	5.4377	-2.4587	-0.3256	2.3908	-0.6588	0.5028	0.0432	0.4065	0.7417	-0.0361	-0.0601	-0.4071	-0.2249	0.0005	0.017	-0.0111	-0.0362	0.0075	-0.0733	0.066	0.0141	-50.5373	-17.3674	28.3773
19	1.3046	-1.3209	-0.7566	3.1588	1.6556	1.7523	0.049	0.0815	0.2292	-0.1179	0.0125	0.0357	-0.1783	-0.0935	-0.0615	-0.0352	-0.0089	-0.016	-0.0735	0.0401	0.045	-71.0198	-16.5331	36.8458
20	1.8275	-0.6446	-0.3622	1.3302	0.0954	0.3377	0.0369	0.127	0.2624	-0.0531	0.0138	-0.1241	-0.0946	0.0176	-0.0508	-0.0364	-0.0018	-0.0164	-0.1116	0.0456	0.0139	-61.5709	-17.5696	33.5331
21	0.2253	-0.1553	-0.0479	1.3518	0.4584	0.4184	-0.0054	0.0219	-0.0008	-0.0535	-0.0125	0.1318	-0.012	-0.0352	0.0179	-0.0327	-0.0037	-0.0347	-0.0228	0.0288	0.0473	-68.7251	-49.9094	30.5679
22	0.3134	-0.103	-0.0371	1.315	0.3155	0.18	0.0145	0.0424	0.0564	-0.106	0.0105	0.0375	-0.0543	0.002	-0.025	-0.0461	0.0019	-0.026	-0.0477	0.0381	-0.0174	-63.7945	-45.4826	30.0715
23	0.451	0.0446	-0.0554	1.0441	0.1326	0.5098	-0.0189	0.0283	0.0452	-0.1517	-0.003	0.0288	-0.0829	0.0122	0.0218	-0.1075	0.0164	-0.0168	-0.1158	0.0432	-0.0673	-58.3332	-45.5426	26.7503
24	3.7482	-1.0114	-0.5514	3.5112	0.7426	1.7077	-0.0652	-0.0162	-0.2701	-0.0109	0.0115	0.0249	0.2198	0.0625	0.0537	0.0327	0.0032	-0.0274	-0.0596	-0.0038	0.0067	-67.058	-88.9272	16.7119
25	-0.2236	0.1931	0.4034	1.4037	-0.4054	0.2253	-0.0051	-0.0174	-0.0229	-0.041	0.0129	-0.0081	0.0362	0.0219	-0.0078	0.1096	0.0012	-0.061	-0.1749	0.1553	0.0852	-45.0628	-91.8871	46.4429
26	4.8303	1.5081	-0.5162	4.3173	-1.1567	2.2224	-0.0492	-0.3047	-0.5917	-0.0657	-0.1615	-0.184	0.2588	0.2332	0.2107	-0.0172	0.0636	-0.0068	-0.0243	0.0426	0.0711	-45.532	-81.0735	45.1113
27	2.0193	0.8081	0.5873	1.7344	0.5604	2.1193	-0.0853	-0.231	-0.189	0.1108	-0.0346	0.1496	0.1934	-0.1399	0.1199	-0.0454	-0.0032	0.0461	-0.1174	0.0022	-0.0413	-66.6134	-79.4385	48.4695
28	2.6654	0.7781	-0.709	1.2579	-0.3442	0.6901	-0.0642	-0.2112	-0.3156	0.1744	-0.0275	-0.0584	0.0497	0.0828	0.0917	-0.0132	0.0292	-0.006	-0.0898	0.0385	-0.0292	-55.8567	-78.8514	48.8783
29	0.3917	0.155	-0.0126	1.5975	0.2075	0.3766	-0.0088	-0.0192	-0.0005	0.1347	-0.0035	0.1325	0.0351	-0.0273	0.0123	-0.0333	0.0005	0.002	-0.0151	0.0199	0.0055	-61.6051	-51.5875	52.8958
30	0.9296	-0.4512	-1.2149	1.1244	0.7485	2.5348	-0.0205	0.1381	-0.0287	-0.1144	-0.0897	0.1721	-0.104	-0.0437	0.1102	-0.0466	-0.0197	-0.0109	-0.0531	-0.0049	0.0237	-72.4342	-71.7427	41.6332
