PDB-5uqq: Crystal structure of 2-methylcitrate synthase from Aspergillus fu...

ID or keywords:

Entry

Database: PDB / ID: 5uqq

Title

Crystal structure of 2-methylcitrate synthase from Aspergillus fumigatus

Components

2-methylcitrate synthase, mitochondrial

Keywords

TRANSFERASE / mcsA / 2-methylcitrate synthase / citrate synthase

Function / homology

Function and homology information

2-methylcitrate synthase / 2-methylcitrate synthase activity / propionate catabolic process, 2-methylcitrate cycle / citrate synthase (unknown stereospecificity) / propionate catabolic process / : / tricarboxylic acid cycle / carbohydrate metabolic process / mitochondrial matrix
Similarity search - Function

Biological species

Neosartorya fumigata (mold)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.3 Å

Authors

Schlachter, C. / Chruszcz, M.

Citation

Journal: Biol.Chem. / Year: 2019
Title: Comparative studies of Aspergillus fumigatus 2-methylcitrate synthase and human citrate synthase.
Authors: Schlachter, C.R. / Klapper, V. / Radford, T. / Chruszcz, M.

History

Deposition	Feb 8, 2017	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 14, 2018	Provider: repository / Type: Initial release
Revision 1.1	Jun 17, 2020	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2	Mar 6, 2024	Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Validation report

Summary document	5uqq_validation.pdf.gz	491.5 KB	Display	wwPDB validaton report
Full document	5uqq_full_validation.pdf.gz	504.4 KB	Display
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Data in CIF	5uqq_validation.cif.gz	146.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/uq/5uqq ftp://data.pdbj.org/pub/pdb/validation_reports/uq/5uqq	HTTPS FTP

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Related structure data

Related structure data	5uqoC 5uqrC 5uqsC 5uquC 5uzpC 5uzqC 5uzrC 6bolC 6bomC 6bonC 6booC 6bopC C: citing same article (ref.)
Similar structure data	6bom-2 6bop-2 5uqo-d 6bom-1 2rkw-d 5uzq-1 3dsr-d 3ssa-d 2r2n-2 5xmq-1 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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

Related structure data

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#93 - Sep 2007 Citrate Synthase similarity (10) #154 - Oct 2012 Citric Acid Cycle similarity (7)

Deposited unit

B: 2-methylcitrate synthase, mitochondrial

C: 2-methylcitrate synthase, mitochondrial

A: 2-methylcitrate synthase, mitochondrial

D: 2-methylcitrate synthase, mitochondrial

E: 2-methylcitrate synthase, mitochondrial

F: 2-methylcitrate synthase, mitochondrial

hetero molecules

306 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

B: 2-methylcitrate synthase, mitochondrial

C: 2-methylcitrate synthase, mitochondrial

hetero molecules

defined by author&software
102 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

A: 2-methylcitrate synthase, mitochondrial

D: 2-methylcitrate synthase, mitochondrial

defined by author&software
102 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

E: 2-methylcitrate synthase, mitochondrial

F: 2-methylcitrate synthase, mitochondrial

defined by author&software
102 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	82.393, 130.012, 261.535
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Component-ID: _ / Refine code: _

