PDB-4r8k: Crystal structure of the guinea pig L-asparaginase 1 catalytic domain

ID or keywords:

Entry

Database: PDB / ID: 4r8k

Title

Crystal structure of the guinea pig L-asparaginase 1 catalytic domain

Components

Uncharacterized protein

Keywords

HYDROLASE / L-asparaginase

Function / homology

Function and homology information

aspartate family amino acid metabolic process / asparaginase / asparaginase activity / cytosol
Similarity search - Function

Biological species

Cavia porcellus (domestic guinea pig)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.2 Å

Authors

Schalk, A.M. / Lavie, A.

Citation

Journal: J.Biol.Chem. / Year: 2014
Title: Identification and Structural Analysis of an l-Asparaginase Enzyme from Guinea Pig with Putative Tumor Cell Killing Properties.
Authors: Schalk, A.M. / Nguyen, H.A. / Rigouin, C. / Lavie, A.

History

Deposition	Sep 2, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 22, 2014	Provider: repository / Type: Initial release
Revision 1.1	Oct 29, 2014	Group: Database references
Revision 1.2	Dec 10, 2014	Group: Database references
Revision 1.3	Sep 20, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_ref_seq_dif / struct_site 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4r8k.cif.gz	552.6 KB	Display	PDBx/mmCIF format
PDB format	pdb4r8k.ent.gz	455.6 KB	Display	PDB format
PDBx/mmJSON format	4r8k.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	4r8k_validation.pdf.gz	516.8 KB	Display	wwPDB validaton report
Full document	4r8k_full_validation.pdf.gz	545.9 KB	Display
Data in XML	4r8k_validation.xml.gz	104.9 KB	Display
Data in CIF	4r8k_validation.cif.gz	145.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/r8/4r8k ftp://data.pdbj.org/pub/pdb/validation_reports/r8/4r8k	HTTPS FTP

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Related structure data

Related structure data	4r8lC 2himS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	5dne-d 5dnc-d 5dnd-d 4r8l-d 1foh-2 2dtu-4 4hny-2 5h01-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

