PDB-3kr5: Structure of a protease 4

ID or keywords:

Entry

Database: PDB / ID: 3kr5

Title

Structure of a protease 4

Components

M17 leucyl aminopeptidase

Keywords

HYDROLASE / protease / Aminopeptidase

Function / homology

Function and homology information

Hydrolases; Acting on peptide bonds (peptidases); Dipeptidases / leucyl aminopeptidase / metallodipeptidase activity / peptide catabolic process / metalloaminopeptidase activity / carboxypeptidase activity / peptidase activity / manganese ion binding / proteolysis / zinc ion binding ...
Similarity search - Function

Biological species

Plasmodium falciparum (malaria parasite P. falciparum)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.56 Å

Authors

McGowan, S. / Whisstock, J.C.

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Structure of the Plasmodium falciparum M17 aminopeptidase and significance for the design of drugs targeting the neutral exopeptidases
Authors: McGowan, S. / Oellig, C.A. / Birru, W.A. / Caradoc-Davies, T.T. / Stack, C.M. / Lowther, J. / Skinner-Adams, T. / Mucha, A. / Kafarski, P. / Grembecka, J. / Trenholme, K.R. / Buckle, A.M. / ...

History

Deposition	Nov 17, 2009	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Feb 2, 2010	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Nov 10, 2021	Group: Database references / Derived calculations Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3	Nov 1, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	3kr5.cif.gz	2.3 MB	Display	PDBx/mmCIF format
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Validation report

Summary document	3kr5_validation.pdf.gz	3.8 MB	Display	wwPDB validaton report
Full document	3kr5_full_validation.pdf.gz	4 MB	Display
Data in XML	3kr5_validation.xml.gz	248.8 KB	Display
Data in CIF	3kr5_validation.cif.gz	340.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/kr/3kr5 ftp://data.pdbj.org/pub/pdb/validation_reports/kr/3kr5	HTTPS FTP

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Related structure data

Related structure data	3kqxSC 3kqzC 3kr4C S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4zy2-2 3kqz-1 4zy1-2 3kqz-2 3kqx-2 5cbm-1 4r6t-2 4r76-2 6eee-1 3kr4-1 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	#193 - Jan 2016 Siderocalin similarity (1) #255 - Mar 2021 Cisplatin and DNA similarity (1) #35 - Nov 2002 Ferritin and Transferrin similarity (1) #37 - Jan 2003 Serum Albumin similarity (1)

Deposited unit

A: M17 leucyl aminopeptidase

B: M17 leucyl aminopeptidase

C: M17 leucyl aminopeptidase

D: M17 leucyl aminopeptidase

E: M17 leucyl aminopeptidase

F: M17 leucyl aminopeptidase

G: M17 leucyl aminopeptidase

H: M17 leucyl aminopeptidase

I: M17 leucyl aminopeptidase

J: M17 leucyl aminopeptidase

K: M17 leucyl aminopeptidase

L: M17 leucyl aminopeptidase

hetero molecules

721 kDa, 12 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: M17 leucyl aminopeptidase

B: M17 leucyl aminopeptidase

C: M17 leucyl aminopeptidase

D: M17 leucyl aminopeptidase

E: M17 leucyl aminopeptidase

F: M17 leucyl aminopeptidase

hetero molecules

defined by author&software
360 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

G: M17 leucyl aminopeptidase

H: M17 leucyl aminopeptidase

I: M17 leucyl aminopeptidase

J: M17 leucyl aminopeptidase

K: M17 leucyl aminopeptidase

L: M17 leucyl aminopeptidase

hetero molecules

defined by author&software
361 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	172.080, 174.160, 227.706
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
3	1	C
4	1	D
5	1	E
6	1	F
7	1	G
8	1	H
9	1	I
10	1	J
11	1	K
12	1	L

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Refine code	Auth asym-ID	Auth seq-ID
1	1	1	1	A	277 - 603
2	1	1	1	B	277 - 603
3	1	1	1	C	277 - 603
4	1	1	1	D	277 - 603
5	1	1	1	E	277 - 603
6	1	1	1	F	277 - 603
7	1	1	1	G	277 - 603
8	1	1	1	H	277 - 603
9	1	1	1	I	277 - 603
10	1	1	1	J	277 - 603
11	1	1	1	K	277 - 603
12	1	1	1	L	277 - 603

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Protein , 1 types, 12 molecules ABCDEFGHIJKL

#1: Protein	M17 leucyl aminopeptidase / Malarial protease Mass: 58708.973 Da / Num. of mol.: 12 / Fragment: residues 84-605 / Mutation: N152Q, N515Q, N546Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum) Strain: 3D7 / Plasmid: pTrc-His2b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 Rosetta2 / References: UniProt: Q8IL11, leucyl aminopeptidase

