PDB-9hra: Crystal Structure of the Coxiella burnetii 2-methylisocitrate lya...

ID or keywords:

Entry

Database: PDB / ID: 9hra

Title

Crystal Structure of the Coxiella burnetii 2-methylisocitrate lyase Bound to Products Succinic and Pyruvic Acid

Components

2-methylisocitrate lyase

Keywords

CYTOSOLIC PROTEIN / PrpB / methylisocitrate lyase / carbon-carbon lyase / EC 4.1.3.30

Function / homology

Function and homology information

methylisocitrate lyase / propionate catabolic process, 2-methylcitrate cycle / methylisocitrate lyase activity / magnesium ion binding
Similarity search - Function

Biological species

Coxiella burnetii (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.48 Å

Authors

Stuart, W. / Isupov, M. / Harmer, N.J.

Funding support

United Kingdom, 1items

Citation

Journal: J.Biol.Chem. / Year: 2025
Title: Structure and catalytic mechanism of methylisocitrate lyase, a potential drug target against Coxiella burnetii.
Authors: Stuart, W.S. / Jenkins, C.H. / Ireland, P.M. / Isupov, M.N. / Norville, I.H. / Harmer, N.J.

History

Deposition	Dec 17, 2024	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Aug 13, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9hra.cif.gz	447.2 KB	Display	PDBx/mmCIF format
PDB format	pdb9hra.ent.gz	366.7 KB	Display	PDB format
PDBx/mmJSON format	9hra.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9hra_validation.pdf.gz	4.4 MB	Display	wwPDB validaton report
Full document	9hra_full_validation.pdf.gz	4.3 MB	Display
Data in XML	9hra_validation.xml.gz	98.6 KB	Display
Data in CIF	9hra_validation.cif.gz	127.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/hr/9hra ftp://data.pdbj.org/pub/pdb/validation_reports/hr/9hra	HTTPS FTP

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Related structure data

Related structure data	9hgkC 9hgoC 9hgqC 9hhsC 9hhyC C: citing same article (ref.)
Similar structure data	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	#50 - Feb 2004 Glycolytic Enzymes similarity (2) #102 - Jun 2008 Lactate Dehydrogenase similarity (1) #263 - Nov 2021 Acetohydroxyacid Synthase similarity (1)

Deposited unit

A: 2-methylisocitrate lyase

B: 2-methylisocitrate lyase

D: 2-methylisocitrate lyase

F: 2-methylisocitrate lyase

G: 2-methylisocitrate lyase

I: 2-methylisocitrate lyase

J: 2-methylisocitrate lyase

L: 2-methylisocitrate lyase

hetero molecules

257 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: 2-methylisocitrate lyase

B: 2-methylisocitrate lyase

D: 2-methylisocitrate lyase

F: 2-methylisocitrate lyase

hetero molecules

defined by author&software
Evidence: gel filtration
128 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

