PDB-3dwc: Trypanosoma Cruzi Metallocarboxypeptidase 1

ID or keywords:

Entry

Database: PDB / ID: 3dwc

Title

Trypanosoma Cruzi Metallocarboxypeptidase 1

Components

Metallocarboxypeptidase

Keywords

HYDROLASE / metallocarboxypeptidase / cowrin family of metallocarboxypeptidases / Carboxypeptidase

Function / homology

Function and homology information

carboxypeptidase Taq / metallocarboxypeptidase activity
Similarity search - Function

Biological species

Trypanosoma cruzi (eukaryote)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.1 Å

Authors

Niemirowicz, G. / Fernandez, D. / Sola, M. / Cazzulo, J.J. / Aviles, F.X. / Gomis-Ruth, F.X.

Citation

Journal: Mol.Microbiol. / Year: 2008
Title: The molecular analysis of Trypanosoma cruzi metallocarboxypeptidase 1 provides insight into fold and substrate specificity
Authors: Niemirowicz, G. / Fernandez, D. / Sola, M. / Cazzulo, J.J. / Aviles, F.X. / Gomis-Ruth, F.X.

History

Deposition	Jul 22, 2008	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Sep 9, 2008	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Nov 1, 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 / 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn.ptnr2_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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PDBx/mmCIF format	3dwc.cif.gz	422.5 KB	Display	PDBx/mmCIF format
PDB format	pdb3dwc.ent.gz	345.3 KB	Display	PDB format
PDBx/mmJSON format	3dwc.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	3dwc_validation.pdf.gz	511.8 KB	Display	wwPDB validaton report
Full document	3dwc_full_validation.pdf.gz	537.7 KB	Display
Data in XML	3dwc_validation.xml.gz	80.5 KB	Display
Data in CIF	3dwc_validation.cif.gz	115.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/dw/3dwc ftp://data.pdbj.org/pub/pdb/validation_reports/dw/3dwc	HTTPS FTP

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Related structure data

Related structure data	1k9xS S: Starting model for refinement
Similar structure data	3gzj-2 1k9x-1 21913 3dkh-d 1ka2-1 5zvg-d 5wvu-2 3qpk-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
Related items in Molecule of the Month	#235 - Jul 2019 AMPA Receptor similarity (1) #104 - Aug 2008 Selenocysteine Synthase similarity (1) #142 - Oct 2011 PDB Pioneers similarity (1)

Deposited unit

A: Metallocarboxypeptidase

B: Metallocarboxypeptidase

C: Metallocarboxypeptidase

D: Metallocarboxypeptidase

hetero molecules

234 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Metallocarboxypeptidase

B: Metallocarboxypeptidase

hetero molecules

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

2

C: Metallocarboxypeptidase

D: Metallocarboxypeptidase

hetero molecules

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

Unit cell

Length a, b, c (Å)	89.400, 136.250, 117.860
Angle α, β, γ (deg.)	90.00, 103.06, 90.00
Int Tables number	4
Space group name H-M	P12₁1

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Protein , 1 types, 4 molecules ABCD

#1: Protein	Metallocarboxypeptidase / TCMCP-1 Mass: 57967.145 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trypanosoma cruzi (eukaryote) / Gene: mcar-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6ZXC0, carboxypeptidase Taq

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Non-polymers , 6 types, 1148 molecules

#2: Chemical	ChemComp-CO / COBALT (II) ION Mass: 58.933 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Co
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO₄
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Chemical	ChemComp-GLY / GLYCINE Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₅NO₂
#6: Chemical	ChemComp-ALA / ALANINE Type: L-peptide linking / Mass: 89.093 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₇NO₂
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1120 / 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: 3.01 Å³/Da / Density % sol: 59.18 %

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 1 Å
Detector	Type: ADSC QUANTUM 210 / Detector: CCD
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.1→46.23 Å / Num. obs: 156037 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.3 % / B_iso Wilson estimate: 31.1 Å² / R_merge(I) obs: 0.084 / Net I/σ(I): 17.8
Reflection shell	Resolution: 2.1→2.21 Å / Redundancy: 6.3 % / R_merge(I) obs: 0.574 / Mean I/σ(I) obs: 4.1 / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0019	refinement
ADSC	Quantum	data collection
XDS		data reduction
SCALA		data scaling
AMoRE		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1K9X

1k9x

Resolution: 2.1→46.23 Å / Cor.coef. F_o:F_c: 0.957 / Cor.coef. F_o:F_c free: 0.935 / SU B: 9.377 / SU ML: 0.113 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.169 / ESU R Free: 0.156 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.22114	3915	2.4 %	RANDOM
R_work	0.17928	-	-	-
obs	0.18037	147734	100 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 30.974 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.45 Å²	0 Å²	-1.47 Å²
2-	-	-2.18 Å²	0 Å²
3-	-	-	1.97 Å²

Refinement step

Cycle: LAST / Resolution: 2.1→46.23 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	16009	0	132	1120	17261

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.016	0.022	16456
X-RAY DIFFRACTION	r_bond_other_d	0.003	0.02	11628
X-RAY DIFFRACTION	r_angle_refined_deg	1.48	1.974	22154
X-RAY DIFFRACTION	r_angle_other_deg	0.969	3	28167
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.732	5	1985
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.177	23.64	805
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.569	15	3003
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.911	15	140
X-RAY DIFFRACTION	r_chiral_restr	0.089	0.2	2334
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	18133
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	3384
X-RAY DIFFRACTION	r_nbd_refined	0.211	0.2	3805
X-RAY DIFFRACTION	r_nbd_other	0.195	0.2	12050
X-RAY DIFFRACTION	r_nbtor_refined	0.181	0.2	7930
X-RAY DIFFRACTION	r_nbtor_other	0.09	0.2	8261
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.165	0.2	940
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined	0.02	0.2	1
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.298	0.2	12
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.286	0.2	65
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.16	0.2	12
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	1.08	1.5	12907
X-RAY DIFFRACTION	r_mcbond_other	0.206	1.5	4047
X-RAY DIFFRACTION	r_mcangle_it	1.25	2	15856
X-RAY DIFFRACTION	r_scbond_it	2.278	3	7592
X-RAY DIFFRACTION	r_scangle_it	3.287	4.5	6298
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.1→2.154 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.353	1	-
R_work	0.211	11786	-
obs	-	-	100 %

