PDB-9bpl: Crystal structure of Adenylosuccinate Lyase from Leishmania major

ID or keywords:

Entry

Database: PDB / ID: 9bpl

Title

Crystal structure of Adenylosuccinate Lyase from Leishmania major

Components

Adenylosuccinate lyase

Keywords

LYASE / Adenylossucinate lyase / ASL / Leishmania major

Function / homology

Function and homology information

adenylosuccinate lyase / N6-(1,2-dicarboxyethyl)AMP AMP-lyase (fumarate-forming) activity / (S)-2-(5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamido) succinate lyase (fumarate-forming) activity / 'de novo' AMP biosynthetic process / 'de novo' IMP biosynthetic process / nucleoplasm / cytoplasm
Similarity search - Function

Biological species

Leishmania major (eukaryote)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 1.97 Å

Authors

Rosa e Silva, I. / Mantovani, M. / Nagem, R. / Cardona, A. / Reboredo, E. / Thiemann, O.

Funding support

Brazil, 1items

Citation

Journal: To Be Published
Title: Crystal Structure of Adenylosuccinate lyase from Leishmania major
Authors: Rosa e Silva, I. / Mantovani, M. / Nagem, R. / Cardona, A. / Reboredo, E. / Thiemann, O.

History

Deposition	May 7, 2024	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 8, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9bpl.cif.gz	445.3 KB	Display	PDBx/mmCIF format
PDB format	pdb9bpl.ent.gz	304.2 KB	Display	PDB format
PDBx/mmJSON format	9bpl.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9bpl_validation.pdf.gz	1.5 MB	Display	wwPDB validaton report
Full document	9bpl_full_validation.pdf.gz	1.5 MB	Display
Data in XML	9bpl_validation.xml.gz	42.9 KB	Display
Data in CIF	9bpl_validation.cif.gz	58.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/bp/9bpl ftp://data.pdbj.org/pub/pdb/validation_reports/bp/9bpl	HTTPS FTP

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Related structure data

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	#127 - Jul 2010 Crystallins similarity (7) #154 - Oct 2012 Citric Acid Cycle similarity (7)

Deposited unit

A: Adenylosuccinate lyase

B: Adenylosuccinate lyase

hetero molecules

108 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Adenylosuccinate lyase

B: Adenylosuccinate lyase

hetero molecules

A: Adenylosuccinate lyase

B: Adenylosuccinate lyase

hetero molecules

defined by author&software
Evidence: native gel electrophoresis, Proposed assembly by PISA A 1 0 0 0 0 1 0 0 0 0 1 0 B 1 0 0 0 0 1 0 0 0 0 1 0 A -1 0 0 130.020 0 -1 0 0 0 0 1 0 B -1 0 0 130.020 0 -1 0 0 0 0 1 0
217 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	130.020, 130.020, 316.770
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	98
Space group name H-M	I4₁22
Space group name Hall	I4bw2bw
Symmetry operation	#1: x,y,z #2: -y+1/2,x,z+3/4 #3: y+1/2,-x,z+3/4 #4: x+1/2,-y,-z+3/4 #5: -x+1/2,y,-z+3/4 #6: -x,-y,z #7: y,x,-z #8: -y,-x,-z #9: x+1/2,y+1/2,z+1/2 #10: -y+1,x+1/2,z+5/4 #11: y+1,-x+1/2,z+5/4 #12: x+1,-y+1/2,-z+5/4 #13: -x+1,y+1/2,-z+5/4 #14: -x+1/2,-y+1/2,z+1/2 #15: y+1/2,x+1/2,-z+1/2 #16: -y+1/2,-x+1/2,-z+1/2

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
d_1	ens_1	(chain "A" and (resid 14 through 22 or resid 25...
d_2	ens_1	(chain "B" and (resid 14 through 73 or (resid 74...

NCS domain segments:

Ens-ID: ens_1

Dom-ID	Component-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
d_1	1	VAL	VAL	PRO	PRO	A	A	14 - 22	14 - 22
d_1	2	ILE	ILE	THR	THR	A	A	25 - 116	25 - 116
d_1	3	ASP	ASP	PHE	PHE	A	A	119 - 209	119 - 209
d_1	4	VAL	VAL	THR	THR	A	A	211 - 221	211 - 221
d_1	5	LEU	LEU	LEU	LEU	A	A	223 - 294	223 - 294
d_1	6	ASP	ASP	LYS	LYS	A	A	296 - 313	296 - 313
d_1	7	HIS	HIS	GLU	GLU	A	A	326 - 334	326 - 334
d_1	8	ALA	ALA	LEU	LEU	A	A	336 - 419	336 - 419
d_1	9	ARG	ARG	LEU	LEU	A	A	421 - 434	421 - 434
d_1	10	HIS	HIS	PRO	PRO	A	A	440 - 479	440 - 479
d_1	11	GOL	GOL	GOL	GOL	A	C	501
d_2	1	VAL	VAL	ARG	ARG	B	B	14 - 94	14 - 94
d_2	2	THR	THR	GLY	GLY	B	B	96 - 135	96 - 135
d_2	3	GLU	GLU	ALA	ALA	B	B	137 - 138	137 - 138
d_2	4	LYS	LYS	PHE	PHE	B	B	140 - 209	140 - 209
d_2	5	VAL	VAL	THR	THR	B	B	211 - 221	211 - 221
d_2	6	LEU	LEU	LEU	LEU	B	B	223 - 294	223 - 294
d_2	7	ASP	ASP	GLU	GLU	B	B	296 - 334	296 - 334
d_2	8	ALA	ALA	LEU	LEU	B	B	336 - 419	336 - 419
d_2	9	ARG	ARG	LEU	LEU	B	B	421 - 434	421 - 434
d_2	10	HIS	HIS	PRO	PRO	B	B	440 - 479	440 - 479
d_2	11	GOL	GOL	GOL	GOL	B	K	502

