PDB-9hnc: Crystal structure of potassium-independent L-asparaginase from Ph...

ID or keywords:

Entry

Database: PDB / ID: 9hnc

Title

Crystal structure of potassium-independent L-asparaginase from Phaseolus vulgaris (PvAIII, PvAspG2)

Components

beta-aspartyl-peptidase

Keywords

HYDROLASE / L-asparaginase / beta-aspartylpeptidase / common bean / potassium-idenpendent enzyme

Function / homology

beta-aspartyl-peptidase / Peptidase T2, asparaginase 2 / Asparaginase / asparaginase activity / Nucleophile aminohydrolases, N-terminal / beta-aspartyl-peptidase

Function and homology information

Biological species

Phaseolus vulgaris (French bean)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.879 Å

Authors

Loch, J.I. / Pierog, I. / Imiolczyk, B. / Barciszewski, J. / Marsolais, F. / Gilski, M. / Jaskolski, M.

Funding support

Poland, 1items

Citation

Journal: Acta Crystallogr D Struct Biol / Year: 2025
Title: Unique double-helical packing of protein molecules in the crystal of potassium-independent L-asparaginase from common bean.
Authors: Loch, J.I. / Pierog, I. / Imiolczyk, B. / Barciszewski, J. / Marsolais, F. / Gilski, M. / Jaskolski, M.

History

Deposition	Dec 10, 2024	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	May 14, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9hnc.cif.gz	1.6 MB	Display	PDBx/mmCIF format
PDB format	pdb9hnc.ent.gz		Display	PDB format
PDBx/mmJSON format	9hnc.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/hn/9hnc ftp://data.pdbj.org/pub/pdb/validation_reports/hn/9hnc	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
Experimental dataset #1	Data reference: 10.60884/0K7B68 / Data set type: diffraction image data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#166 - Oct 2013 Proteasome similarity (1) #80 - Aug 2006 AAA+ Proteases similarity (1) #176 - Aug 2014 Dynein similarity (1) #60 - Dec 2004 Ubiquitin similarity (1)

Deposited unit

AAA: beta-aspartyl-peptidase

BBB: beta-aspartyl-peptidase

CCC: beta-aspartyl-peptidase

DDD: beta-aspartyl-peptidase

EEE: beta-aspartyl-peptidase

FFF: beta-aspartyl-peptidase

GGG: beta-aspartyl-peptidase

HHH: beta-aspartyl-peptidase

III: beta-aspartyl-peptidase

JJJ: beta-aspartyl-peptidase

KKK: beta-aspartyl-peptidase

LLL: beta-aspartyl-peptidase

MMM: beta-aspartyl-peptidase

NNN: beta-aspartyl-peptidase

OOO: beta-aspartyl-peptidase

PPP: beta-aspartyl-peptidase

hetero molecules

549 kDa, 16 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

AAA: beta-aspartyl-peptidase

BBB: beta-aspartyl-peptidase

hetero molecules

defined by author
Evidence: gel filtration, asymmeric unit contains 8 heteroteramers (dimers of heterodimers) made of chains: AB, CD, EF, GH, IJ, KL, MN, OP
68.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

CCC: beta-aspartyl-peptidase

DDD: beta-aspartyl-peptidase

hetero molecules

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

3

EEE: beta-aspartyl-peptidase

FFF: beta-aspartyl-peptidase

hetero molecules

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

4

GGG: beta-aspartyl-peptidase

HHH: beta-aspartyl-peptidase

hetero molecules

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

5

III: beta-aspartyl-peptidase

JJJ: beta-aspartyl-peptidase

hetero molecules

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

6

KKK: beta-aspartyl-peptidase

LLL: beta-aspartyl-peptidase

hetero molecules

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

7

MMM: beta-aspartyl-peptidase

NNN: beta-aspartyl-peptidase

hetero molecules

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

8

OOO: beta-aspartyl-peptidase

PPP: beta-aspartyl-peptidase

hetero molecules

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

Unit cell

Length a, b, c (Å)	123.764, 123.645, 187.679
Angle α, β, γ (deg.)	90.000, 90.063, 90.000
Int Tables number	3
Space group name H-M	P121

Components on special symmetry positions

ID	Model	Components
1	1	KKK-623- HOH

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Protein , 1 types, 16 molecules AAABBBCCCDDDEEEFFFGGGHHHIIIJJJKKKLLLMMMNNNOOOPPP

#1: Protein	beta-aspartyl-peptidase Mass: 33983.523 Da / Num. of mol.: 16 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Phaseolus vulgaris (French bean) / Gene: PHAVU_003G182400g / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): XL10 Gold / References: UniProt: V7CAP3, beta-aspartyl-peptidase

