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

ID or keywords:

Entry

Database: PDB / ID: 9hhy

Title

Crystal Structure of the Coxiella burnetii 2-methylisocitrate lyase Bound to Inhibitor Isocitric 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: 2.33 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	Nov 22, 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	9hhy.cif.gz	685.9 KB	Display	PDBx/mmCIF format
PDB format	pdb9hhy.ent.gz	564.1 KB	Display	PDB format
PDBx/mmJSON format	9hhy.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9hhy_validation.pdf.gz	8.6 MB	Display	wwPDB validaton report
Full document	9hhy_full_validation.pdf.gz	8.6 MB	Display
Data in XML	9hhy_validation.xml.gz	152 KB	Display
Data in CIF	9hhy_validation.cif.gz	193.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/hh/9hhy ftp://data.pdbj.org/pub/pdb/validation_reports/hh/9hhy	HTTPS FTP

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Related structure data

Related structure data	9hgkC 9hgoC 9hgqC 9hhsC 9hraC 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	#129 - Sep 2010 Isocitrate Dehydrogenase similarity (1) #154 - Oct 2012 Citric Acid Cycle similarity (1) #89 - May 2007 Aconitase and Iron Regulatory Protein 1 similarity (1) #50 - Feb 2004 Glycolytic Enzymes similarity (2)

Deposited unit

A: 2-methylisocitrate lyase

B: 2-methylisocitrate lyase

C: 2-methylisocitrate lyase

D: 2-methylisocitrate lyase

E: 2-methylisocitrate lyase

F: 2-methylisocitrate lyase

G: 2-methylisocitrate lyase

H: 2-methylisocitrate lyase

I: 2-methylisocitrate lyase

J: 2-methylisocitrate lyase

K: 2-methylisocitrate lyase

L: 2-methylisocitrate lyase

hetero molecules

418 kDa, 12 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: 2-methylisocitrate lyase

B: 2-methylisocitrate lyase

C: 2-methylisocitrate lyase

D: 2-methylisocitrate lyase

hetero molecules

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

2

E: 2-methylisocitrate lyase

F: 2-methylisocitrate lyase

H: 2-methylisocitrate lyase

K: 2-methylisocitrate lyase

hetero molecules

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

3

G: 2-methylisocitrate lyase

I: 2-methylisocitrate lyase

J: 2-methylisocitrate lyase

L: 2-methylisocitrate lyase

hetero molecules

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

Unit cell

Length a, b, c (Å)	93.785, 115.550, 195.241
Angle α, β, γ (deg.)	90.00, 92.34, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS ensembles :

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Protein , 1 types, 12 molecules ABCDEFGHIJKL

#1: Protein	2-methylisocitrate lyase / 2-MIC / MICL / (2R / 3S)-2-methylisocitrate lyase Mass: 34358.168 Da / Num. of mol.: 12 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 , 7 types, 952 molecules

#2: Chemical	ChemComp-ICT / ISOCITRIC ACID Mass: 192.124 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C₆H₈O₇ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	... ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 32 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Cl
#6: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#7: Chemical	ChemComp-PGE / TRIETHYLENE GLYCOL Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₁₄O₄
#8: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 881 / 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: 2.56 Å³/Da / Density % sol: 52.02 %
Crystal grow	Temperature: 292 K / Method: microbatch Details: Clear Strategy I D7: 0.3 M sodium acetate trihydrate, 0.1 M sodium cacodylate pH 6.5, 8% w/v PEG 20,000, 8% v/v PEG 500 MME

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
Detector	Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Dec 13, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9763 Å / Relative weight: 1
Reflection	Resolution: 2.33→59.24 Å / Num. obs: 177721 / % possible obs: 99.98 % / Redundancy: 7.04 % / CC_1/2: 0.9945 / Net I/σ(I): 8.29
Reflection shell	Resolution: 2.33→2.37 Å / Num. unique obs: 8831 / CC_1/2: 0.2991

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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: 2.33→59.24 Å / Cor.coef. F_o:F_c: 0.955 / Cor.coef. F_o:F_c free: 0.933 / SU B: 15.71 / SU ML: 0.318 / Cross valid method: THROUGHOUT / ESU R: 0.352 / ESU R Free: 0.255 / Stereochemistry target values: MAXIMUM LIKELIHOOD

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.26523	8841	5 %	RANDOM
R_work	0.214	-	-	-
obs	0.21657	168617	99.83 %	-

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: 68.925 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	2.57 Å²	0 Å²	1.57 Å²
2-	-	-1.87 Å²	0 Å²
3-	-	-	-0.82 Å²

Refinement step

Cycle: 1 / Resolution: 2.33→59.24 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	26526	0	326	881	27733