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	1.0082	0.2511	0.4962	0.965	-0.0138	0.6365	-0.0107	-0.0893	0.1026	0.0639	-0.0179	-0.0336	-0.0339	-0.0221	0.0286	-0.1914	0.0104	0.041	-0.1327	-0.0196	-0.1733	45.6572	69.7202	93.8721
2	6.9795	3.9788	-3.3456	4.7356	0.8472	4.6785	-0.0888	-0.0688	-0.2711	0.4346	-0.3452	1.0786	0.3584	-0.5907	0.434	0.0002	-0.0002	0.0003	0.0001	-0.0001	0.0003	35.8212	56.7162	110.9694
3	1.5099	-0.3408	0.2423	0.8849	-0.1393	0.5144	0.0194	0.1162	-0.1718	-0.0715	-0.0053	0.0953	0.0558	0.0095	-0.0141	-0.1477	-0.0214	0.039	-0.0674	-0.0008	-0.0874	-0.341	66.8553	77.7876
4	6.8007	-4.3938	-3.8564	7.7485	-2.6314	7.5322	-0.0203	0.3082	-0.4017	-0.6549	-0.4648	-1.1714	0.8895	0.5303	0.4851	0.0002	0.0003	0.0003	0.0002	0.0002	0.0004	10.8696	54.2932	60.4849
5	1	-0.2106	0.4219	1.1846	-0.1082	0.7004	-0.0644	-0.0066	0.0881	0.0244	0.059	-0.0534	-0.1317	0.1077	0.0055	-0.0652	0.0134	0.0269	-0.0689	-0.0337	-0.1645	49.6073	64.2944	48.2373
6	4.3749	-2.8	-2.2873	8.1826	-3.1076	6.1636	0.2459	0.6975	0.7602	-1.2232	-0.3473	0.0903	-0.9981	-0.381	0.1015	0.0005	0.0004	0.0001	0.0002	0.0002	0.0003	58.9813	81.6662	34.8008
7	1.144	-0.0762	0.705	0.8041	0.2733	1.0145	0.0828	-0.0287	-0.0859	-0.0657	-0.0269	-0.0227	0.1701	-0.0982	-0.0559	0.0022	-0.0293	-0.004	-0.1291	0.0179	-0.1442	15.3864	68.5103	14.5522
8	3.7643	7.7063	-1.8936	21.1998	9.3051	32.9897	0.6432	-0.5128	0.3983	1.9048	-0.2396	-0.4653	0.8047	-0.6736	-0.4036	-0.0003	0.0006	0.0003	-0.0004	-0.0003	0.0002	4.2352	83.3858	31.6142
9	0.0722	-0.0348	0.0828	0.1011	-0.0333	0.1179	-0.0013	-0.0183	0.0057	-0.0249	0.0089	0.034	0.0255	0.0063	-0.0076	0.1162	-0.0148	0.0269	0.1498	-0.0095	0.0986	28.1693	67.4973	63.2133

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	X-RAY DIFFRACTION	1	A	A	0 - 95	2 - 97
2	X-RAY DIFFRACTION	1	A	A	151 - 500	153 - 502
3	X-RAY DIFFRACTION	1	A	E	999
4	X-RAY DIFFRACTION	2	A	A	96 - 150	98 - 152
5	X-RAY DIFFRACTION	3	B	B	0 - 95	2 - 97
6	X-RAY DIFFRACTION	3	B	B	151 - 503	153 - 505
7	X-RAY DIFFRACTION	3	B	P	999
8	X-RAY DIFFRACTION	4	B	B	96 - 150	98 - 152
9	X-RAY DIFFRACTION	5	C	C	0 - 95	2 - 97
10	X-RAY DIFFRACTION	5	C	C	151 - 500	153 - 502
11	X-RAY DIFFRACTION	5	C	I	999
12	X-RAY DIFFRACTION	6	C	C	96 - 150	98 - 152
13	X-RAY DIFFRACTION	7	D	D	-1 - 95	1 - 97
14	X-RAY DIFFRACTION	7	D	D	151 - 500	153 - 502
15	X-RAY DIFFRACTION	7	D	M	999
16	X-RAY DIFFRACTION	8	D	D	96 - 107	98 - 109
17	X-RAY DIFFRACTION	8	D	D	127 - 150	129 - 152
18	X-RAY DIFFRACTION	9	A	F - H	604 - 610
19	X-RAY DIFFRACTION	9	B	Q - U	602 - 612
20	X-RAY DIFFRACTION	9	C	J - L	603 - 613
21	X-RAY DIFFRACTION	9	D	N - O	601 - 608
22	X-RAY DIFFRACTION	9	B	V - W	701 - 702
23	X-RAY DIFFRACTION	9	A	X - CA	703 - 711
24	X-RAY DIFFRACTION	9	B	DA - FA	706 - 709
25	X-RAY DIFFRACTION	9	A	GA	1001 - 2119
26	X-RAY DIFFRACTION	9	B	HA	1004 - 2093
27	X-RAY DIFFRACTION	9	C	IA	1021 - 2114
28	X-RAY DIFFRACTION	9	D	JA	1013 - 2120

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