PDB-5mux: Crystal structure of 2-methylcitrate dehydratase (MmgE) from Baci...

ID or keywords:

Entry

Database: PDB / ID: 5mux

Title

Crystal structure of 2-methylcitrate dehydratase (MmgE) from Bacillus subtilis.

Components

2-methylcitrate dehydratase

Keywords

LYASE / dehydratase

Function / homology

Function and homology information

2-methylcitrate dehydratase activity / propionate metabolic process, methylcitrate cycle / Lyases; Carbon-oxygen lyases; Hydro-lyases / sporulation resulting in formation of a cellular spore / tricarboxylic acid cycle / 2 iron, 2 sulfur cluster binding
Similarity search - Function

Biological species

Bacillus subtilis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2 Å

Authors

Baker, G.E. / Race, P.R.

Citation

Journal: To Be Published
Title: Crystal structure of 2-methylcitrate dehydratase (MmgE) from Bacillus subtilis.
Authors: Baker, G.E. / Race, P.R.

History

Deposition	Jan 14, 2017	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Feb 14, 2018	Provider: repository / Type: Initial release
Revision 1.1	Oct 16, 2019	Group: Data collection / Category: reflns_shell
Revision 1.2	May 8, 2024	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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	5mux.cif.gz	555.4 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	5mux_validation.pdf.gz	483.8 KB	Display	wwPDB validaton report
Full document	5mux_full_validation.pdf.gz	504.7 KB	Display
Data in XML	5mux_validation.xml.gz	100.9 KB	Display
Data in CIF	5mux_validation.cif.gz	145.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/mu/5mux ftp://data.pdbj.org/pub/pdb/validation_reports/mu/5mux	HTTPS FTP

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Related structure data

Similar structure data	6ik6-1 4ywo-1 5j8q-1 6xx8-d 4cz8-d 6r6u-d 5ul4-d 2po3-d 2qne-d 2hp0-d 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

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#228 - Dec 2018 Directed Evolution of Enzymes similarity (1)

Deposited unit

A: 2-methylcitrate dehydratase

B: 2-methylcitrate dehydratase

C: 2-methylcitrate dehydratase

D: 2-methylcitrate dehydratase

E: 2-methylcitrate dehydratase

F: 2-methylcitrate dehydratase

hetero molecules

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

1

A: 2-methylcitrate dehydratase

B: 2-methylcitrate dehydratase

hetero molecules

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

2

C: 2-methylcitrate dehydratase

D: 2-methylcitrate dehydratase

hetero molecules

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

3

E: 2-methylcitrate dehydratase

F: 2-methylcitrate dehydratase

hetero molecules

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

Unit cell

Length a, b, c (Å)	90.831, 194.409, 90.869
Angle α, β, γ (deg.)	90.00, 92.74, 90.00
Int Tables number	4
Space group name H-M	P12₁1

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	MET	MET	ASP	ASP	A	A	1 - 468	1 - 468
2	1	MET	MET	ASP	ASP	B	B	1 - 468	1 - 468
1	2	MET	MET	ASP	ASP	A	A	1 - 468	1 - 468
2	2	MET	MET	ASP	ASP	C	C	1 - 468	1 - 468
1	3	MET	MET	ASP	ASP	A	A	1 - 468	1 - 468
2	3	MET	MET	ASP	ASP	D	D	1 - 468	1 - 468
1	4	MET	MET	ASP	ASP	A	A	1 - 468	1 - 468
2	4	MET	MET	ASP	ASP	E	E	1 - 468	1 - 468
1	5	PRO	PRO	ASP	ASP	A	A	2 - 468	2 - 468
2	5	PRO	PRO	ASP	ASP	F	F	2 - 468	2 - 468
1	6	MET	MET	MET	MET	B	B	1 - 472	1 - 472
2	6	MET	MET	MET	MET	C	C	1 - 472	1 - 472
1	7	MET	MET	PHE	PHE	B	B	1 - 470	1 - 470
2	7	MET	MET	PHE	PHE	D	D	1 - 470	1 - 470
1	8	MET	MET	MET	MET	B	B	1 - 472	1 - 472
2	8	MET	MET	MET	MET	E	E	1 - 472	1 - 472
1	9	PRO	PRO	ASP	ASP	B	B	2 - 468	2 - 468
2	9	PRO	PRO	ASP	ASP	F	F	2 - 468	2 - 468
1	10	MET	MET	PHE	PHE	C	C	1 - 470	1 - 470
2	10	MET	MET	PHE	PHE	D	D	1 - 470	1 - 470
1	11	MET	MET	MET	MET	C	C	1 - 472	1 - 472
2	11	MET	MET	MET	MET	E	E	1 - 472	1 - 472
1	12	PRO	PRO	ASP	ASP	C	C	2 - 468	2 - 468
2	12	PRO	PRO	ASP	ASP	F	F	2 - 468	2 - 468
1	13	MET	MET	PHE	PHE	D	D	1 - 470	1 - 470
2	13	MET	MET	PHE	PHE	E	E	1 - 470	1 - 470
1	14	PRO	PRO	ASP	ASP	D	D	2 - 468	2 - 468
2	14	PRO	PRO	ASP	ASP	F	F	2 - 468	2 - 468
1	15	PRO	PRO	ASP	ASP	E	E	2 - 468	2 - 468
2	15	PRO	PRO	ASP	ASP	F	F	2 - 468	2 - 468

