PDB-6bop: Crystal structure of 2-methylcitrate synthase from Aspergillus fu...

ID or keywords:

Entry

Database: PDB / ID: 6bop

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: 2.71 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	Nov 20, 2017	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 28, 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	Oct 4, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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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PDBx/mmCIF format	6bop.cif.gz	657.4 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	6bop_validation.pdf.gz	442.8 KB	Display	wwPDB validaton report
Full document	6bop_full_validation.pdf.gz	450.4 KB	Display
Data in XML	6bop_validation.xml.gz	57.3 KB	Display
Data in CIF	6bop_validation.cif.gz	79.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/bo/6bop ftp://data.pdbj.org/pub/pdb/validation_reports/bo/6bop	HTTPS FTP

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Related structure data

Related structure data	5uqoSC 5uqqC 5uqrC 5uqsC 5uquC 5uzpC 5uzqC 5uzrC 6bolC 6bomC 6bonC 6booC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5uqq-3 4x0p-2 6bom-3 5uqs-d 5uqo-d 6k5v-3 6k5v-2 4x0p-3 6bom-2 6k5v-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) 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	#93 - Sep 2007 Citrate Synthase similarity (10) #154 - Oct 2012 Citric Acid Cycle similarity (7)

Deposited unit

B: 2-methylcitrate synthase, mitochondrial

A: 2-methylcitrate synthase, mitochondrial

C: 2-methylcitrate synthase, mitochondrial

D: 2-methylcitrate synthase, mitochondrial

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

1

B: 2-methylcitrate synthase, mitochondrial

D: 2-methylcitrate synthase, mitochondrial

defined by author&software
Evidence: gel filtration
97.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

A: 2-methylcitrate synthase, mitochondrial

C: 2-methylcitrate synthase, mitochondrial

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

Unit cell

Length a, b, c (Å)	80.654, 100.451, 209.918
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:

ID	Ens-ID	Details
1	1	B
2	1	A
1	2	B
2	2	C
1	3	B
2	3	D
1	4	A
2	4	C
1	5	A
2	5	D
1	6	C
2	6	D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: _ / Auth seq-ID: 31 - 464 / Label seq-ID: 7 - 440

Dom-ID	Ens-ID	Auth asym-ID	Label asym-ID
1	1	B	A
2	1	A	B
1	2	B	A
2	2	C	C
1	3	B	A
2	3	D	D
1	4	A	B
2	4	C	C
1	5	A	B
2	5	D	D
1	6	C	C
2	6	D	D

NCS ensembles :

ID
1
2
3
4
5
6

#1: Protein	2-methylcitrate synthase, mitochondrial / Methylcitrate synthase / (2S / 3S)-2-methylcitrate synthase / Citrate synthase 1 Mass: 48571.453 Da / Num. of mol.: 4 / Mutation: G352A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Neosartorya fumigata (mold) / Gene: mcsA, cit1 / Production host: Escherichia coli (E. coli) References: UniProt: Q50I20, 2-methylcitrate synthase, citrate synthase (unknown stereospecificity)
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 170 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

2-methylcitrate synthase, mitochondrial / Methylcitrate synthase / (2S / 3S)-2-methylcitrate synthase / Citrate synthase 1

Mass: 48571.453 Da / Num. of mol.: 4 / Mutation: G352A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Neosartorya fumigata (mold) / Gene: mcsA, cit1 / Production host:

Escherichia coli (E. coli)
References: UniProt: Q50I20, 2-methylcitrate synthase, citrate synthase (unknown stereospecificity)

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 170 / 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: 2.19 Å³/Da / Density % sol: 43.79 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1 M Tris, pH 8.5 25% PEG3350

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
Detector	Type: RAYONIX MX300-HS / Detector: CCD / Date: Jun 23, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.7→40 Å / Num. obs: 42989 / % possible obs: 91.1 % / Observed criterion σ(I): -3 / Redundancy: 4.4 % / R_merge(I) obs: 0.105 / R_pim(I) all: 0.065 / R_rim(I) all: 0.14 / R_sym value: 0.105 / Net I/σ(I): 12.3
Reflection shell	Resolution: 2.7→2.75 Å / Redundancy: 4.3 % / R_merge(I) obs: 0.424 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 2185 / R_pim(I) all: 0.218 / R_rim(I) all: 0.45 / R_sym value: 0.424 / % possible all: 94.8

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0158	refinement
HKL-2000		data reduction
HKL-2000		data scaling
MOLREP		phasing
HKL-3000		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5UQO

5uqo

Resolution: 2.71→40 Å / Cor.coef. F_o:F_c: 0.937 / Cor.coef. F_o:F_c free: 0.9 / Cross valid method: THROUGHOUT / ESU R Free: 0.383 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.233	2113	4.9 %	RANDOM
R_work	0.18676	-	-	-
obs	0.189	40851	90.95 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 37.425 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.23 Å²	0 Å²	0 Å²
2-	-	1.52 Å²	-0 Å²
3-	-	-	-1.28 Å²

Refinement step

Cycle: 1 / Resolution: 2.71→40 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	13486	0	0	170	13656