NCS oper: (Code: givenMatrix: (-0.687717846028, 0.725940260116, -0.0074096556277), (0.725945061539, 0.687748087256, 0.00251716161285), (0.00692328544116, -0.00364790594814, -0.999969379982)Vector: ...

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Protein , 1 types, 2 molecules AB

#1: Protein	Adenylosuccinate lyase / ASL / Adenylosuccinase Mass: 53775.270 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Leishmania major (eukaryote) / Gene: LMJF_04_0460 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9U0T7, adenylosuccinate lyase

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Non-polymers , 6 types, 427 molecules

#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: SO₄ / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO₄
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 415 / 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: 3.14 Å³/Da / Density % sol: 60.86 %
Crystal grow	Temperature: 291.15 K / Method: vapor diffusion Details: 3 uL of protein solution at 10 mg.mL-1 (in a buffer containing 5 mM KPO4, 5 mM NaCl, 100 uM ADS) and 3 uL of reservoir solution (1.6 M ammonium sulfate, 0.1 M MES pH 6.5, 10% dioxane)

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Data collection

Diffraction	Mean temperature: 80 K / Serial crystal experiment: N
Diffraction source	Source: ROTATING ANODE / Type: RIGAKU ULTRAX 18 / Wavelength: 1.542 Å
Detector	Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jan 25, 2005
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.542 Å / Relative weight: 1
Reflection	Resolution: 1.97→25.25 Å / Num. obs: 95392 / % possible obs: 99.8 % / Redundancy: 14.2 % / B_iso Wilson estimate: 30.88 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.104 / R_pim(I) all: 0.028 / R_rim(I) all: 0.108 / Net I/σ(I): 18.7
Reflection shell	Resolution: 1.97→2 Å / R_merge(I) obs: 1.373 / Num. unique obs: 4603 / CC_1/2: 0.792 / R_pim(I) all: 0.382 / % possible all: 99.2

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Processing

Software

Name	Version	Classification
PHENIX	1.19.2_4158	refinement
PHENIX	1.19.2_4158	refinement
iMOSFLM		data reduction
pointless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.97→25.25 Å / SU ML: 0.2355 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.9307
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2394	4714	4.96 %
R_work	0.2108	90295	-
obs	0.2122	95009	99.38 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 42.56 Å²

Refinement step

Cycle: LAST / Resolution: 1.97→25.25 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7027	0	48	415	7490

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	7280
X-RAY DIFFRACTION	f_angle_d	0.9832	9880
X-RAY DIFFRACTION	f_chiral_restr	0.0541	1124
X-RAY DIFFRACTION	f_plane_restr	0.009	1257
X-RAY DIFFRACTION	f_dihedral_angle_d	15.1148	982