#1: Protein

M17 leucyl aminopeptidase / Malarial protease

Mass: 58708.973 Da / Num. of mol.: 12 / Fragment: residues 84-605 / Mutation: N152Q, N515Q, N546Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / Plasmid: pTrc-His2b / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21 DE3 Rosetta2 / References: UniProt: Q8IL11, leucyl aminopeptidase

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Non-polymers , 6 types, 2414 molecules

#2: Chemical	ChemComp-CO3 / CARBONATE ION Mass: 60.009 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: CO₃
#3: Chemical	... ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: Zn
#4: Chemical	ChemComp-BEY / (2S)-3-[(R)-[(1S)-1-amino-3-phenylpropyl](hydroxy)phosphoryl]-2-benzylpropanoic acid Mass: 361.372 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C₁₉H₂₄NO₄P
#5: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: SO₄
#6: Chemical	... ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 Mass: 238.278 Da / Num. of mol.: 37 / Source method: obtained synthetically / Formula: C₁₀H₂₂O₆ / Comment: precipitant*YM
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 2314 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.51 Å³/Da / Density % sol: 50.97 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 40% PEG 400, 0.1M Tris pH 8.5, 0.2M LiSO4, 1mM TCEP, 1mM ZnCl2, 1mM Co4/BEY, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95376 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 9, 2009
Radiation	Monochromator: Double crystal silicon 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.95376 Å / Relative weight: 1
Reflection	Resolution: 2.56→78.9 Å / Num. obs: 217885 / % possible obs: 100 % / Redundancy: 12.2 % / R_merge(I) obs: 0.549 / R_sym value: 0.164 / Net I/σ(I): 4.1 / Num. measured all: 2662653
Reflection shell	Resolution: 2.56→2.74 Å / Redundancy: 12.4 % / R_merge(I) obs: 1.299 / Mean I/σ(I) obs: 2.1 / Num. unique all: 390909 / R_sym value: 0.384 / % possible all: 100

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Processing

Software

Name	Version	Classification
Blu-Ice		data collection
MOLREP		phasing
REFMAC	5.5.0102	refinement
MOSFLM		data reduction
SCALA		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3KQX

3kqx

Resolution: 2.56→77.7 Å / Cor.coef. F_o:F_c: 0.932 / Cor.coef. F_o:F_c free: 0.886 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 28.392 / SU ML: 0.281 / Cross valid method: THROUGHOUT / ESU R: 2.209 / ESU R Free: 0.359 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.27766	10910	5 %	RANDOM
R_work	0.22	-	-	-
obs	0.22288	206865	98.79 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso max: 295.39 Å² / B_iso mean: 24.299 Å² / B_iso min: 2 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-2.8 Å²	0 Å²	0 Å²
2-	-	1.53 Å²	0 Å²
3-	-	-	1.27 Å²

Refinement step

Cycle: LAST / Resolution: 2.56→77.7 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	47309	0	821	2314	50444

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.022	48955
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.456	1.975	66200
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.361	5	6131
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	39.293	25.282	1967
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.686	15	8174
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	20.19	15	104
X-RAY DIFFRACTION	r_chiral_restr	0.104	0.2	7548
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.021	36112
X-RAY DIFFRACTION	r_gen_planes_other
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	1.335	3	30585
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	2.53	5	49154
X-RAY DIFFRACTION	r_scbond_it	4.222	7	18370
X-RAY DIFFRACTION	r_scangle_it	6.394	10	17046
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Ens-ID: 1 / Number: 2422 / Refine-ID: X-RAY DIFFRACTION

Dom-ID	Auth asym-ID	Type	Rms dev position (Å)	Weight position
1	A	tight positional	0.05	0.05
2	B	tight positional	0.05	0.05
3	C	tight positional	0.06	0.05
4	D	tight positional	0.05	0.05
5	E	tight positional	0.06	0.05
6	F	tight positional	0.06	0.05
7	G	tight positional	0.05	0.05
8	H	tight positional	0.05	0.05
9	I	tight positional	0.06	0.05
10	J	tight positional	0.05	0.05
11	K	tight positional	0.05	0.05
12	L	tight positional	0.05	0.05
1	A	tight thermal	0.12	0.5
2	B	tight thermal	0.12	0.5
3	C	tight thermal	0.13	0.5
4	D	tight thermal	0.12	0.5
5	E	tight thermal	0.13	0.5
6	F	tight thermal	0.13	0.5
7	G	tight thermal	0.13	0.5
8	H	tight thermal	0.12	0.5
9	I	tight thermal	0.12	0.5
10	J	tight thermal	0.12	0.5
11	K	tight thermal	0.12	0.5
12	L	tight thermal	0.13	0.5

LS refinement shell

Resolution: 2.556→2.622 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.362	665	-
R_work	0.298	12788	-
obs	-	-	83.52 %