31	0.4982	0.4873	0.4472	1.6577	0.9563	1.2327	0.0402	-0.0631	0.0019	0.1162	-0.0247	-0.0701	0.044	-0.0083	-0.0155	-0.066	0.0153	-0.0121	-0.0643	0.0258	-0.0279	-54.347	-46.2752	50.7016
32	0.4326	-0.1355	-0.0179	1.0421	0.2248	0.8262	0.0017	-0.0507	-0.012	0.1247	0.0548	-0.0482	0.0472	0.032	-0.0565	-0.0979	0.0015	-0.0152	-0.0894	0.0348	-0.0448	-51.9057	-51.9926	50.7496
33	4.24	1.4815	-1.0773	10.2246	-0.0271	1.3941	0.0325	-0.0374	0.762	0.3886	0.1063	-0.144	-0.2508	0.111	-0.1388	0.0125	0.0118	-0.0006	-0.1493	-0.0371	0.039	-54.552	-8.2585	63.8994

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN A AND RESID 9-13
2	X-RAY DIFFRACTION	2	CHAIN A AND RESID 20-44
3	X-RAY DIFFRACTION	3	CHAIN A AND RESID 45-121
4	X-RAY DIFFRACTION	4	CHAIN A AND RESID 122-242
5	X-RAY DIFFRACTION	5	CHAIN A AND RESID 243-314
6	X-RAY DIFFRACTION	6	CHAIN A AND RESID 325-380
7	X-RAY DIFFRACTION	7	CHAIN A AND RESID 381-444
8	X-RAY DIFFRACTION	8	CHAIN A AND RESID 449-467
9	X-RAY DIFFRACTION	9	CHAIN B AND RESID 9-19
10	X-RAY DIFFRACTION	10	CHAIN B AND RESID 20-48
11	X-RAY DIFFRACTION	11	CHAIN B AND RESID 49-121
12	X-RAY DIFFRACTION	12	CHAIN B AND RESID 122-242
13	X-RAY DIFFRACTION	13	CHAIN B AND RESID 243-377
14	X-RAY DIFFRACTION	14	CHAIN B AND RESID 378-406
15	X-RAY DIFFRACTION	15	CHAIN B AND RESID 407-455
16	X-RAY DIFFRACTION	16	CHAIN B AND RESID 456-466
17	X-RAY DIFFRACTION	17	CHAIN C AND RESID 9-14
18	X-RAY DIFFRACTION	18	CHAIN C AND RESID 20-48
19	X-RAY DIFFRACTION	19	CHAIN C AND RESID 49-77
20	X-RAY DIFFRACTION	20	CHAIN C AND RESID 78-149
21	X-RAY DIFFRACTION	21	CHAIN C AND RESID 150-241
22	X-RAY DIFFRACTION	22	CHAIN C AND RESID 242-325
23	X-RAY DIFFRACTION	23	CHAIN C AND RESID 326-399
24	X-RAY DIFFRACTION	24	CHAIN C AND RESID 400-467
25	X-RAY DIFFRACTION	25	CHAIN D AND RESID 9-14
26	X-RAY DIFFRACTION	26	CHAIN D AND RESID 20-44
27	X-RAY DIFFRACTION	27	CHAIN D AND RESID 45-77
28	X-RAY DIFFRACTION	28	CHAIN D AND RESID 78-121
29	X-RAY DIFFRACTION	29	CHAIN D AND RESID 122-222
30	X-RAY DIFFRACTION	30	CHAIN D AND RESID 223-259
31	X-RAY DIFFRACTION	31	CHAIN D AND RESID 260-314
32	X-RAY DIFFRACTION	32	CHAIN D AND RESID 325-398
33	X-RAY DIFFRACTION	33	CHAIN D AND RESID 399-467

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