PDB-5nsm: unliganded Structure of Leucyl aminopeptidase from Trypanosoma brucei

Basic information

• Entry: Database: PDB / ID: 5nsm
• Title: unliganded Structure of Leucyl aminopeptidase from Trypanosoma brucei
• Components: Aminopeptidase, putative
• Keywords: HYDROLASE / M17 leucyl aminopeptidase / aminopeptidase / tryanosoma brucei

Function / homology

Function:

metalloaminopeptidase activity / aminopeptidase activity / manganese ion binding / peptidase activity / proteolysis / cytoplasm

Domain/homology:

Zn-dependent exopeptidases / Probable aminopeptidase NPEPL1, N-terminal / M17 aminopeptidase N-terminal domain 2 / Cytosol aminopeptidase signature. / Peptidase M17, leucyl aminopeptidase, C-terminal / Peptidase M17, leucine aminopeptidase/peptidase B / Cytosol aminopeptidase family, catalytic domain / Zn peptidases / Aminopeptidase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta

Component:

BICARBONATE ION / : / Aminopeptidase, putative

• Biological species: Trypanosoma brucei brucei (eukaryote)
• Method: X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
• Authors: Timm, J. / Wilson, K.
• Citation: Journal: mSphere / Year: 2018; Title: Structural Characterization of Acidic M17 Leucine Aminopeptidases from the TriTryps and Evaluation of Their Role in Nutrient Starvation inTrypanosoma brucei.; Authors: Timm, J. / Valente, M. / Garcia-Caballero, D. / Wilson, K.S. / Gonzalez-Pacanowska, D.

History

Deposition	Apr 26, 2017	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Aug 2, 2017	Provider: repository / Type: Initial release
Revision 1.1	Aug 30, 2017	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2	Feb 21, 2018	Group: Database references / Category: citation / Item: _citation.title
Revision 1.3	Mar 28, 2018	Group: Data collection / Database references / Category: citation / Item: _citation.title / _citation.year
Revision 1.4	Jan 17, 2024	Group: Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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

Assembly

Deposited unit

A: Aminopeptidase, putative

B: Aminopeptidase, putative

C: Aminopeptidase, putative

D: Aminopeptidase, putative

E: Aminopeptidase, putative

F: Aminopeptidase, putative

G: Aminopeptidase, putative

H: Aminopeptidase, putative

I: Aminopeptidase, putative

J: Aminopeptidase, putative

K: Aminopeptidase, putative

L: Aminopeptidase, putative

hetero molecules

Summary:

• 667 kDa, 12 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	667,068	48
Polymers	665,018	12
Non-polymers	2,051	36
Water	11,908	661

1

A: Aminopeptidase, putative

B: Aminopeptidase, putative

D: Aminopeptidase, putative

hetero molecules

J: Aminopeptidase, putative

K: Aminopeptidase, putative

L: Aminopeptidase, putative

hetero molecules

Summary:

• defined by author&software
• Evidence: light scattering
• 334 kDa, 6 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	333,534	24
Polymers	332,509	6
Non-polymers	1,025	18
Water	108	6

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1
crystal symmetry operation	1_455	x-1,y,z	1

Calculated values:

Buried area	30360 Å2
ΔGint	-143 kcal/mol
Surface area	92290 Å2
Method	PISA

2

J: Aminopeptidase, putative

K: Aminopeptidase, putative

L: Aminopeptidase, putative

hetero molecules

A: Aminopeptidase, putative

B: Aminopeptidase, putative

D: Aminopeptidase, putative

hetero molecules

Summary:

• defined by author&software
• 334 kDa, 6 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	333,534	24
Polymers	332,509	6
Non-polymers	1,025	18
Water	108	6

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1
crystal symmetry operation	1_655	x+1,y,z	1

Calculated values:

Buried area	30360 Å2
ΔGint	-143 kcal/mol
Surface area	92290 Å2
Method	PISA

3

C: Aminopeptidase, putative

E: Aminopeptidase, putative

F: Aminopeptidase, putative

G: Aminopeptidase, putative

H: Aminopeptidase, putative

I: Aminopeptidase, putative

hetero molecules

Summary:

• defined by author&software
• 334 kDa, 6 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	333,534	24
Polymers	332,509	6
Non-polymers	1,025	18
Water	108	6

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

Calculated values:

Buried area	30340 Å2
ΔGint	-144 kcal/mol
Surface area	92280 Å2
Method	PISA

Unit cell

Length a, b, c (Å)	87.368, 143.760, 270.085
Angle α, β, γ (deg.)	90.00, 95.47, 90.00
Int Tables number	4
Space group name H-M	P1211