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.006	0.012	27308
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.195	1.637	36829
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.113	5	3444
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.402	22.584	1362
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.783	15	4588
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.295	15	164
X-RAY DIFFRACTION	r_chiral_restr	0.096	0.2	3624
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	20457
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	14.276	13.485	13812
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	18.71	25.177	17244
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	15.816	14.149	13496
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	21.983	96.76	40671
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	8994	0.06
1	2	B	8994	0.06
2	1	A	9068	0.05
2	2	C	9068	0.05
3	1	A	9125	0.07
3	2	D	9125	0.07
4	1	A	8976	0.06
4	2	E	8976	0.06
5	1	A	9023	0.05
5	2	F	9023	0.05
6	1	A	8912	0.07
6	2	G	8912	0.07
7	1	A	9027	0.05
7	2	H	9027	0.05
8	1	A	9025	0.07
8	2	I	9025	0.07
9	1	A	9077	0.05
9	2	J	9077	0.05
10	1	A	9049	0.06
10	2	K	9049	0.06
11	1	A	8851	0.07
11	2	L	8851	0.07
12	1	B	9055	0.05
12	2	C	9055	0.05
13	1	B	9035	0.06
13	2	D	9035	0.06
14	1	B	8949	0.06
14	2	E	8949	0.06
15	1	B	9007	0.05
15	2	F	9007	0.05
16	1	B	8937	0.07
16	2	G	8937	0.07
17	1	B	9057	0.04
17	2	H	9057	0.04
18	1	B	8998	0.06
18	2	I	8998	0.06
19	1	B	9042	0.05
19	2	J	9042	0.05
20	1	B	9022	0.06
20	2	K	9022	0.06
21	1	B	8834	0.06
21	2	L	8834	0.06
22	1	C	9147	0.05
22	2	D	9147	0.05
23	1	C	9038	0.05
23	2	E	9038	0.05
24	1	C	9055	0.05
24	2	F	9055	0.05
25	1	C	9018	0.06
25	2	G	9018	0.06
26	1	C	9072	0.05
26	2	H	9072	0.05
27	1	C	9053	0.06
27	2	I	9053	0.06
28	1	C	9137	0.05
28	2	J	9137	0.05
29	1	C	9149	0.05
29	2	K	9149	0.05
30	1	C	8867	0.06
30	2	L	8867	0.06
31	1	D	9049	0.05
31	2	E	9049	0.05
32	1	D	9063	0.05
32	2	F	9063	0.05
33	1	D	9025	0.07
33	2	G	9025	0.07
34	1	D	9067	0.06
34	2	H	9067	0.06
35	1	D	9135	0.06
35	2	I	9135	0.06
36	1	D	9136	0.05
36	2	J	9136	0.05
37	1	D	9125	0.05
37	2	K	9125	0.05
38	1	D	8855	0.07
38	2	L	8855	0.07
39	1	E	8941	0.06
39	2	F	8941	0.06
40	1	E	8940	0.06
40	2	G	8940	0.06
41	1	E	8946	0.05
41	2	H	8946	0.05
42	1	E	8999	0.05
42	2	I	8999	0.05
43	1	E	8992	0.05
43	2	J	8992	0.05
44	1	E	9018	0.05
44	2	K	9018	0.05
45	1	E	8730	0.07
45	2	L	8730	0.07
46	1	F	8994	0.06
46	2	G	8994	0.06
47	1	F	9065	0.06
47	2	H	9065	0.06
48	1	F	8995	0.06
48	2	I	8995	0.06
49	1	F	9061	0.05
49	2	J	9061	0.05
50	1	F	9054	0.05
50	2	K	9054	0.05
51	1	F	8880	0.07
51	2	L	8880	0.07
52	1	G	8938	0.07
52	2	H	8938	0.07
53	1	G	9018	0.06
53	2	I	9018	0.06
54	1	G	8983	0.06
54	2	J	8983	0.06
55	1	G	8988	0.06
55	2	K	8988	0.06
56	1	G	8745	0.08
56	2	L	8745	0.08
57	1	H	8980	0.06
57	2	I	8980	0.06
58	1	H	9044	0.06
58	2	J	9044	0.06
59	1	H	9067	0.05
59	2	K	9067	0.05
60	1	H	8931	0.06
60	2	L	8931	0.06
61	1	I	9051	0.05
61	2	J	9051	0.05
62	1	I	9050	0.05
62	2	K	9050	0.05
63	1	I	8757	0.08
63	2	L	8757	0.08
64	1	J	9149	0.05
64	2	K	9149	0.05
65	1	J	8867	0.07
65	2	L	8867	0.07
66	1	K	8842	0.07
66	2	L	8842	0.07

LS refinement shell

Resolution: 2.33→2.39 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.435	697	-
R_work	0.426	12151	-
obs	-	-	98.19 %

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