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	0.5761	0.0276	-0.1747	0.2643	0.0172	0.196	0.009	-0.035	0.0122	0.021	-0.0026	0.0499	-0.0235	-0.0466	-0.0063	0.0282	0.0048	-0.0031	0.0261	0.0034	0.0131	73.631	82.817	40.179
2	0.2521	0.0479	0.146	0.0961	0.0647	0.418	-0.0095	-0.0063	0.02	0.0258	0.0218	-0.0744	0.0082	0.1086	-0.0123	0.0308	0.0056	-0.0147	0.0408	-0.0187	0.0777	119.668	69.469	13.438
3	0.2629	-0.1547	-0.1191	0.4828	0.2824	0.4121	0.0044	0.0536	-0.0684	-0.065	-0.021	-0.0013	0.0115	-0.0273	0.0165	0.0299	-0.0024	0.0004	0.0325	-0.0049	0.0319	71.355	58.107	-8.823
4	0.3569	-0.1429	-0.0917	0.3446	0.0185	0.1728	-0.0346	-0.0294	0.0146	0.0417	0.0272	0.0701	-0.0058	-0.0489	0.0074	0.0268	-0.0093	-0.0018	0.0415	0.0029	0.0246	56.972	41.809	27.268
5	0.1961	0.018	0.1507	0.2129	0.0955	0.4633	0.0013	0.0546	-0.0271	-0.0518	0.0165	-0.0115	0.0028	0.0138	-0.0179	0.033	0.0044	0.0091	0.0246	0.0004	0.0402	105.707	30.957	6.023
6	0.7269	0.0891	0.026	0.3057	0.0072	0.2734	0.013	-0.067	0.009	0.0571	-0.0039	-0.0975	-0.0029	0.0386	-0.009	0.0332	0.0169	-0.0163	0.0421	0.002	0.0345	101.086	55.002	53.894
7	0.6065	-0.0252	-0.1397	0.164	0.0584	0.1634	-0.0137	-0.0688	-0.0189	0.0199	0.0049	0.0466	-0.0001	-0.037	0.0088	0.0311	0.0082	-0.0055	0.0351	0.0033	0.0252	76.309	82.81	155.343
8	0.3367	0.0354	0.2315	0.1593	0.0452	0.5516	-0.0242	0.0051	0.026	0.035	0.0177	-0.0872	-0.008	0.1189	0.0066	0.0267	0.0084	-0.0119	0.0381	-0.0057	0.063	122.409	69.436	128.769
9	0.2224	-0.0886	-0.0924	0.4085	0.2038	0.3163	0.0029	0.0618	-0.0715	-0.0784	-0.0113	0.0066	0.0067	-0.0159	0.0083	0.0272	0.0018	0.0021	0.0353	-0.0139	0.0277	73.596	58.097	106.452
10	0.4622	-0.1387	-0.1184	0.3515	0.0347	0.2035	-0.0324	-0.0203	0.0408	0.0469	0.0161	0.0539	-0.0196	-0.0624	0.0162	0.0338	-0.0061	-0.0069	0.0445	-0.0035	0.0245	59.54	41.814	142.3
11	0.1765	0.014	0.1363	0.1974	0.0728	0.5322	-0.0032	0.0477	-0.027	-0.0549	0.0241	-0.0034	-0.0001	0.0156	-0.021	0.0302	0.0027	0.0032	0.0253	-0.0018	0.0374	108.331	30.918	121.082
12	0.867	0.1067	0.0615	0.3667	-0.0222	0.2164	-0.0144	-0.0652	0.05	0.0443	0.0018	-0.098	-0.0048	0.0482	0.0126	0.0248	0.0114	-0.013	0.0433	0.0007	0.0359	104.541	55.56	169.33

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	86 - 603
2	X-RAY DIFFRACTION	2	B	86 - 603
3	X-RAY DIFFRACTION	3	C	86 - 603
4	X-RAY DIFFRACTION	4	D	86 - 603
5	X-RAY DIFFRACTION	5	E	86 - 602
6	X-RAY DIFFRACTION	6	F	86 - 603
7	X-RAY DIFFRACTION	7	G	86 - 603
8	X-RAY DIFFRACTION	8	H	86 - 603
9	X-RAY DIFFRACTION	9	I	86 - 603
10	X-RAY DIFFRACTION	10	J	86 - 603
11	X-RAY DIFFRACTION	11	K	86 - 603
12	X-RAY DIFFRACTION	12	L	86 - 603

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Protein , 1 types, 12 molecules ABCDEFGHIJKL

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Non-polymers , 6 types, 2414 molecules

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-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Protein , 1 types, 12 molecules ABCDEFGHIJKL

-
Non-polymers , 6 types, 2414 molecules

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
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

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Yorodumi