G: 2-methylisocitrate lyase

I: 2-methylisocitrate lyase

J: 2-methylisocitrate lyase

L: 2-methylisocitrate lyase

hetero molecules

defined by author&software
129 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	105.199, 101.203, 115.683
Angle α, β, γ (deg.)	90.00, 91.15, 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	SER	SER	LEU	LEU	A	A	0 - 283	2 - 285
2	1	SER	SER	LEU	LEU	B	B	0 - 283	2 - 285
1	2	SER	SER	GLN	GLN	A	A	0 - 282	2 - 284
2	2	SER	SER	GLN	GLN	D	C	0 - 282	2 - 284
1	3	MET	MET	LEU	LEU	A	A	1 - 283	3 - 285
2	3	MET	MET	LEU	LEU	F	D	1 - 283	3 - 285
1	4	SER	SER	PHE	PHE	A	A	0 - 284	2 - 286
2	4	SER	SER	PHE	PHE	G	E	0 - 284	2 - 286
1	5	SER	SER	PHE	PHE	A	A	0 - 284	2 - 286
2	5	SER	SER	PHE	PHE	I	F	0 - 284	2 - 286
1	6	SER	SER	LEU	LEU	A	A	0 - 283	2 - 285
2	6	SER	SER	LEU	LEU	J	G	0 - 283	2 - 285
1	7	SER	SER	PHE	PHE	A	A	0 - 284	2 - 286
2	7	SER	SER	PHE	PHE	L	H	0 - 284	2 - 286
1	8	SER	SER	LEU	LEU	B	B	0 - 283	2 - 285
2	8	SER	SER	LEU	LEU	D	C	0 - 283	2 - 285
1	9	MET	MET	GLN	GLN	B	B	1 - 282	3 - 284
2	9	MET	MET	GLN	GLN	F	D	1 - 282	3 - 284
1	10	SER	SER	GLN	GLN	B	B	0 - 282	2 - 284
2	10	SER	SER	GLN	GLN	G	E	0 - 282	2 - 284
1	11	SER	SER	LEU	LEU	B	B	0 - 283	2 - 285
2	11	SER	SER	LEU	LEU	I	F	0 - 283	2 - 285
1	12	SER	SER	LEU	LEU	B	B	0 - 283	2 - 285
2	12	SER	SER	LEU	LEU	J	G	0 - 283	2 - 285
1	13	SER	SER	LEU	LEU	B	B	0 - 283	2 - 285
2	13	SER	SER	LEU	LEU	L	H	0 - 283	2 - 285
1	14	MET	MET	GLN	GLN	D	C	1 - 282	3 - 284
2	14	MET	MET	GLN	GLN	F	D	1 - 282	3 - 284
1	15	SER	SER	GLN	GLN	D	C	0 - 282	2 - 284
2	15	SER	SER	GLN	GLN	G	E	0 - 282	2 - 284
1	16	SER	SER	LEU	LEU	D	C	0 - 283	2 - 285
2	16	SER	SER	LEU	LEU	I	F	0 - 283	2 - 285
1	17	SER	SER	LEU	LEU	D	C	0 - 283	2 - 285
2	17	SER	SER	LEU	LEU	J	G	0 - 283	2 - 285
1	18	SER	SER	LEU	LEU	D	C	0 - 283	2 - 285
2	18	SER	SER	LEU	LEU	L	H	0 - 283	2 - 285
1	19	MET	MET	LEU	LEU	F	D	1 - 283	3 - 285
2	19	MET	MET	LEU	LEU	G	E	1 - 283	3 - 285
1	20	MET	MET	PHE	PHE	F	D	1 - 284	3 - 286
2	20	MET	MET	PHE	PHE	I	F	1 - 284	3 - 286
1	21	MET	MET	LEU	LEU	F	D	1 - 283	3 - 285
2	21	MET	MET	LEU	LEU	J	G	1 - 283	3 - 285
1	22	MET	MET	PHE	PHE	F	D	1 - 284	3 - 286
2	22	MET	MET	PHE	PHE	L	H	1 - 284	3 - 286
1	23	SER	SER	PHE	PHE	G	E	0 - 284	2 - 286
2	23	SER	SER	PHE	PHE	I	F	0 - 284	2 - 286
1	24	SER	SER	LEU	LEU	G	E	0 - 283	2 - 285
2	24	SER	SER	LEU	LEU	J	G	0 - 283	2 - 285
1	25	SER	SER	PHE	PHE	G	E	0 - 284	2 - 286
2	25	SER	SER	PHE	PHE	L	H	0 - 284	2 - 286
1	26	SER	SER	LEU	LEU	I	F	0 - 283	2 - 285
2	26	SER	SER	LEU	LEU	J	G	0 - 283	2 - 285
1	27	SER	SER	LYS	LYS	I	F	0 - 285	2 - 287
2	27	SER	SER	LYS	LYS	L	H	0 - 285	2 - 287
1	28	SER	SER	GLN	GLN	J	G	0 - 282	2 - 284
2	28	SER	SER	GLN	GLN	L	H	0 - 282	2 - 284

NCS ensembles :

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Protein , 1 types, 8 molecules ABDFGIJL

#1: Protein	2-methylisocitrate lyase / 2-MIC / MICL / (2R / 3S)-2-methylisocitrate lyase Mass: 31526.178 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Coxiella burnetii (bacteria) / Gene: prpB, CBU_0771 / Production host: Escherichia coli (E. coli) / References: UniProt: Q83DG5, methylisocitrate lyase

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Non-polymers , 9 types, 619 molecules