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
1	2	A
2	2	C
1	3	A
2	3	D
1	4	A
2	4	E
1	5	A
2	5	F
1	6	A
2	6	G
1	7	A
2	7	H
1	8	A
2	8	I
1	9	A
2	9	J
1	10	A
2	10	K
1	11	A
2	11	L
1	12	B
2	12	C
1	13	B
2	13	D
1	14	B
2	14	E
1	15	B
2	15	F
1	16	B
2	16	G
1	17	B
2	17	H
1	18	B
2	18	I
1	19	B
2	19	J
1	20	B
2	20	K
1	21	B
2	21	L
1	22	C
2	22	D
1	23	C
2	23	E
1	24	C
2	24	F
1	25	C
2	25	G
1	26	C
2	26	H
1	27	C
2	27	I
1	28	C
2	28	J
1	29	C
2	29	K
1	30	C
2	30	L
1	31	D
2	31	E
1	32	D
2	32	F
1	33	D
2	33	G
1	34	D
2	34	H
1	35	D
2	35	I
1	36	D
2	36	J
1	37	D
2	37	K
1	38	D
2	38	L
1	39	E
2	39	F
1	40	E
2	40	G
1	41	E
2	41	H
1	42	E
2	42	I
1	43	E
2	43	J
1	44	E
2	44	K
1	45	E
2	45	L
1	46	F
2	46	G
1	47	F
2	47	H
1	48	F
2	48	I
1	49	F
2	49	J
1	50	F
2	50	K
1	51	F
2	51	L
1	52	G
2	52	H
1	53	G
2	53	I
1	54	G
2	54	J
1	55	G
2	55	K
1	56	G
2	56	L
1	57	H
2	57	I
1	58	H
2	58	J
1	59	H
2	59	K
1	60	H
2	60	L
1	61	I
2	61	J
1	62	I
2	62	K
1	63	I
2	63	L
1	64	J
2	64	K
1	65	J
2	65	L
1	66	K
2	66	L

NCS domain segments:

Component-ID: 0 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 0 / Auth seq-ID: 3 - 521 / Label seq-ID: 3 - 521

Dom-ID	Ens-ID	Auth asym-ID	Label asym-ID
1	1	A	A
2	1	B	B
1	2	A	A
2	2	C	C
1	3	A	A
2	3	D	D
1	4	A	A
2	4	E	E
1	5	A	A
2	5	F	F
1	6	A	A
2	6	G	G
1	7	A	A
2	7	H	H
1	8	A	A
2	8	I	I
1	9	A	A
2	9	J	J
1	10	A	A
2	10	K	K
1	11	A	A
2	11	L	L
1	12	B	B
2	12	C	C
1	13	B	B
2	13	D	D
1	14	B	B
2	14	E	E
1	15	B	B
2	15	F	F
1	16	B	B
2	16	G	G
1	17	B	B
2	17	H	H
1	18	B	B
2	18	I	I
1	19	B	B
2	19	J	J
1	20	B	B
2	20	K	K
1	21	B	B
2	21	L	L
1	22	C	C
2	22	D	D
1	23	C	C
2	23	E	E
1	24	C	C
2	24	F	F
1	25	C	C
2	25	G	G
1	26	C	C
2	26	H	H
1	27	C	C
2	27	I	I
1	28	C	C
2	28	J	J
1	29	C	C
2	29	K	K
1	30	C	C
2	30	L	L
1	31	D	D
2	31	E	E
1	32	D	D
2	32	F	F
1	33	D	D
2	33	G	G
1	34	D	D
2	34	H	H
1	35	D	D
2	35	I	I
1	36	D	D
2	36	J	J
1	37	D	D
2	37	K	K
1	38	D	D
2	38	L	L
1	39	E	E
2	39	F	F
1	40	E	E
2	40	G	G
1	41	E	E
2	41	H	H
1	42	E	E
2	42	I	I
1	43	E	E
2	43	J	J
1	44	E	E
2	44	K	K
1	45	E	E
2	45	L	L
1	46	F	F
2	46	G	G
1	47	F	F
2	47	H	H
1	48	F	F
2	48	I	I
1	49	F	F
2	49	J	J
1	50	F	F
2	50	K	K
1	51	F	F
2	51	L	L
1	52	G	G
2	52	H	H
1	53	G	G
2	53	I	I
1	54	G	G
2	54	J	J
1	55	G	G
2	55	K	K
1	56	G	G
2	56	L	L
1	57	H	H
2	57	I	I
1	58	H	H
2	58	J	J
1	59	H	H
2	59	K	K
1	60	H	H
2	60	L	L
1	61	I	I
2	61	J	J
1	62	I	I
2	62	K	K
1	63	I	I
2	63	L	L
1	64	J	J
2	64	K	K
1	65	J	J
2	65	L	L
1	66	K	K
2	66	L	L