NCS ensembles :

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

#1: Protein	2-methylcitrate dehydratase / 2-MC dehydratase / (2S / 3S)-2-methylcitrate dehydratase / Probable aconitate hydratase / Aconitase Mass: 52977.348 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria) Gene: prpD, mmgE, yqiP, BSU24130 / Production host: Escherichia coli (E. coli) References: UniProt: P45859, 2-methylcitrate dehydratase, aconitate hydratase
#2: Chemical	ChemComp-TLA / L(+)-TARTARIC ACID Mass: 150.087 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₄H₆O₆
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1026 / 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: 2.52 Å³/Da / Density % sol: 51.21 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop Details: 0.2 M potassium/sodium tartrate, 20 % w/v PEG 3350.

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

Diamond

/ Beamline: I24 / Wavelength: 0.9686 Å

Detector

Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 7, 2015

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.9686 Å / Relative weight: 1

Reflection twin

Crystal-ID	ID	Operator	Domain-ID	Fraction
1	1	H, K, L	1	0.525
1	1	L, -K, H	2	0.475

Reflection

Resolution: 2→30.8 Å / Num. obs: 200076 / % possible obs: 99.5 % / Redundancy: 6.3 % / CC_1/2: 0.64 / Net I/σ(I): 4.5

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0103	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2→30.8 Å / Cor.coef. F_o:F_c: 0.954 / Cor.coef. F_o:F_c free: 0.925 / SU B: 2.059 / SU ML: 0.06 / Cross valid method: THROUGHOUT / ESU R: 0.03 / ESU R Free: 0.028 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.18926	10311	4.9 %	RANDOM
R_work	0.15094	-	-	-
obs	0.15279	200076	99.39 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 19.941 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-2.59 Å²	0 Å²	-12.56 Å²
2-	-	-5.54 Å²	0 Å²
3-	-	-	8.13 Å²

Refinement step

Cycle: 1 / Resolution: 2→30.8 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	22020	0	60	1026	23106

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.014	0.019	22550
X-RAY DIFFRACTION	r_bond_other_d	0.008	0.02	21421
X-RAY DIFFRACTION	r_angle_refined_deg	1.484	1.961	30625
X-RAY DIFFRACTION	r_angle_other_deg	1.289	3	49263
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.72	5	2818
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.827	23.729	1003
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.847	15	3790
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	21.318	15	157
X-RAY DIFFRACTION	r_chiral_restr	0.141	0.2	3473
X-RAY DIFFRACTION	r_gen_planes_refined	0.017	0.021	25432
X-RAY DIFFRACTION	r_gen_planes_other	0.011	0.02	5051
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	2.628	1.801	11290
X-RAY DIFFRACTION	r_mcbond_other	2.628	1.801	11289
X-RAY DIFFRACTION	r_mcangle_it	3.602	2.691	14102
X-RAY DIFFRACTION	r_mcangle_other	3.601	2.691	14103
X-RAY DIFFRACTION	r_scbond_it	3.525	2.143	11260
X-RAY DIFFRACTION	r_scbond_other	3.525	2.143	11257
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	5.072	3.083	16522
X-RAY DIFFRACTION	r_long_range_B_refined	6.434	14.714	26298
X-RAY DIFFRACTION	r_long_range_B_other	6.433	14.695	26213
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	A	58852	0.08
1	2	B	58852	0.08
2	1	A	59246	0.07
2	2	C	59246	0.07
3	1	A	58924	0.08
3	2	D	58924	0.08
4	1	A	58592	0.08
4	2	E	58592	0.08
5	1	A	55820	0.09
5	2	F	55820	0.09
6	1	B	59464	0.07
6	2	C	59464	0.07
7	1	B	58974	0.08
7	2	D	58974	0.08
8	1	B	58928	0.08
8	2	E	58928	0.08
9	1	B	55536	0.09
9	2	F	55536	0.09
10	1	C	59738	0.07
10	2	D	59738	0.07
11	1	C	59644	0.08
11	2	E	59644	0.08
12	1	C	55788	0.08
12	2	F	55788	0.08
13	1	D	59080	0.07
13	2	E	59080	0.07
14	1	D	56058	0.08
14	2	F	56058	0.08
15	1	E	55742	0.08
15	2	F	55742	0.08

LS refinement shell

Resolution: 1.999→2.051 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.287	752	-
R_work	0.22	14528	-
obs	-	-	97.96 %

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