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.019	13829
X-RAY DIFFRACTION	r_bond_other_d	0	0.02	13017
X-RAY DIFFRACTION	r_angle_refined_deg	1.575	1.969	18775
X-RAY DIFFRACTION	r_angle_other_deg	3.684	3	30221
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.287	5	1735
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	38.328	24.141	594
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.466	15	2326
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.196	15	74
X-RAY DIFFRACTION	r_chiral_restr	0.09	0.2	2086
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.021	15357
X-RAY DIFFRACTION	r_gen_planes_other	0.011	0.02	2741
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	1.115	2.441	6943
X-RAY DIFFRACTION	r_mcbond_other	1.114	2.441	6942
X-RAY DIFFRACTION	r_mcangle_it	1.966	3.658	8671
X-RAY DIFFRACTION	r_mcangle_other	1.966	3.658	8672
X-RAY DIFFRACTION	r_scbond_it	1.211	2.582	6886
X-RAY DIFFRACTION	r_scbond_other	1.211	2.582	6887
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	2.135	3.804	10103
X-RAY DIFFRACTION	r_long_range_B_refined	3.442	27.98	15171
X-RAY DIFFRACTION	r_long_range_B_other	3.44	27.978	15166
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	27322	0.07
1	2	A	27322	0.07
2	1	B	27202	0.08
2	2	C	27202	0.08
3	1	B	26800	0.09
3	2	D	26800	0.09
4	1	A	27254	0.08
4	2	C	27254	0.08
5	1	A	26984	0.08
5	2	D	26984	0.08
6	1	C	26746	0.09
6	2	D	26746	0.09

LS refinement shell

Resolution: 2.709→2.779 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.344	173	-
R_work	0.269	2974	-
obs	-	-	92.02 %

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	0.5581	-0.0748	0.0758	0.7012	-0.335	0.8677	0.0339	-0.0313	-0.0294	-0.1057	0.0375	0.0826	0.0831	-0.0421	-0.0714	0.1365	0.0145	-0.0199	0.0083	0.0088	0.1387	17.605	56.261	15.049
2	1.3953	0.0873	-0.8797	3.1625	1.3514	2.2685	-0.0854	-0.1691	0.1151	-0.355	0.0158	0.2458	-0.2159	-0.0491	0.0697	0.0747	0.0314	0.0011	0.0487	-0.003	0.2007	9.287	81.299	27.957
3	1.1174	0.1342	-0.4836	0.413	-0.064	0.6714	0.0255	-0.1513	0.01	-0.0994	-0.0402	0.1033	-0.0742	0.1322	0.0147	0.1674	0.0014	-0.0086	0.0387	0.0227	0.124	22.581	66.788	17.255
4	0.7606	0.2038	-0.0264	0.6673	0.0877	0.0377	-0.0022	0.0508	0.0486	-0.0247	0.0061	-0.015	-0.0449	0.0136	-0.0038	0.1203	0.0117	-0.0207	0.0621	0.0071	0.1222	-3.231	22.133	31.773
5	0.7774	-0.1514	0.9664	0.5924	0.438	2.0146	0.0262	0.0354	0.0321	0.0475	-0.0435	-0.1424	0.1273	0.03	0.0174	0.0704	-0.0018	0.0115	0.066	0.0287	0.185	16.714	8.037	48.419
6	0.7231	-0.0727	0.1641	0.331	-0.0084	0.0503	0.0334	-0.0642	0.0591	0.0824	-0.0879	0.0593	-0.0001	-0.0262	0.0545	0.1529	-0.0042	-0.0133	0.0893	-0.0223	0.1595	-2.572	11.522	37.292
7	0.4762	0.0746	-0.0926	0.7273	-0.1175	0.5773	0.0121	-0.0481	-0.0132	-0.039	0.0015	-0.0642	-0.0288	0.1113	-0.0135	0.131	0.006	0.0216	0.045	-0.0165	0.1063	47.728	62.125	22.282
8	1.1595	0.9304	1.5299	3.3074	2.0559	3.1314	-0.0444	0.3123	-0.1958	-0.1095	0.3598	-0.1099	-0.1385	0.4633	-0.3155	0.1299	0.0955	-0.0268	0.1918	-0.0904	0.0694	57.358	45.497	1.318
9	0.144	-0.101	0.2126	0.0769	-0.1439	1.9244	0.1152	0.0265	-0.0227	-0.1017	-0.0088	0.0385	-0.0398	0.2033	-0.1064	0.222	-0.026	-0.0337	0.0372	0.0386	0.2381	38.968	62.641	14.513
10	0.85	-0.0423	-0.5398	0.5223	0.3159	0.7307	-0.0195	-0.0052	-0.0317	0.0373	0.0038	0.0485	0.0429	-0.0058	0.0158	0.0722	0.0113	-0.0314	0.0549	0.0117	0.1281	-27.094	6.369	45.247
11	4.6216	-1.6084	-0.6643	3.511	-1.0187	4.764	0.4165	1.455	0.0005	-0.6162	-0.518	0.035	0.1353	-0.7634	0.1014	0.1272	0.188	0.0075	0.74	0.0343	0.0158	-39.406	12.902	19.04
12	0.8371	-0.2058	-0.9847	0.1885	0.3392	1.2689	0.1686	0.3488	-0.0767	-0.0334	-0.1525	-0.0633	-0.1669	-0.4173	-0.0162	0.0773	0.0683	-0.0451	0.235	-0.0398	0.1157	-32.415	9.089	30.688

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	31 - 307
2	X-RAY DIFFRACTION	2	A	308 - 398
3	X-RAY DIFFRACTION	3	A	399 - 464
4	X-RAY DIFFRACTION	4	B	31 - 307
5	X-RAY DIFFRACTION	5	B	308 - 398
6	X-RAY DIFFRACTION	6	B	399 - 464
7	X-RAY DIFFRACTION	7	C	31 - 310
8	X-RAY DIFFRACTION	8	C	311 - 418
9	X-RAY DIFFRACTION	9	C	419 - 464
10	X-RAY DIFFRACTION	10	D	29 - 309
11	X-RAY DIFFRACTION	11	D	310 - 362
12	X-RAY DIFFRACTION	12	D	363 - 464

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