PDB-4mmo: The crystal structure of a M20 family metallo-carboxypeptidase Ss...

ID or keywords:

Entry

Database: PDB / ID: 4mmo

Title

The crystal structure of a M20 family metallo-carboxypeptidase Sso-CP2 from Sulfolobus solfataricus

Components

Sso-CP2 metallo-carboxypetidase

Keywords

HYDROLASE / M20 family peptidase / metallo protein / protease / metalloprotease / metal-binding hydrolase / carboxypeptidase

Function / homology

Function and homology information

hydrolase activity / metal ion binding
Similarity search - Function

Biological species

Sulfolobus solfataricus (archaea)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.3363 Å

Authors

Dupuy, J. / Dutoit, R. / Durisotti, V. / Demarez, M. / Borel, F. / Van Elder, D. / Legrain, C. / Bauvois, C.

Citation

Journal: To be Published
Title: Biochemical characterization of a novel thermostable dinuclear carboxypeptidase from the thermoacidophilic archaeum Sulfolobus solfataricus.
Authors: Bauvois, C. / Demarez, M. / Durisotti, V. / Roovers, M. / Dutoit, R. / Gigot, D. / Dupuy, J. / Wattiez, R. / Legrain, C.

History

Deposition	Sep 9, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 15, 2014	Provider: repository / Type: Initial release
Revision 1.1	Nov 15, 2017	Group: Refinement description / Category: software / Item: _software.name
Revision 1.2	Dec 20, 2017	Group: Database references / Category: pdbx_database_related
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_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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	4mmo.cif.gz	467.8 KB	Display	PDBx/mmCIF format
PDB format	pdb4mmo.ent.gz	391.4 KB	Display	PDB format
PDBx/mmJSON format	4mmo.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/mm/4mmo ftp://data.pdbj.org/pub/pdb/validation_reports/mm/4mmo	HTTPS FTP

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Related structure data

Related structure data	3dljS S: Starting model for refinement
Similar structure data	2a96-d 1noc-d 3vvp-d 1b7e-1 1kjy-3 3ck9-d 1r20-2 1aqw-d 5zjg-d 6ltd-1 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	#110 - Feb 2009 Auxin and TIR1 Ubiquitin Ligase similarity (4)

Deposited unit

A: Sso-CP2 metallo-carboxypetidase

B: Sso-CP2 metallo-carboxypetidase

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	86.070, 89.370, 161.420
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Sso-CP2 metallo-carboxypetidase Mass: 49027.035 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Strain: ATCC 35092 / DSM 1617 / JCM 11322 / P2 / Gene: SSO2737 / Plasmid: pET-30b(SSO2737) / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) pLysS / References: UniProt: Q97V97
#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO₄
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 318 / 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: 3.17 Å³/Da / Density % sol: 61.15 %
Crystal grow	Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 4.3 Details: SsoCP2 (120 uM) was mixed 2:2 with well buffer (100 mM acetate HCl pH 4.3 with 12% PEG 8000,(NH4)2SO4 500 mM and 20 % glycerol) with 500 uL well buffer., VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.979798 Å
Detector	Type: MAR CCD 165 mm / Detector: CCD / Date: Jul 3, 2006
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.979798 Å / Relative weight: 1
Reflection	Resolution: 2.336→50 Å / Num. all: 53510 / Num. obs: 53076 / % possible obs: 99.2 % / Observed criterion σ(F): -3 / Redundancy: 7.7 % / B_iso Wilson estimate: 46.91 Å² / R_merge(I) obs: 0.06374 / Net I/σ(I): 22.33
Reflection shell	Resolution: 2.336→2.42 Å / Redundancy: 7.6 % / R_merge(I) obs: 0.7355 / Mean I/σ(I) obs: 3.04 / Num. unique all: 3877 / % possible all: 96.4

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Processing

Software

Name	Version	Classification
MAR345		data collection
BALBES		phasing
PHENIX	(phenix.refine: 1.8.2_1309)	refinement
XDS		data reduction
XSCALE		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3DLJ

3dlj

Resolution: 2.3363→46.097 Å / SU ML: 0.28 / σ(F): 1.99 / Phase error: 27.25 / Stereochemistry target values: ML
Details: DUE TO INCOMPLETE ELECTRON DENSITY, SEVERAL LOOPS (FORMED BY RESIDUES 1-7, 18-19, 73-86, 92-102, 135-139, 369 and 400-414) OF THE MONOMER B CATALYTIC DOMAIN ARE MISSING.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2533	2651	5 %	RANDOM
R_work	0.206	-	-	-
obs	0.2084	53035	99.13 %	-
all	-	53076	-	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.3363→46.097 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6254	0	32	318	6604

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	6409
X-RAY DIFFRACTION	f_angle_d	0.836	8691
X-RAY DIFFRACTION	f_dihedral_angle_d	12.225	2340
X-RAY DIFFRACTION	f_chiral_restr	0.045	1002
X-RAY DIFFRACTION	f_plane_restr	0.003	1099