Dom-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	THR	THR	LYS	LYS	B	A	30 - 464	27 - 461
2	1	THR	THR	LYS	LYS	C	B	30 - 464	27 - 461
1	2	ALA	ALA	LYS	LYS	B	A	31 - 464	28 - 461
2	2	ALA	ALA	LYS	LYS	A	C	31 - 464	28 - 461
1	3	ALA	ALA	LEU	LEU	B	A	31 - 463	28 - 460
2	3	ALA	ALA	LEU	LEU	D	D	31 - 463	28 - 460
1	4	ALA	ALA	LEU	LEU	B	A	31 - 463	28 - 460
2	4	ALA	ALA	LEU	LEU	E	E	31 - 463	28 - 460
1	5	ALA	ALA	LYS	LYS	B	A	31 - 464	28 - 461
2	5	ALA	ALA	LYS	LYS	F	F	31 - 464	28 - 461
1	6	ALA	ALA	LYS	LYS	C	B	31 - 464	28 - 461
2	6	ALA	ALA	LYS	LYS	A	C	31 - 464	28 - 461
1	7	ALA	ALA	LEU	LEU	C	B	31 - 463	28 - 460
2	7	ALA	ALA	LEU	LEU	D	D	31 - 463	28 - 460
1	8	ALA	ALA	LEU	LEU	C	B	31 - 463	28 - 460
2	8	ALA	ALA	LEU	LEU	E	E	31 - 463	28 - 460
1	9	ALA	ALA	LYS	LYS	C	B	31 - 464	28 - 461
2	9	ALA	ALA	LYS	LYS	F	F	31 - 464	28 - 461
1	10	ALA	ALA	LEU	LEU	A	C	31 - 463	28 - 460
2	10	ALA	ALA	LEU	LEU	D	D	31 - 463	28 - 460
1	11	ALA	ALA	LEU	LEU	A	C	31 - 463	28 - 460
2	11	ALA	ALA	LEU	LEU	E	E	31 - 463	28 - 460
1	12	ALA	ALA	LYS	LYS	A	C	31 - 465	28 - 462
2	12	ALA	ALA	LYS	LYS	F	F	31 - 465	28 - 462
1	13	ALA	ALA	LYS	LYS	D	D	31 - 464	28 - 461
2	13	ALA	ALA	LYS	LYS	E	E	31 - 464	28 - 461
1	14	ALA	ALA	LEU	LEU	D	D	31 - 463	28 - 460
2	14	ALA	ALA	LEU	LEU	F	F	31 - 463	28 - 460
1	15	ALA	ALA	LEU	LEU	E	E	31 - 463	28 - 460
2	15	ALA	ALA	LEU	LEU	F	F	31 - 463	28 - 460

NCS ensembles :

ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

#1: Protein	2-methylcitrate synthase, mitochondrial / Methylcitrate synthase / (2S / 3S)-2-methylcitrate synthase / Citrate synthase 1 Mass: 51029.078 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Neosartorya fumigata (mold) / Gene: mcsA, cit1 / Plasmid: pJExpress411 / Cell line (production host): BL-21(DE3) / Production host: Escherichia coli (E. coli) References: UniProt: Q50I20, 2-methylcitrate synthase, citrate synthase (unknown stereospecificity)
#2: Chemical	ChemComp-SRT / S,R MESO-TARTARIC ACID Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₆O₆
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1449 / 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: 46.23 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / Details: 0.2 M NaTartrate, 20% PEG3350 pH 7.85

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 16, 2013
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.3→50 Å / Num. obs: 118739 / % possible obs: 99.67 % / Observed criterion σ(I): -3 / Redundancy: 4.9 % / R_merge(I) obs: 0.081 / R_pim(I) all: 0.052 / R_rim(I) all: 0.117 / R_sym value: 0.081 / Net I/σ(I): 18.4
Reflection shell	Resolution: 2.3→2.33 Å / Redundancy: 4.8 % / R_merge(I) obs: 0.528 / Mean I/σ(I) obs: 2.35 / Num. unique obs: 4770 / CC_1/2: 0.809 / R_pim(I) all: 0.354 / R_rim(I) all: 0.777 / R_sym value: 0.528 / % possible all: 99.7

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0158	refinement
HKL-2000		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.3→31.41 Å / Cor.coef. F_o:F_c: 0.956 / Cor.coef. F_o:F_c free: 0.941 / Cross valid method: THROUGHOUT / ESU R: 0.36 / ESU R Free: 0.215 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.21434	6278	5 %	RANDOM
R_work	0.18524	-	-	-
obs	0.1867	118739	99.67 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å

Displacement parameters

B_iso mean: 42.189 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.45 Å²	-0 Å²	0 Å²
2-	-	0.34 Å²	-0 Å²
3-	-	-	0.11 Å²

Refinement step

Cycle: 1 / Resolution: 2.3→31.41 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	20274	0	10	1449	21733