#2: Chemical	ChemComp-SIN / SUCCINIC ACID Mass: 118.088 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₄H₆O₄ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-PYR / PYRUVIC ACID Mass: 88.062 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₃H₄O₃ / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	... ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C₂H₆O₂
#5: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#6: Chemical	... ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: Cl
#7: Chemical	ChemComp-DMS / DIMETHYL SULFOXIDE Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₆OS / Comment: DMSO, precipitant*YM
#8: Chemical	ChemComp-PGE / TRIETHYLENE GLYCOL Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₁₄O₄
#9: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#10: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 543 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	Y
Has protein modification	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.24 Å³/Da / Density % sol: 45.09 %
Crystal grow	Temperature: 292 K / Method: microbatch / pH: 6 Details: Ligand Friendly Screen B7: 0.1 M MES pH 6, 0.2 M NaCl, 20% PEG 6K, 10% Ethylene glycol

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9537 Å
Detector	Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Nov 26, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9537 Å / Relative weight: 1
Reflection	Resolution: 2.48→52.59 Å / Num. obs: 86032 / % possible obs: 99.91 % / Redundancy: 7.05 % / CC_1/2: 0.9695 / Net I/σ(I): 4.83
Reflection shell	Resolution: 2.48→2.52 Å / Num. unique obs: 4189 / CC_1/2: 0.2558

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
xia2		data reduction
DIALS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.48→52.59 Å / Cor.coef. F_o:F_c: 0.948 / Cor.coef. F_o:F_c free: 0.915 / SU B: 20.119 / SU ML: 0.379 / Cross valid method: THROUGHOUT / ESU R: 0.711 / ESU R Free: 0.304 / Stereochemistry target values: MAXIMUM LIKELIHOOD

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.25701	4243	4.9 %	RANDOM
R_work	0.20843	-	-	-
obs	0.21089	81674	99.76 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 53.907 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.22 Å²	-0 Å²	-2.62 Å²
2-	-	2.04 Å²	-0 Å²
3-	-	-	-0.72 Å²

Refinement step

Cycle: 1 / Resolution: 2.48→52.59 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	17149	0	271	543	17963

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.005	0.012	17676
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.076	1.636	23811
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.191	5	2228
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.482	22.872	867
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.161	15	2947
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.384	15	94
X-RAY DIFFRACTION	r_chiral_restr	0.091	0.2	2347
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	13187
X-RAY DIFFRACTION	r_gen_planes_other
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	10.079	10.341	8957
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	14.611	19.285	11170
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	12.023	11.172	8719
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined	19.075	73.769	26326
X-RAY DIFFRACTION	r_long_range_B_other
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	8679	0.07
1	2	B	8679	0.07
2	1	A	8687	0.06
2	2	D	8687	0.06
3	1	A	8704	0.07
3	2	F	8704	0.07
4	1	A	8740	0.06
4	2	G	8740	0.06
5	1	A	8737	0.06
5	2	I	8737	0.06
6	1	A	8691	0.06
6	2	J	8691	0.06
7	1	A	8648	0.06
7	2	L	8648	0.06
8	1	B	8688	0.06
8	2	D	8688	0.06
9	1	B	8743	0.06
9	2	F	8743	0.06
10	1	B	8658	0.06
10	2	G	8658	0.06
11	1	B	8701	0.07
11	2	I	8701	0.07
12	1	B	8669	0.06
12	2	J	8669	0.06
13	1	B	8644	0.06
13	2	L	8644	0.06
14	1	D	8702	0.07
14	2	F	8702	0.07
15	1	D	8712	0.06
15	2	G	8712	0.06
16	1	D	8739	0.07
16	2	I	8739	0.07
17	1	D	8672	0.06
17	2	J	8672	0.06
18	1	D	8661	0.06
18	2	L	8661	0.06
19	1	F	8711	0.06
19	2	G	8711	0.06
20	1	F	8812	0.06
20	2	I	8812	0.06
21	1	F	8706	0.05
21	2	J	8706	0.05
22	1	F	8692	0.06
22	2	L	8692	0.06
23	1	G	8734	0.07
23	2	I	8734	0.07
24	1	G	8677	0.06
24	2	J	8677	0.06
25	1	G	8665	0.06
25	2	L	8665	0.06
26	1	I	8686	0.06
26	2	J	8686	0.06
27	1	I	8719	0.07
27	2	L	8719	0.07
28	1	J	8644	0.06
28	2	L	8644	0.06

LS refinement shell

Resolution: 2.48→2.544 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.384	320	-
R_work	0.394	5832	-
obs	-	-	97.73 %

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