Deposited unit

A: Uncharacterized protein

B: Uncharacterized protein

C: Uncharacterized protein

D: Uncharacterized protein

E: Uncharacterized protein

F: Uncharacterized protein

G: Uncharacterized protein

H: Uncharacterized protein

hetero molecules

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

1

A: Uncharacterized protein

B: Uncharacterized protein

C: Uncharacterized protein

D: Uncharacterized protein

hetero molecules

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

2

E: Uncharacterized protein

F: Uncharacterized protein

G: Uncharacterized protein

H: Uncharacterized protein

hetero molecules

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

Unit cell

Length a, b, c (Å)	98.550, 123.310, 120.560
Angle α, β, γ (deg.)	90.00, 92.35, 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	PRO	PRO	A	A	7 - 361	30 - 384
2	1	SER	SER	PRO	PRO	B	B	7 - 361	30 - 384
1	2	GLU	GLU	LEU	LEU	A	A	8 - 360	31 - 383
2	2	GLU	GLU	LEU	LEU	C	C	8 - 360	31 - 383
1	3	GLU	GLU	LEU	LEU	A	A	8 - 360	31 - 383
2	3	GLU	GLU	LEU	LEU	D	D	8 - 360	31 - 383
1	4	SER	SER	PRO	PRO	A	A	7 - 361	30 - 384
2	4	SER	SER	PRO	PRO	E	E	7 - 361	30 - 384
1	5	GLU	GLU	LEU	LEU	A	A	8 - 360	31 - 383
2	5	GLU	GLU	LEU	LEU	F	F	8 - 360	31 - 383
1	6	GLU	GLU	LEU	LEU	A	A	8 - 360	31 - 383
2	6	GLU	GLU	LEU	LEU	G	G	8 - 360	31 - 383
1	7	GLU	GLU	LEU	LEU	A	A	8 - 360	31 - 383
2	7	GLU	GLU	LEU	LEU	H	H	8 - 360	31 - 383
1	8	GLU	GLU	THR	THR	B	B	8 - 362	31 - 385
2	8	GLU	GLU	THR	THR	C	C	8 - 362	31 - 385
1	9	GLU	GLU	THR	THR	B	B	8 - 362	31 - 385
2	9	GLU	GLU	THR	THR	D	D	8 - 362	31 - 385
1	10	SER	SER	PRO	PRO	B	B	7 - 361	30 - 384
2	10	SER	SER	PRO	PRO	E	E	7 - 361	30 - 384
1	11	GLU	GLU	PRO	PRO	B	B	8 - 361	31 - 384
2	11	GLU	GLU	PRO	PRO	F	F	8 - 361	31 - 384
1	12	GLU	GLU	PRO	PRO	B	B	8 - 361	31 - 384
2	12	GLU	GLU	PRO	PRO	G	G	8 - 361	31 - 384
1	13	GLU	GLU	PRO	PRO	B	B	8 - 361	31 - 384
2	13	GLU	GLU	PRO	PRO	H	H	8 - 361	31 - 384
1	14	GLU	GLU	THR	THR	C	C	8 - 362	31 - 385
2	14	GLU	GLU	THR	THR	D	D	8 - 362	31 - 385
1	15	GLU	GLU	PRO	PRO	C	C	8 - 361	31 - 384
2	15	GLU	GLU	PRO	PRO	E	E	8 - 361	31 - 384
1	16	GLU	GLU	LEU	LEU	C	C	8 - 360	31 - 383
2	16	GLU	GLU	LEU	LEU	F	F	8 - 360	31 - 383
1	17	GLU	GLU	LEU	LEU	C	C	8 - 360	31 - 383
2	17	GLU	GLU	LEU	LEU	G	G	8 - 360	31 - 383
1	18	GLU	GLU	LEU	LEU	C	C	8 - 360	31 - 383
2	18	GLU	GLU	LEU	LEU	H	H	8 - 360	31 - 383
1	19	GLU	GLU	PRO	PRO	D	D	8 - 361	31 - 384
2	19	GLU	GLU	PRO	PRO	E	E	8 - 361	31 - 384
1	20	GLU	GLU	LEU	LEU	D	D	8 - 360	31 - 383
2	20	GLU	GLU	LEU	LEU	F	F	8 - 360	31 - 383
1	21	GLU	GLU	LEU	LEU	D	D	8 - 360	31 - 383
2	21	GLU	GLU	LEU	LEU	G	G	8 - 360	31 - 383
1	22	GLU	GLU	LEU	LEU	D	D	8 - 360	31 - 383
2	22	GLU	GLU	LEU	LEU	H	H	8 - 360	31 - 383
1	23	GLU	GLU	PRO	PRO	E	E	8 - 361	31 - 384
2	23	GLU	GLU	PRO	PRO	F	F	8 - 361	31 - 384
1	24	GLU	GLU	PRO	PRO	E	E	8 - 361	31 - 384
2	24	GLU	GLU	PRO	PRO	G	G	8 - 361	31 - 384
1	25	GLU	GLU	PRO	PRO	E	E	8 - 361	31 - 384
2	25	GLU	GLU	PRO	PRO	H	H	8 - 361	31 - 384
1	26	GLU	GLU	PRO	PRO	F	F	8 - 361	31 - 384
2	26	GLU	GLU	PRO	PRO	G	G	8 - 361	31 - 384
1	27	GLU	GLU	PRO	PRO	F	F	8 - 361	31 - 384
2	27	GLU	GLU	PRO	PRO	H	H	8 - 361	31 - 384
1	28	GLU	GLU	PRO	PRO	G	G	8 - 361	31 - 384
2	28	GLU	GLU	PRO	PRO	H	H	8 - 361	31 - 384

NCS ensembles :

#1: Protein	Uncharacterized protein / L-Asparaginase 1 Mass: 41977.418 Da / Num. of mol.: 8 / Fragment: catalytic domain (UNP residues 1-362) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cavia porcellus (domestic guinea pig) / Gene: ASPG / Plasmid: pET14b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) C41 / References: UniProt: H0W0T5, asparaginase
#2: Chemical	ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES Mass: 238.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₈H₁₈N₂O₄S / Comment: pH buffer*YM
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 892 / Source method: isolated from a natural source / Formula: H₂O
Sequence details	AUTHORS STATE THAT THE CRYSTALLIZATION EXPERIMENTS WERE SET UP WITH N-TERMINAL HIS-TAGGED FULL ...AUTHORS STATE THAT THE CRYSTALLIZATION EXPERIMENTS WERE SET UP WITH N-TERMINAL HIS-TAGGED FULL LENGTH (1-565) PROTEIN. HOWEVER, UPON SOLVING THE STRUCTURE IT BECAME CLEAR THAT THE C-TERMINAL DOMAIN HAD BEEN CLEAVED OFF IN THE DROP, LEAVING ONLY THE ASPARAGINASE CATALYTIC DOMAIN. SINCE THE EXACT LOCATION OF THE CLEAVAGE SITE IS UNKNOWN, THE SEQRES RECORDS IN THE PDB FILE ONLY INCLUDE THE 23-RESIDUE HIS TAG AND UNIPROT SEQUENCE DATABASE RESIDUES 1 THROUGH 362.