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.019	20832
X-RAY DIFFRACTION	r_bond_other_d	0	0.02	19572
X-RAY DIFFRACTION	r_angle_refined_deg	1.509	1.97	28286
X-RAY DIFFRACTION	r_angle_other_deg	3.641	3	45441
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.27	5	2616
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	38.054	24.118	896
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.511	15	3497
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.673	15	113
X-RAY DIFFRACTION	r_chiral_restr	0.085	0.2	3137
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.021	23179
X-RAY DIFFRACTION	r_gen_planes_other	0.011	0.02	4138
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	1.102	2.197	10465
X-RAY DIFFRACTION	r_mcbond_other	1.102	2.197	10464
X-RAY DIFFRACTION	r_mcangle_it	1.925	3.29	13079
X-RAY DIFFRACTION	r_mcangle_other	1.925	3.29	13080
X-RAY DIFFRACTION	r_scbond_it	1.273	2.37	10367
X-RAY DIFFRACTION	r_scbond_other	1.273	2.369	10364
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	2.225	3.473	15205
X-RAY DIFFRACTION	r_long_range_B_refined	5.281	41.164	88080
X-RAY DIFFRACTION	r_long_range_B_other	5.281	41.162	88079
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	B	27856	0.07
1	2	C	27856	0.07
2	1	B	27992	0.07
2	2	A	27992	0.07
3	1	B	27664	0.08
3	2	D	27664	0.08
4	1	B	27848	0.07
4	2	E	27848	0.07
5	1	B	27564	0.08
5	2	F	27564	0.08
6	1	C	27846	0.07
6	2	A	27846	0.07
7	1	C	27746	0.07
7	2	D	27746	0.07
8	1	C	27862	0.07
8	2	E	27862	0.07
9	1	C	27710	0.07
9	2	F	27710	0.07
10	1	A	27628	0.07
10	2	D	27628	0.07
11	1	A	27924	0.06
11	2	E	27924	0.06
12	1	A	27824	0.07
12	2	F	27824	0.07
13	1	D	27748	0.08
13	2	E	27748	0.08
14	1	D	27772	0.07
14	2	F	27772	0.07
15	1	E	27572	0.07
15	2	F	27572	0.07

LS refinement shell

Resolution: 2.3→2.359 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.281	455	-
R_work	0.258	8584	-
obs	-	-	98.84 %

