PDB-7ebe: Crystal structure of Isocitrate lyase-1 from Candida albicans

ID or keywords:

Entry

Database: PDB / ID: 7ebe

Title

Crystal structure of Isocitrate lyase-1 from Candida albicans

Components

Isocitrate lyase

Keywords

LYASE / Isocitrate lyase / glyoxylate cycle / ubiquitination

Function / homology

Function and homology information

methylisocitrate lyase activity / glyoxysome / isocitrate lyase activity / glyoxylate cycle / tricarboxylic acid cycle / peroxisome / metal ion binding
Similarity search - Function

Biological species

Candida albicans (yeast)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.69 Å

Authors

Hiragi, K. / Nishio, K. / Moriyama, S. / Hamaguchi, T. / Mizoguchi, A. / Yonekura, K. / Tani, K. / Mizushima, T.

Citation

Journal: J Struct Biol / Year: 2021
Title: Structural insights into the targeting specificity of ubiquitin ligase for S. cerevisiae isocitrate lyase but not C. albicans isocitrate lyase.
Authors: Keito Hiragi / Kazuya Nishio / Shu Moriyama / Tasuku Hamaguchi / Akira Mizoguchi / Koji Yonekura / Kazutoshi Tani / Tsunehiro Mizushima /

Abstract: In Saccharomyces cerevisiae, the glyoxylate cycle is controlled through the posttranslational regulation of its component enzymes, such as isocitrate lyase (ICL), which catalyzes the first unique ...

History

Deposition	Mar 9, 2021	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Jun 23, 2021	Provider: repository / Type: Initial release
Revision 1.1	Nov 29, 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	7ebe.cif.gz	827 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	7ebe_validation.pdf.gz	535.4 KB	Display	wwPDB validaton report
Full document	7ebe_full_validation.pdf.gz	625.3 KB	Display
Data in XML	7ebe_validation.xml.gz	151.9 KB	Display
Data in CIF	7ebe_validation.cif.gz	198.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/eb/7ebe ftp://data.pdbj.org/pub/pdb/validation_reports/eb/7ebe	HTTPS FTP

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Related structure data

Related structure data	31053C 7ebcSC 7ebfC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	7ebe-2 7ebc-d 1dqu-1 5nqd-1 5nqd-2 5e9f-d 1g8k-6 5e9g-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) 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)