NCS ensembles :

ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66

Components

#1: Protein

A B C D E F G H I J K L
Aminopeptidase, putative /

Details:

Mass: 55418.141 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei brucei (strain 927/4 GUTat10.1) (eukaryote)
Strain: 927/4 GUTat10.1 / Gene: Tb11.02.4440 / Production host: Escherichia coli (E. coli) / References: UniProt: Q385B0

#2: Chemical

A-601 B-601 C-601 D-601 E-601 F-601 G-601 H-601 I-601 J-601 K-601 L-601
ChemComp-BCT / BICARBONATE ION / Bicarbonate

Details:

Mass: 61.017 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: CHO₃ / Comment: pH buffer*YM

#3: Chemical

A-602 A-603 B-602 B-603 C-602 C-603 D-602 D-603 E-602 E-603 F-602 F-603 G-602 G-603 H-602 H-603 I-602 I-603 J-602 J-603 ...
ChemComp-MN / MANGANESE (II) ION

Details:

Mass: 54.938 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: Mn

#4: Water

ChemComp-HOH / water / Water

Details:

Mass: 18.015 Da / Num. of mol.: 661 / Source method: isolated from a natural source / Formula: H₂O

Experimental details

Experiment

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

Sample preparation

• Crystal: Density Matthews: 2.54 ų/Da / Density % sol: 51.54 %
• Crystal grow: Temperature: 293 K / Method: vapor diffusion, hanging drop; Details: 0.1 M Tris pH 6.8, 0.2 M MgCl2, 11 % (w/v) PEG 8000, 10 microM ZnCl2, 10 mM L-leucine

Data collection

• Diffraction: Mean temperature: 100 K
• Diffraction source: Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
• Detector: Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 27, 2014
• Radiation: Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
• Radiation wavelength: Wavelength: 0.9795 Å / Relative weight: 1
• Reflection: Resolution: 2.4→32.73 Å / Num. obs: 244412 / % possible obs: 94.5 % / Redundancy: 3.3 % / R_merge(I) obs: 0.117 / Net I/σ(I): 5.7
• Reflection shell: Resolution: 2.4→2.44 Å / Redundancy: 2.9 % / R_merge(I) obs: 0.351 / Mean I/σ(I) obs: 2 / Num. unique all: 11362 / % possible all: 88.7

Processing

Software

Name	Version	Classification
REFMAC	5.8.0135	refinement
MOSFLM		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure: MOLECULAR REPLACEMENT
Starting model: 5NSK

5nsk

Resolution: 2.4→32.73 Å / Cor.coef. F_o:F_c: 0.934 / Cor.coef. F_o:F_c free: 0.921 / SU B: 9.662 / SU ML: 0.217 / Cross valid method: THROUGHOUT / ESU R: 0.51 / ESU R Free: 0.25 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	Rfactor	Num. reflection	% reflection	Selection details
Rfree	0.22508	11981	4.9 %	RANDOM
Rwork	0.20595	-	-	-
obs	0.20689	232199	94.27 %	-

• 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: 34.619 Ų

	Baniso -1	Baniso -2	Baniso -3
1-	3.46 Å2	0 Å2	-1.16 Å2
2-	-	-1.65 Å2	0 Å2
3-	-	-	-1.56 Å2

Refinement step

Cycle: 1 / Resolution: 2.4→32.73 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	45554	0	72	661	46287