#1: Protein

beta-aspartyl-peptidase

Mass: 33983.523 Da / Num. of mol.: 16
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Phaseolus vulgaris (French bean) / Gene: PHAVU_003G182400g / Plasmid: pQE30 / Production host:

Escherichia coli (E. coli) / Strain (production host): XL10 Gold / References: UniProt: V7CAP3, beta-aspartyl-peptidase

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Non-polymers , 6 types, 2563 molecules

#2: Chemical	... ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 33 / Source method: obtained synthetically / Formula: Na
#3: Chemical	... ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 25 / Source method: obtained synthetically / Formula: SO₄
#4: Chemical	... ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 29 / Source method: obtained synthetically / Formula: Cl
#5: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C₂H₆O₂
#6: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 2466 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	N
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: 2.64 Å³/Da / Density % sol: 53.43 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 2.0 M ammonium sulfate and 5% v/v 2-propanol

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

PETRA III, EMBL c/o DESY

/ Beamline: P13 (MX1) / Wavelength: 0.72931 Å

Detector

Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 13, 2022

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.72931 Å / Relative weight: 1

Reflection twin

Type	Crystal-ID	ID	Operator	Domain-ID	Fraction
pseudo-merohedral	1	1	H, K, L	1	0.8246
pseudo-merohedral	2	2	-h,-k,l	2	0.0602
pseudo-merohedral	3	3	K, H, -L	3	0.0561
pseudo-merohedral	4	4	-K, -H, -L	4	0.0591

Reflection

Resolution: 1.879→47.69 Å / Num. obs: 451021 / % possible obs: 98.7 % / Redundancy: 6.93 % / CC_1/2: 0.998 / R_merge(I) obs: 0.083 / R_rim(I) all: 0.074 / Net I/σ(I): 13.43

Reflection shell

Resolution: 1.879→1.99 Å / R_merge(I) obs: 0.813 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 73624 / CC_1/2: 0.98 / R_rim(I) all: 0.774

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0258	refinement
XDS		data reduction
XDS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.879→47.688 Å / Cor.coef. F_o:F_c: 0.964 / Cor.coef. F_o:F_c free: 0.954 / SU B: 4.459 / SU ML: 0.064 / Cross valid method: FREE R-VALUE / ESU R: 0.026 / ESU R Free: 0.025

	R_factor	Num. reflection	% reflection
R_free	0.2111	6207	1.376 %
R_work	0.1824	444784	-
all	0.183	-	-
obs	-	450991	98.373 %

Solvent computation

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

Displacement parameters

B_iso mean: 30.984 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	5.505 Å²	0 Å²	0.758 Å²
2-	-	5.128 Å²	0 Å²
3-	-	-	-10.633 Å²

Refinement step

Cycle: LAST / Resolution: 1.879→47.688 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	34011	0	229	2466	36706

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.013	34706
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	32997
X-RAY DIFFRACTION	r_angle_refined_deg	1.717	1.624	47059
X-RAY DIFFRACTION	r_angle_other_deg	1.418	1.571	76366
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.969	5	4629
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	31.09	21.999	1586
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.328	15	5741
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.364	15	245
X-RAY DIFFRACTION	r_chiral_restr	0.09	0.2	4746
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.02	39298
X-RAY DIFFRACTION	r_gen_planes_other	0.004	0.02	6773
X-RAY DIFFRACTION	r_nbd_refined	0.21	0.2	7338
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.182	0.2	31826
X-RAY DIFFRACTION	r_nbtor_refined	0.153	0.2	16846
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.085	0.2	15734
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.16	0.2	2114
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.102	0.2	16
X-RAY DIFFRACTION	r_metal_ion_refined	0.124	0.2	59
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.235	0.2	49
X-RAY DIFFRACTION	r_nbd_other	0.26	0.2	172
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.219	0.2	18
X-RAY DIFFRACTION	r_xyhbond_nbd_other	0.16	0.2	2
X-RAY DIFFRACTION	r_mcbond_it	1.69	2.674	18537
X-RAY DIFFRACTION	r_mcbond_other	1.69	2.674	18536
X-RAY DIFFRACTION	r_mcangle_it	2.37	4.001	23123
X-RAY DIFFRACTION	r_mcangle_other	2.37	4.001	23124
X-RAY DIFFRACTION	r_scbond_it	2.266	3.061	16169
X-RAY DIFFRACTION	r_scbond_other	2.262	3.057	16150
X-RAY DIFFRACTION	r_scangle_it	3.435	4.471	23924
X-RAY DIFFRACTION	r_scangle_other	3.434	4.466	23895
X-RAY DIFFRACTION	r_lrange_it	4.966	33.666	38401
X-RAY DIFFRACTION	r_lrange_other	4.959	33.647	38362