Deposited unit

A: Isocitrate lyase

B: Isocitrate lyase

C: Isocitrate lyase

D: Isocitrate lyase

E: Isocitrate lyase

F: Isocitrate lyase

G: Isocitrate lyase

H: Isocitrate lyase

hetero molecules

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

1

A: Isocitrate lyase

B: Isocitrate lyase

C: Isocitrate lyase

D: Isocitrate lyase

hetero molecules

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

2

E: Isocitrate lyase

F: Isocitrate lyase

G: Isocitrate lyase

H: Isocitrate lyase

hetero molecules

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

Unit cell

Length a, b, c (Å)	80.971, 139.910, 200.301
Angle α, β, γ (deg.)	90.00, 92.55, 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	PRO	PRO	GLU	GLU	A	A	2 - 540	8 - 546
2	1	PRO	PRO	GLU	GLU	B	B	2 - 540	8 - 546
1	2	PRO	PRO	LYS	LYS	A	A	2 - 544	8 - 550
2	2	PRO	PRO	LYS	LYS	C	C	2 - 544	8 - 550
1	3	PRO	PRO	LYS	LYS	A	A	2 - 544	8 - 550
2	3	PRO	PRO	LYS	LYS	D	D	2 - 544	8 - 550
1	4	PRO	PRO	LYS	LYS	A	A	2 - 544	8 - 550
2	4	PRO	PRO	LYS	LYS	E	E	2 - 544	8 - 550
1	5	PRO	PRO	PHE	PHE	A	A	2 - 543	8 - 549
2	5	PRO	PRO	PHE	PHE	F	F	2 - 543	8 - 549
1	6	THR	THR	PHE	PHE	A	A	4 - 543	10 - 549
2	6	THR	THR	PHE	PHE	G	G	4 - 543	10 - 549
1	7	THR	THR	GLN	GLN	A	A	4 - 536	10 - 542
2	7	THR	THR	GLN	GLN	H	H	4 - 536	10 - 542
1	8	PRO	PRO	ASP	ASP	B	B	2 - 541	8 - 547
2	8	PRO	PRO	ASP	ASP	C	C	2 - 541	8 - 547
1	9	PRO	PRO	GLU	GLU	B	B	2 - 540	8 - 546
2	9	PRO	PRO	GLU	GLU	D	D	2 - 540	8 - 546
1	10	PRO	PRO	GLU	GLU	B	B	2 - 540	8 - 546
2	10	PRO	PRO	GLU	GLU	E	E	2 - 540	8 - 546
1	11	PRO	PRO	GLU	GLU	B	B	2 - 540	8 - 546
2	11	PRO	PRO	GLU	GLU	F	F	2 - 540	8 - 546
1	12	THR	THR	ASP	ASP	B	B	4 - 541	10 - 547
2	12	THR	THR	ASP	ASP	G	G	4 - 541	10 - 547
1	13	THR	THR	GLN	GLN	B	B	4 - 536	10 - 542
2	13	THR	THR	GLN	GLN	H	H	4 - 536	10 - 542
1	14	PRO	PRO	LYS	LYS	C	C	2 - 544	8 - 550
2	14	PRO	PRO	LYS	LYS	D	D	2 - 544	8 - 550
1	15	PRO	PRO	LYS	LYS	C	C	2 - 544	8 - 550
2	15	PRO	PRO	LYS	LYS	E	E	2 - 544	8 - 550
1	16	PRO	PRO	LYS	LYS	C	C	2 - 544	8 - 550
2	16	PRO	PRO	LYS	LYS	F	F	2 - 544	8 - 550
1	17	THR	THR	PHE	PHE	C	C	4 - 543	10 - 549
2	17	THR	THR	PHE	PHE	G	G	4 - 543	10 - 549
1	18	THR	THR	GLY	GLY	C	C	4 - 537	10 - 543
2	18	THR	THR	GLY	GLY	H	H	4 - 537	10 - 543
1	19	PRO	PRO	LYS	LYS	D	D	2 - 544	8 - 550
2	19	PRO	PRO	LYS	LYS	E	E	2 - 544	8 - 550
1	20	PRO	PRO	LYS	LYS	D	D	2 - 544	8 - 550
2	20	PRO	PRO	LYS	LYS	F	F	2 - 544	8 - 550
1	21	THR	THR	PHE	PHE	D	D	4 - 543	10 - 549
2	21	THR	THR	PHE	PHE	G	G	4 - 543	10 - 549
1	22	THR	THR	GLN	GLN	D	D	4 - 536	10 - 542
2	22	THR	THR	GLN	GLN	H	H	4 - 536	10 - 542
1	23	PRO	PRO	LYS	LYS	E	E	2 - 544	8 - 550
2	23	PRO	PRO	LYS	LYS	F	F	2 - 544	8 - 550
1	24	THR	THR	PHE	PHE	E	E	4 - 543	10 - 549
2	24	THR	THR	PHE	PHE	G	G	4 - 543	10 - 549
1	25	THR	THR	GLN	GLN	E	E	4 - 536	10 - 542
2	25	THR	THR	GLN	GLN	H	H	4 - 536	10 - 542
1	26	THR	THR	PHE	PHE	F	F	4 - 543	10 - 549
2	26	THR	THR	PHE	PHE	G	G	4 - 543	10 - 549
1	27	THR	THR	GLN	GLN	F	F	4 - 536	10 - 542
2	27	THR	THR	GLN	GLN	H	H	4 - 536	10 - 542
1	28	THR	THR	GLY	GLY	G	G	4 - 537	10 - 543
2	28	THR	THR	GLY	GLY	H	H	4 - 537	10 - 543

NCS ensembles :

#1: Protein	Isocitrate lyase Mass: 62336.523 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Candida albicans (yeast) / Production host: Escherichia coli (E. coli) / References: UniProt: Q59RB8, isocitrate lyase
#2: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#3: Chemical	ChemComp-FMT / FORMIC ACID Mass: 46.025 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: CH₂O₂
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 298 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	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: 2.31 Å³/Da / Density % sol: 46.73 %
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 22%(w/v)PEG 3350, 0.2M magnesium formate