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	0.6575	0.1118	0.0555	0.2419	-0.0513	0.7497	0.0177	0.0479	-0.0807	-0.0083	0.036	0.0139	0.0916	-0.1725	-0.0538	0.1302	-0.0149	-0.0043	0.1809	0.0138	0.1657	-6.545	-49.756	20.668
2	2.8169	-0.3502	-0.1937	0.6484	1.0285	5.668	0.0211	-0.4813	0.5517	-0.3062	0.0881	-0.2725	-0.8256	0.1173	-0.1092	0.3045	0.0579	0.0972	0.1847	-0.05	0.2325	-17.561	-19.619	23.066
3	0.6007	-0.1005	0.1006	0.0367	0.0952	0.6624	0.03	0.0428	0.0039	-0.0281	-0.0474	-0.0046	-0.1242	-0.1951	0.0173	0.1541	0.0389	0.0185	0.2254	0.0198	0.1411	-11.721	-34.633	19.017
4	2.5675	-0.8002	-1.2068	0.9885	0.4657	1.8101	-0.1365	-0.1905	-0.4912	0.1233	0.1054	0.1326	0.2298	0.1174	0.0311	0.1692	0.0026	-0.053	0.0996	0.0573	0.1511	-11.209	-35.762	71.71
5	0.5638	-0.2234	0.3084	0.6147	0.0905	0.6713	0.0071	0.0969	-0.0448	-0.0426	0.0609	-0.029	0.0383	0.1131	-0.0681	0.1526	-0.0083	-0.0217	0.1827	-0.0231	0.1355	-0.937	-25.686	58.135
6	0.356	-0.049	0.1489	0.5586	0.3736	0.3941	-0.0258	0.0644	0	0.0268	0.1357	-0.0798	0.0143	0.1166	-0.1099	0.1515	-0.0043	-0.0199	0.2066	-0.0348	0.1528	5.933	-15.178	70.027
7	0.7245	0.1248	0.0232	0.7946	-0.1268	0.6586	-0.0411	-0.0715	0.1419	0.0548	0.0018	0.1131	-0.1343	0.0246	0.0393	0.1802	-0.0004	-0.0384	0.1025	-0.0257	0.1714	-25.394	-4.791	65.248
8	1.2123	0.5032	0.7536	1.3312	1.1787	2.1383	0.0259	0.0733	0.0347	0.1479	-0.0997	0.0193	0.2232	-0.0999	0.0737	0.1314	0.0119	-0.0117	0.1415	-0.029	0.1614	-44.923	-23.856	57.664
9	0.8216	0.6755	0.1639	0.7142	0.1237	0.1836	-0.054	-0.0177	0.0749	0.0959	-0.0694	0.0715	-0.0402	0.0668	0.1235	0.2058	0.0146	-0.0041	0.1728	0	0.1291	-18.663	-16.026	70.062
10	0.6939	0.0107	-0.0577	0.2568	0.0062	1.0069	0.0133	-0.0313	0.0768	0.0175	0.014	-0.0233	-0.0935	0.072	-0.0272	0.14	-0.0028	0.0036	0.1405	0.001	0.1603	21.013	-35.385	24.576
11	1.7942	-0.0707	0.4281	2.398	-0.3562	1.4888	-0.0177	0.1384	-0.1693	-0.2743	-0.0271	-0.097	0.1291	0.1961	0.0448	0.1212	0.0374	0.0322	0.1548	-0.0361	0.1567	35.359	-56.301	12.315
12	0.5572	0.0745	-0.2494	0.5939	0.304	0.7868	-0.0037	0.0703	0.0826	-0.0191	0.0183	-0.0379	-0.0672	0.0025	-0.0146	0.123	0.0041	0.0109	0.1666	0.0234	0.1486	11.494	-38.471	16.355
13	0.56	-0.2925	0.1831	0.4869	-0.3343	0.7466	0.1202	-0.0393	-0.2839	-0.4201	0.0478	0.4171	0.1638	-0.0417	-0.168	0.5045	-0.0688	-0.3978	0.0223	0.0505	0.3939	-32.516	16.169	25.525
14	2.3326	-0.3443	-0.2433	3.7261	-1.2306	1.122	0.5382	-0.1848	-0.2406	-0.4543	-0.0668	0.4033	-0.0031	-0.017	-0.4714	0.5381	-0.0004	-0.2101	0.0969	0.0199	0.3413	-46.035	40.874	23.247
15	0.4811	-0.4179	0.3349	1.2527	-0.5735	0.6472	0.1541	0.0031	-0.2296	-0.554	0.0086	0.4632	0.0055	0.0615	-0.1627	0.6324	-0.0696	-0.3526	0.0586	0.0167	0.253	-23.697	22.161	18.336
16	0.7362	0.1153	0.1809	0.6922	0.3282	0.4803	0.0419	0.0653	-0.0144	-0.3646	0.0511	0.0768	-0.0724	0.0989	-0.0929	0.4652	-0.0496	-0.1112	0.0654	-0.006	0.0928	-4.754	30.452	24.952
17	1.5252	-0.7698	1.8974	3.7167	-3.4009	8.8866	0.0002	0.3235	-0.5086	-0.1704	0.1538	-0.4383	0.0071	0.2171	-0.154	0.1603	-0.0349	0.0108	0.1959	-0.268	0.4179	5.57	2.385	13.894
18	1.4654	0.4157	0.1299	1.5244	0.5577	0.2489	-0.1663	0.4166	-0.3091	-0.5808	0.288	-0.2377	-0.2523	0.1529	-0.1217	0.5354	-0.1051	-0.0128	0.2271	-0.1721	0.1719	-0.571	17.139	17.637

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	31 - 309
2	X-RAY DIFFRACTION	2	A	310 - 355
3	X-RAY DIFFRACTION	3	A	356 - 465
4	X-RAY DIFFRACTION	4	B	30 - 75
5	X-RAY DIFFRACTION	5	B	76 - 217
6	X-RAY DIFFRACTION	6	B	218 - 465
7	X-RAY DIFFRACTION	7	C	29 - 310
8	X-RAY DIFFRACTION	8	C	311 - 422
9	X-RAY DIFFRACTION	9	C	423 - 465
10	X-RAY DIFFRACTION	10	D	31 - 311
11	X-RAY DIFFRACTION	11	D	312 - 422
12	X-RAY DIFFRACTION	12	D	423 - 464
13	X-RAY DIFFRACTION	13	E	31 - 310
14	X-RAY DIFFRACTION	14	E	311 - 422
15	X-RAY DIFFRACTION	15	E	423 - 464
16	X-RAY DIFFRACTION	16	F	31 - 311
17	X-RAY DIFFRACTION	17	F	312 - 357
18	X-RAY DIFFRACTION	18	F	358 - 465

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