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.014	0.019	46699
X-RAY DIFFRACTION	r_bond_other_d	0.008	0.02	43734
X-RAY DIFFRACTION	r_angle_refined_deg	1.397	1.966	63650
X-RAY DIFFRACTION	r_angle_other_deg	2.323	3	100420
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.884	5	6234
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.511	24.463	1824
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.544	15	6767
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.568	15	205
X-RAY DIFFRACTION	r_chiral_restr	0.074	0.2	7489
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.021	54162
X-RAY DIFFRACTION	r_gen_planes_other	0.006	0.02	10143
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	1.673	3.462	24930
X-RAY DIFFRACTION	r_mcbond_other	1.673	3.462	24929
X-RAY DIFFRACTION	r_mcangle_it	2.664	5.19	31145
X-RAY DIFFRACTION	r_mcangle_other	2.664	5.19	31146
X-RAY DIFFRACTION	r_scbond_it	1.938	3.613	21769
X-RAY DIFFRACTION	r_scbond_other	1.934	3.612	21734
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	3.112	5.365	32463
X-RAY DIFFRACTION	r_long_range_B_refined	4.434	27.267	49862
X-RAY DIFFRACTION	r_long_range_B_other	4.407	27.258	49721
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	61292	0.05
1	2	B	61292	0.05
2	1	A	62434	0.02
2	2	C	62434	0.02
3	1	A	61328	0.05
3	2	D	61328	0.05
4	1	A	61598	0.05
4	2	E	61598	0.05
5	1	A	61042	0.04
5	2	F	61042	0.04
6	1	A	62268	0.03
6	2	G	62268	0.03
7	1	A	61316	0.05
7	2	H	61316	0.05
8	1	A	61376	0.04
8	2	I	61376	0.04
9	1	A	62328	0.02
9	2	J	62328	0.02
10	1	A	60518	0.05
10	2	K	60518	0.05
11	1	A	61264	0.04
11	2	L	61264	0.04
12	1	B	61146	0.05
12	2	C	61146	0.05
13	1	B	60740	0.05
13	2	D	60740	0.05
14	1	B	62110	0.02
14	2	E	62110	0.02
15	1	B	60570	0.05
15	2	F	60570	0.05
16	1	B	61212	0.05
16	2	G	61212	0.05
17	1	B	62086	0.02
17	2	H	62086	0.02
18	1	B	60570	0.05
18	2	I	60570	0.05
19	1	B	61096	0.05
19	2	J	61096	0.05
20	1	B	61484	0.02
20	2	K	61484	0.02
21	1	B	60540	0.05
21	2	L	60540	0.05
22	1	C	61428	0.05
22	2	D	61428	0.05
23	1	C	61442	0.05
23	2	E	61442	0.05
24	1	C	61158	0.04
24	2	F	61158	0.04
25	1	C	62264	0.02
25	2	G	62264	0.02
26	1	C	61102	0.05
26	2	H	61102	0.05
27	1	C	61336	0.04
27	2	I	61336	0.04
28	1	C	62088	0.03
28	2	J	62088	0.03
29	1	C	60628	0.05
29	2	K	60628	0.05
30	1	C	61150	0.04
30	2	L	61150	0.04
31	1	D	60786	0.06
31	2	E	60786	0.06
32	1	D	62016	0.03
32	2	F	62016	0.03
33	1	D	61184	0.05
33	2	G	61184	0.05
34	1	D	60524	0.05
34	2	H	60524	0.05
35	1	D	62004	0.03
35	2	I	62004	0.03
36	1	D	61346	0.04
36	2	J	61346	0.04
37	1	D	60326	0.05
37	2	K	60326	0.05
38	1	D	61974	0.02
38	2	L	61974	0.02
39	1	E	60574	0.05
39	2	F	60574	0.05
40	1	E	61336	0.05
40	2	G	61336	0.05
41	1	E	62116	0.03
41	2	H	62116	0.03
42	1	E	60902	0.05
42	2	I	60902	0.05
43	1	E	61354	0.05
43	2	J	61354	0.05
44	1	E	61314	0.03
44	2	K	61314	0.03
45	1	E	60714	0.05
45	2	L	60714	0.05
46	1	F	61076	0.04
46	2	G	61076	0.04
47	1	F	60420	0.05
47	2	H	60420	0.05
48	1	F	61896	0.02
48	2	I	61896	0.02
49	1	F	61052	0.05
49	2	J	61052	0.05
50	1	F	60164	0.05
50	2	K	60164	0.05
51	1	F	61910	0.03
51	2	L	61910	0.03
52	1	G	61168	0.05
52	2	H	61168	0.05
53	1	G	61096	0.05
53	2	I	61096	0.05
54	1	G	62074	0.03
54	2	J	62074	0.03
55	1	G	60526	0.05
55	2	K	60526	0.05
56	1	G	61050	0.04
56	2	L	61050	0.04
57	1	H	60546	0.05
57	2	I	60546	0.05
58	1	H	61108	0.05
58	2	J	61108	0.05
59	1	H	61364	0.02
59	2	K	61364	0.02
60	1	H	60518	0.05
60	2	L	60518	0.05
61	1	I	61306	0.05
61	2	J	61306	0.05
62	1	I	60150	0.05
62	2	K	60150	0.05
63	1	I	61984	0.03
63	2	L	61984	0.03
64	1	J	60414	0.05
64	2	K	60414	0.05
65	1	J	61440	0.04
65	2	L	61440	0.04
66	1	K	60124	0.05
66	2	L	60124	0.05

LS refinement shell

Resolution: 2.4→2.462 Å / Total num. of bins used: 20

	Rfactor	Num. reflection	% reflection
Rfree	0.297	805	-
Rwork	0.273	16011	-
obs	-	-	88.51 %