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 23, 2020
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9 Å / Relative weight: 1
Reflection	Resolution: 2.69→200.1 Å / Num. obs: 122958 / % possible obs: 99.5 % / Redundancy: 3.5 % / CC_1/2: 0.998 / R_merge(I) obs: 0.0693 / R_pim(I) all: 0.0387 / R_rim(I) all: 0.0732 / Net I/σ(I): 13.5
Reflection shell	Resolution: 2.69→2.79 Å / R_merge(I) obs: 0.595 / Num. unique obs: 12109 / CC_1/2: 0.849 / R_pim(I) all: 0.366 / R_rim(I) all: 0.7

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0135	refinement
XDS		data reduction
XDS		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 7EBC

7ebc

Resolution: 2.69→47.11 Å / Cor.coef. F_o:F_c: 0.95 / Cor.coef. F_o:F_c free: 0.934 / SU B: 19.114 / SU ML: 0.357 / Cross valid method: THROUGHOUT / ESU R Free: 0.369 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.24797	6148	5 %	RANDOM
R_work	0.21468	-	-	-
obs	0.21634	116812	99.52 %	-

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: 74.4 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.02 Å²	0 Å²	0.02 Å²
2-	-	-0.02 Å²	-0 Å²
3-	-	-	-0.01 Å²

Refinement step

Cycle: 1 / Resolution: 2.69→47.11 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	33985	0	44	298	34327

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.002	0.019	34795
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	33047
X-RAY DIFFRACTION	r_angle_refined_deg	0.398	1.943	47048
X-RAY DIFFRACTION	r_angle_other_deg	0.473	3	76238
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	8.705	5	4300
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	40.588	24.562	1576
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	19.754	15	6068
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	21.829	15	160
X-RAY DIFFRACTION	r_chiral_restr	0.036	0.2	5087
X-RAY DIFFRACTION	r_gen_planes_refined	0.002	0.02	39327
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	7913
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	3.744	24.487	17239
X-RAY DIFFRACTION	r_mcbond_other	3.744	24.487	17240
X-RAY DIFFRACTION	r_mcangle_it	5.451	27.539	21526
X-RAY DIFFRACTION	r_mcangle_other	5.451	27.539	21527
X-RAY DIFFRACTION	r_scbond_it	3.898	24.995	17556
X-RAY DIFFRACTION	r_scbond_other	3.898	24.996	17553
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	5.648	27.838	25523
X-RAY DIFFRACTION	r_long_range_B_refined	7.24	39.785	41163
X-RAY DIFFRACTION	r_long_range_B_other	7.24	39.799	41120
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	63718	0.09
1	2	B	63718	0.09
2	1	A	63270	0.09
2	2	C	63270	0.09
3	1	A	64586	0.08
3	2	D	64586	0.08
4	1	A	62690	0.1
4	2	E	62690	0.1
5	1	A	63112	0.1
5	2	F	63112	0.1
6	1	A	63116	0.09
6	2	G	63116	0.09
7	1	A	63044	0.1
7	2	H	63044	0.1
8	1	B	62094	0.1
8	2	C	62094	0.1
9	1	B	63188	0.09
9	2	D	63188	0.09
10	1	B	62560	0.1
10	2	E	62560	0.1
11	1	B	63008	0.1
11	2	F	63008	0.1
12	1	B	62804	0.1
12	2	G	62804	0.1
13	1	B	62694	0.1
13	2	H	62694	0.1
14	1	C	63588	0.09
14	2	D	63588	0.09
15	1	C	61782	0.1
15	2	E	61782	0.1
16	1	C	62052	0.1
16	2	F	62052	0.1
17	1	C	62726	0.09
17	2	G	62726	0.09
18	1	C	62136	0.1
18	2	H	62136	0.1
19	1	D	62684	0.11
19	2	E	62684	0.11
20	1	D	62476	0.11
20	2	F	62476	0.11
21	1	D	62614	0.1
21	2	G	62614	0.1
22	1	D	63216	0.09
22	2	H	63216	0.09
23	1	E	61882	0.11
23	2	F	61882	0.11
24	1	E	61942	0.1
24	2	G	61942	0.1
25	1	E	61228	0.11
25	2	H	61228	0.11
26	1	F	62244	0.11
26	2	G	62244	0.11
27	1	F	61616	0.11
27	2	H	61616	0.11
28	1	G	62204	0.1
28	2	H	62204	0.1

LS refinement shell

Resolution: 2.691→2.761 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.431	443	-
R_work	0.396	8420	-
obs	-	-	97.93 %

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