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 (%)
1.879-1.928	0.314	371	0.237	31289	X-RAY DIFFRACTION	93.7019
1.928-1.981	0.252	419	0.221	31742	X-RAY DIFFRACTION	98.0488
1.981-2.038	0.252	454	0.21	31155	X-RAY DIFFRACTION	98.305
2.038-2.1	0.213	385	0.19	30211	X-RAY DIFFRACTION	98.3731
2.1-2.169	0.226	440	0.181	29288	X-RAY DIFFRACTION	98.6069
2.169-2.245	0.206	416	0.185	28299	X-RAY DIFFRACTION	98.5314
2.245-2.33	0.216	386	0.177	27326	X-RAY DIFFRACTION	98.5982
2.33-2.425	0.219	387	0.177	26434	X-RAY DIFFRACTION	98.7809
2.425-2.532	0.209	358	0.172	25338	X-RAY DIFFRACTION	98.7396
2.532-2.655	0.213	363	0.182	24191	X-RAY DIFFRACTION	98.9961
2.655-2.799	0.204	276	0.171	23173	X-RAY DIFFRACTION	98.9869
2.799-2.968	0.2	269	0.176	21882	X-RAY DIFFRACTION	98.884
2.968-3.172	0.227	296	0.193	20688	X-RAY DIFFRACTION	99.3467
3.172-3.425	0.224	279	0.192	19135	X-RAY DIFFRACTION	99.1168
3.425-3.749	0.204	266	0.178	17728	X-RAY DIFFRACTION	99.2444
3.749-4.189	0.163	227	0.161	16013	X-RAY DIFFRACTION	99.4367
4.189-4.831	0.196	230	0.156	14143	X-RAY DIFFRACTION	99.0149
4.831-5.901	0.253	165	0.194	12068	X-RAY DIFFRACTION	99.2133
5.901-8.282	0.193	139	0.191	9325	X-RAY DIFFRACTION	98.7273
8.282-47.688	0.204	81	0.212	5356	X-RAY DIFFRACTION	98.2117

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	0.0126	-0.0338	-0.0144	0.3775	0.2912	0.3188	0.0215	-0.0124	0.0162	-0.0426	0.0062	-0.0618	0.0278	-0.0527	-0.0277	0.0519	-0.035	0.0189	0.0423	-0.0234	0.0309	31.3867	24.9708	-17.5438
2	0.0816	-0.1527	-0.1276	0.3392	0.2733	0.3466	0.0016	0.0016	0.0022	0.0138	0.0372	-0.0501	-0.0481	-0.045	-0.0388	0.0309	0.033	0.0009	0.0571	-0.0247	0.0414	27.678	45.8486	4.1346
3	0.3631	-0.0979	-0.1299	0.0503	-0.0131	0.2467	0.0457	0.0276	0.0202	-0.0051	-0.0131	0.0218	0.0173	0.0589	-0.0326	0.0295	0.0222	0.0226	0.035	0.0058	0.0395	1.8904	65.3037	28.6658
4	0.3698	0.1406	-0.3222	0.0573	-0.132	0.3715	0.0391	-0.028	0.0243	0.0019	-0.0007	0.0031	0.0097	-0.0434	-0.0384	0.0407	-0.0322	0.0142	0.0528	0.0146	0.0299	-17.6707	61.4017	50.962
5	0.0485	0.0257	0.0152	0.3165	-0.2366	0.2728	-0.0051	0.0017	-0.0146	-0.0266	0.0101	0.0221	-0.0326	0.0316	-0.0051	0.0469	-0.0168	-0.0048	0.0298	0.0225	0.0256	-36.5614	36.648	76.2153
6	0.0989	-0.162	0.1561	0.3032	-0.2452	0.2993	-0.0006	0.0081	-0.0057	0.0311	0.0254	0.0317	0.0417	0.032	-0.0248	0.0478	0.0348	0.0005	0.0399	0.0178	0.0241	-32.962	15.8079	97.7923
7	0.4217	-0.0331	0.2933	0.0486	0.0237	0.3045	0.0227	0.0348	-0.0448	-0.0028	0.0078	-0.0153	-0.0371	-0.0155	-0.0305	0.048	0.0392	-0.0193	0.0468	-0.0147	0.0219	-7.9682	-3.1018	122.9301
8	0.3739	0.1792	0.2797	0.0934	0.1501	0.3	0.0376	-0.0173	-0.0372	-0.0024	0.001	-0.0091	-0.0249	0.047	-0.0385	0.0548	-0.0257	-0.0202	0.0456	-0.0167	0.0318	12.4315	0.504	144.7592
9	0.4159	0.0362	0.3123	0.0656	-0.0339	0.336	0.0094	-0.0271	-0.0347	0.004	0.0118	0.0155	-0.0305	0.0147	-0.0212	0.0288	-0.0255	-0.0202	0.0562	0.0167	0.0255	64.8375	59.008	59.4896
10	0.4071	-0.1961	0.3235	0.1017	-0.1708	0.316	0.0279	0.0221	-0.0404	0.0042	0.0067	0.0122	-0.014	-0.0382	-0.0346	0.0373	0.0253	-0.0193	0.0583	0.0108	0.0301	44.1097	62.3395	37.7849
11	0.0286	-0.0231	-0.0341	0.432	-0.2778	0.2932	0.005	-0.017	-0.0052	0.0435	0.0087	0.0573	-0.0039	0.0504	-0.0137	0.0495	0.001	-0.0001	0.0462	0.029	0.0299	25.4365	86.8824	12.2442
12	0.1074	0.1247	-0.1364	0.3319	-0.2603	0.2838	0.0336	-0.0327	-0.012	-0.0229	0.0071	0.0478	-0.0518	0.0459	-0.0407	0.0641	-0.0469	-0.0058	0.0352	0.0064	0.0313	29.0307	107.4417	-9.4672
13	0.396	-0.0154	-0.2899	0.0327	0.0423	0.3006	0.0375	-0.0174	0.0345	-0.0014	-0.0046	-0.0288	0.0239	-0.0455	-0.0329	0.047	-0.0381	0.0179	0.0485	-0.0031	0.032	53.7859	126.6071	-34.4121
14	0.4028	-0.1556	-0.3054	0.0663	0.137	0.3383	0.0544	0.0351	0.0433	-0.0017	-0.001	-0.0121	0.022	0.0359	-0.0533	0.0634	0.0401	0.0161	0.0396	-0.01	0.0357	74.5545	123.0699	-56.0291
15	0.0909	-0.0263	0.0183	0.3542	0.258	0.2606	0.0071	0.0069	-0.0188	0.0325	0.0054	-0.0274	-0.0232	-0.0344	-0.0124	0.0506	0.0331	-0.0117	0.0318	-0.0177	0.0207	93.3817	98.3511	-81.336
16	0.098	0.183	0.145	0.3546	0.2799	0.3103	-0.0038	0.0069	-0.007	-0.0121	0.0317	-0.0314	0.0439	-0.0283	-0.0279	0.0435	-0.0209	-0.0111	0.0478	-0.0184	0.0283	89.8198	77.6394	-102.9942