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.18 Å³/Da / Density % sol: 43.56 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.1 M HEPES, 15% PEG 4000, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G
Detector	Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 26, 2013
Radiation	Monochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Relative weight: 1
Reflection	Resolution: 2.2→120.46 Å / Num. obs: 146207 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shell	Resolution: 2.2→2.34 Å / % possible all: 98.5

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Processing

Software

Name	Version	Classification
CrystalClear		data collection
MOLREP		phasing
REFMAC	5.8.0069	refinement
XDS		data reduction
XDS		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 2HIM

2him

Resolution: 2.2→29.617 Å / Cor.coef. F_o:F_c: 0.953 / Cor.coef. F_o:F_c free: 0.936 / SU B: 8.835 / SU ML: 0.204 / Cross valid method: THROUGHOUT / ESU R: 0.32 / ESU R Free: 0.216 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.238	7281	5 %	RANDOM
R_work	0.20694	-	-	-
obs	0.20849	138245	99.18 %	-
all	-	145526	-	-

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: 37.191 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.44 Å²	0 Å²	-0.18 Å²
2-	-	0.41 Å²	0 Å²
3-	-	-	-0.83 Å²

Refinement step

Cycle: LAST / Resolution: 2.2→29.617 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	21650	0	120	892	22662

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.019	22250
X-RAY DIFFRACTION	r_bond_other_d	0.006	0.02	22029
X-RAY DIFFRACTION	r_angle_refined_deg	1.339	1.992	30244
X-RAY DIFFRACTION	r_angle_other_deg	1.065	3	50699
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.823	5	2823
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.902	23.725	859
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.983	15	3772
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.817	15	144
X-RAY DIFFRACTION	r_chiral_restr	0.072	0.2	3546
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.021	24676
X-RAY DIFFRACTION	r_gen_planes_other	0.005	0.02	4762
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	2.779	3.532	11304
X-RAY DIFFRACTION	r_mcbond_other	2.778	3.532	11303
X-RAY DIFFRACTION	r_mcangle_it	4.571	5.289	14114
X-RAY DIFFRACTION	r_mcangle_other	4.892	5.241	14096
X-RAY DIFFRACTION	r_scbond_it	3.029	3.908	10946
X-RAY DIFFRACTION	r_scbond_other	3.574	3.934	10947
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	5.836	5.739	16143
X-RAY DIFFRACTION	r_long_range_B_refined	7.94	35.729	17659
X-RAY DIFFRACTION	r_long_range_B_other	7.936	35.798	17404
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	22040	0.05
1	2	B	22040	0.05
2	1	A	22516	0.05
2	2	C	22516	0.05
3	1	A	22458	0.05
3	2	D	22458	0.05
4	1	A	22285	0.05
4	2	E	22285	0.05
5	1	A	22580	0.04
5	2	F	22580	0.04
6	1	A	22544	0.04
6	2	G	22544	0.04
7	1	A	22581	0.04
7	2	H	22581	0.04
8	1	B	22051	0.05
8	2	C	22051	0.05
9	1	B	22204	0.04
9	2	D	22204	0.04
10	1	B	22117	0.05
10	2	E	22117	0.05
11	1	B	22177	0.04
11	2	F	22177	0.04
12	1	B	22180	0.04
12	2	G	22180	0.04
13	1	B	22056	0.05
13	2	H	22056	0.05
14	1	C	22549	0.05
14	2	D	22549	0.05
15	1	C	22226	0.06
15	2	E	22226	0.06
16	1	C	22607	0.05
16	2	F	22607	0.05
17	1	C	22564	0.05
17	2	G	22564	0.05
18	1	C	22588	0.05
18	2	H	22588	0.05
19	1	D	22346	0.05
19	2	E	22346	0.05
20	1	D	22559	0.04
20	2	F	22559	0.04
21	1	D	22652	0.04
21	2	G	22652	0.04
22	1	D	22474	0.05
22	2	H	22474	0.05
23	1	E	22357	0.05
23	2	F	22357	0.05
24	1	E	22318	0.05
24	2	G	22318	0.05
25	1	E	22246	0.05
25	2	H	22246	0.05
26	1	F	22756	0.03
26	2	G	22756	0.03
27	1	F	22722	0.04
27	2	H	22722	0.04
28	1	G	22689	0.04
28	2	H	22689	0.04

LS refinement shell

Resolution: 2.2→2.253 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.377	504	-
R_work	0.341	9854	-
obs	-	-	95.98 %

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