Refine LS restraints NCS

Type: Torsion NCS / Rms dev position: 0.76085265451 Å

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.97-1.99	0.3508	165	0.2954	2934	X-RAY DIFFRACTION	99.07
1.99-2.02	0.2874	151	0.2799	2967	X-RAY DIFFRACTION	99.17
2.02-2.04	0.2795	182	0.2729	2943	X-RAY DIFFRACTION	99.24
2.04-2.07	0.2895	143	0.2665	2996	X-RAY DIFFRACTION	99.34
2.07-2.09	0.3307	177	0.2474	2939	X-RAY DIFFRACTION	99.3
2.09-2.12	0.2356	151	0.2443	2973	X-RAY DIFFRACTION	99.46
2.12-2.15	0.2503	168	0.2336	2979	X-RAY DIFFRACTION	99.46
2.15-2.18	0.3137	151	0.249	2989	X-RAY DIFFRACTION	99.46
2.18-2.22	0.2792	175	0.2456	2963	X-RAY DIFFRACTION	99.56
2.22-2.25	0.348	153	0.3119	2948	X-RAY DIFFRACTION	98.63
2.25-2.29	0.3217	138	0.2682	2974	X-RAY DIFFRACTION	98.7
2.29-2.34	0.2937	169	0.2305	2967	X-RAY DIFFRACTION	99.71
2.34-2.38	0.3185	156	0.2421	3018	X-RAY DIFFRACTION	99.78
2.38-2.43	0.3005	189	0.2383	2968	X-RAY DIFFRACTION	99.75
2.43-2.48	0.2632	134	0.2209	3011	X-RAY DIFFRACTION	99.75
2.48-2.54	0.2237	140	0.2116	3020	X-RAY DIFFRACTION	99.53
2.54-2.6	0.2455	156	0.2182	2995	X-RAY DIFFRACTION	99.75
2.6-2.67	0.2759	146	0.2196	3016	X-RAY DIFFRACTION	99.56
2.67-2.75	0.2798	159	0.2291	2994	X-RAY DIFFRACTION	99.56
2.75-2.84	0.2267	158	0.2287	3004	X-RAY DIFFRACTION	99.22
2.84-2.94	0.2592	162	0.2298	2991	X-RAY DIFFRACTION	98.9
2.94-3.06	0.259	157	0.2288	3026	X-RAY DIFFRACTION	99.34
3.06-3.2	0.2525	147	0.2301	3012	X-RAY DIFFRACTION	99.31
3.2-3.37	0.2467	142	0.2169	3050	X-RAY DIFFRACTION	99.53
3.37-3.58	0.2053	144	0.2021	3044	X-RAY DIFFRACTION	99.35
3.58-3.85	0.2034	156	0.1769	3039	X-RAY DIFFRACTION	99.44
3.85-4.24	0.1865	154	0.1668	3061	X-RAY DIFFRACTION	99.08
4.24-4.85	0.2	146	0.1671	3086	X-RAY DIFFRACTION	99.26
4.85-6.09	0.2254	160	0.1922	3131	X-RAY DIFFRACTION	99.79
6.09-25.25	0.1925	185	0.1848	3257	X-RAY DIFFRACTION	99.65

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	1.40992446648	1.07308371682	-1.26447576887	0.770248304115	-0.695131363188	1.75764044405	0.0484961346159	-0.296650226944	0.106988863778	0.032417469037	-0.273137505207	0.291366696368	-0.259124194769	-1.15651573738	0.084779330232	0.134064288698	-0.211135914943	0.0575874316393	1.23949419062	0.00386650824189	0.421933517953	34.3122305009	0.539196130623	-5.09990863845
2	0.546563759451	0.137117902509	-0.0945743905591	0.50822174697	-0.0921270293111	1.23884218089	-0.0261753872415	0.0116919122308	-0.0682912065314	-0.0346561242018	-0.0163588781895	0.146115557018	0.442520215193	-0.750334701799	0.0351608109884	0.244403321193	-0.176489727745	0.00605639130897	0.430496449641	-0.0237181305477	0.307166705593	49.346755819	-9.44111443858	-18.3090419971
3	5.45462984271	-4.23836662861	0.0533448606304	5.77722308409	1.78103690155	3.9554612762	0.15151841978	0.320127326263	-0.00105420624641	-0.414344438512	-0.0511672013395	-0.369783201663	0.462939656753	0.272577965784	-0.104198454844	0.524846486373	-0.082852759015	0.0594310062507	0.321672717795	-0.032221501089	0.269371945866	71.7624491952	-21.5999174655	-57.5920478983
4	1.26375186161	0.677325819567	0.457809842286	1.63312773991	0.948264922067	2.26412649635	-0.0606756606122	0.0580572951292	-0.302725876286	-0.224410022741	0.196031561709	-0.445292931684	0.658153401182	0.974226652391	-0.167752717956	0.53921194768	0.238473317791	0.061810106804	0.571143157402	0.00625090633995	0.386483265549	86.118663408	-22.9326124701	-26.8557028253
5	0.455735533313	-0.0221934842338	-0.153040286293	0.698627983771	0.232864178189	2.76754175125	-0.0741192115938	-0.0603865769453	-0.152576979417	-0.0228726795478	-0.0095487883058	-0.0113483871669	0.776817642503	0.0961757715697	0.0740072520338	0.30902598116	-0.00690800260731	0.0388078866509	0.184741662436	0.0171394527884	0.260751212198	69.0580611273	-18.1212753155	-14.0742880709
6	9.23988582378	-0.585478102069	-3.91378204732	0.902264940946	0.248856760351	3.10033800759	-0.132528429786	-0.293705719812	-0.0505803676832	0.166501069748	0.0593247251348	0.213067183874	0.302483005953	-0.379208093727	0.063469175418	0.360650144902	-0.0971886964192	0.0786061027932	0.530595976038	0.0472294425121	0.263911373301	45.2977579402	-10.5817179781	25.7589039507

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

ID	Refine TLS-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	chain 'A' and (resid 14 through 129 )	A	A	14 - 129	1 - 114
2	2	chain 'A' and (resid 130 through 395 )	A	A	130 - 395	115 - 365
3	3	chain 'A' and (resid 396 through 479 )	A	A	396 - 479	366 - 445
4	4	chain 'B' and (resid 14 through 129 )	B	K	14 - 129	1 - 112
5	5	chain 'B' and (resid 130 through 395 )	B	K	130 - 395	113 - 364
6	6	chain 'B' and (resid 396 through 479 )	B	K	396 - 479	365 - 444

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