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	AAA	2 - 503
2	X-RAY DIFFRACTION	2	ALL	BBB	1 - 499
3	X-RAY DIFFRACTION	3	ALL	CCC	2 - 490
4	X-RAY DIFFRACTION	4	ALL	DDD	2 - 501
5	X-RAY DIFFRACTION	5	ALL	EEE	2 - 488
6	X-RAY DIFFRACTION	6	ALL	FFF	1 - 499
7	X-RAY DIFFRACTION	7	ALL	GGG	2 - 497
8	X-RAY DIFFRACTION	8	ALL	HHH	2 - 483
9	X-RAY DIFFRACTION	9	ALL	III	2 - 503
10	X-RAY DIFFRACTION	10	ALL	JJJ	2 - 470
11	X-RAY DIFFRACTION	11	ALL	KKK	2 - 464
12	X-RAY DIFFRACTION	12	ALL	LLL	2 - 485
13	X-RAY DIFFRACTION	13	ALL	MMM	2 - 506
14	X-RAY DIFFRACTION	14	ALL	NNN	2 - 507
15	X-RAY DIFFRACTION	15	ALL	OOO	2 - 504
16	X-RAY DIFFRACTION	16	ALL	PPP	2 - 488

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Protein , 1 types, 16 molecules AAABBBCCCDDDEEEFFFGGGHHHIIIJJJKKKLLLMMMNNNOOOPPP

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Non-polymers , 6 types, 2563 molecules

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-Protein , 1 types, 16 molecules AAABBBCCCDDDEEEFFFGGGHHHIIIJJJKKKLLLMMMNNNOOOPPP

-Non-polymers , 6 types, 2563 molecules

-Details

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

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-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

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Movie

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Structure viewers

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Viewer log

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This page

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This web site

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Options

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Open data

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Basic information

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Download

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Validation report

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Related structure data

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Links

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Assembly

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Components

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Protein , 1 types, 16 molecules AAABBBCCCDDDEEEFFFGGGHHHIIIJJJKKKLLLMMMNNNOOOPPP

-
Non-polymers , 6 types, 2563 molecules

-
Details

-
Experimental details

-
Experiment

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Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

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News

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Feb 9, 2022. New format data for meta-information of EMDB entries

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Aug 12, 2020. Covid-19 info

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Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

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Jul 12, 2017. Major update of PDB

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Yorodumi