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 (%)
2.3363-2.3788	0.286	128	0.2471	2423	X-RAY DIFFRACTION	93
2.3788-2.4245	0.3152	139	0.2533	2651	X-RAY DIFFRACTION	100
2.4245-2.474	0.3443	138	0.2504	2626	X-RAY DIFFRACTION	100
2.474-2.5278	0.328	138	0.2504	2625	X-RAY DIFFRACTION	100
2.5278-2.5866	0.321	137	0.2355	2623	X-RAY DIFFRACTION	100
2.5866-2.6513	0.2748	139	0.2337	2636	X-RAY DIFFRACTION	100
2.6513-2.723	0.2749	138	0.2231	2634	X-RAY DIFFRACTION	100
2.723-2.8031	0.2611	140	0.223	2660	X-RAY DIFFRACTION	100
2.8031-2.8935	0.2674	140	0.2288	2646	X-RAY DIFFRACTION	100
2.8935-2.9969	0.3002	139	0.2197	2659	X-RAY DIFFRACTION	100
2.9969-3.1169	0.2891	140	0.2292	2653	X-RAY DIFFRACTION	100
3.1169-3.2587	0.2877	140	0.2142	2657	X-RAY DIFFRACTION	100
3.2587-3.4305	0.254	141	0.2085	2684	X-RAY DIFFRACTION	100
3.4305-3.6453	0.2526	141	0.1952	2665	X-RAY DIFFRACTION	100
3.6453-3.9266	0.2119	141	0.19	2691	X-RAY DIFFRACTION	100
3.9266-4.3215	0.2063	142	0.1724	2690	X-RAY DIFFRACTION	100
4.3215-4.9462	0.1907	143	0.1655	2716	X-RAY DIFFRACTION	100
4.9462-6.2293	0.2672	144	0.2042	2745	X-RAY DIFFRACTION	100
6.2293-46.1057	0.2704	143	0.2278	2700	X-RAY DIFFRACTION	94

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	0.7201	0.1906	-0.449	0.4956	-0.1755	-0.1282	0.0374	0.1085	0.0288	-0.0363	-0.0467	-0.0938	-0.0966	0.1455	-0	0.1208	-0.0257	-0.0152	0.3366	-0.0582	0.117	-8.9152	26.0967	0.2602
2	0.1623	-0.195	0.3865	0.2384	-0.3086	0.7817	-0.0536	0.0754	-0.0142	0.0992	-0.0075	-0.0279	-0.0233	-0.0854	0	0.237	-0.0265	-0.0214	0.1693	-0.0122	0.2145	-11.9401	19.2582	25.578
3	0.1917	0.4159	-0.2268	0.2418	-0.7505	0.0632	-0.0323	-0.0539	-0.2067	0.0065	0.0466	0.1353	0.0374	-0.0998	0	0.1832	0.0072	-0.0418	0.3559	-0.0781	0.2176	-19.3679	19.1239	2.1403
4	0.0053	0.0113	0.0232	0.0044	0.0023	-0.0389	-0.4796	-0.0396	-0.0285	-0.2827	-0.2469	0.0132	0.0387	0.2338	0	0.8026	0.1435	0.3331	1.0859	0.077	0.6816	45.952	-1.9542	34.2443
5	0.0748	0.002	0.0018	-0.0017	0.0117	-0.015	-0.1454	-0.0084	-0.1341	-0.2703	-0.0087	-0.3448	0.0747	0.1421	0	0.6344	-0.0265	0.0662	0.4786	0.0673	0.6316	42.0667	-5.8252	43.3745
6	0.0402	0.0279	-0.0939	0.0939	0.0373	0.0872	-0.0383	0.3518	0.0025	0.2262	-0.2046	0.2584	0.0447	0.3608	0	0.5607	0.0003	-0.0797	0.8121	0.0469	1.0711	41.2214	-7.3567	48.9356
7	0.2335	-0.3861	-0.0019	0.1091	-0.1099	-0.0949	-0.0849	0.0147	0.1295	0.018	0.0178	-0.066	-0.0507	0.0129	0	0.3171	-0.0174	-0.0651	0.1417	0.0337	0.2837	8.8764	7.9485	40.7884
8	0.1354	0.1136	0.1682	0.0747	0.1249	0.2192	-0.1867	-0.0889	0.1809	0.1236	0.0169	0.0559	0.0124	0.0224	-0	0.2884	-0.0743	-0.1262	0.1963	0.063	0.3139	20.1491	15.205	57.9263
9	0.2141	0.072	0.0054	-0.0806	0.0181	-0.0389	-0.155	0.1133	0.4235	0.078	-0.2093	0.0577	0.2748	0.1923	0	0.2402	-0.0258	-0.1166	0.2211	0.0988	0.2586	5.42	12.6735	32.6971
10	0.1813	-0.1287	-0.1255	0.1643	0.0203	0.3932	-0.0691	0.0863	-0.0483	0.0252	0.0026	-0.0393	0.0328	0.0299	0	0.329	0.0154	-0.0643	0.1823	0.0517	0.321	12.0195	-0.7173	47.2174
11	-0.0442	0.0531	0.0387	0.0168	-0.0578	0.0124	0.4883	0.1753	0.4677	-0.413	1.1235	-0.3723	-0.0226	-0.6357	0	0.2319	0.0201	0.0477	-0.0016	-0.5495	0.8465	37.2016	7.9366	58.8363
12	0.0098	0.0308	0.0734	-0.0287	-0.1057	-0.0472	0.0721	-0.1749	0.1039	0.2156	0.3375	-0.2446	0.4876	0.4001	-0	0.5014	0.0281	-0.0883	0.4766	0.0118	0.5221	31.8678	-3.521	52.8371
13	-0.0277	-0.0242	-0.0509	-0.0327	-0.0488	-0.0321	0.8807	-0.0203	0.0188	-0.0912	0.6914	-0.4025	0.2429	-0.0009	0	0.4802	-0.1166	-0.2532	0.5093	-0.0382	0.8152	48.0047	4.6697	55.5822

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 149 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 150 through 388 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 389 through 437 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 8 through 39 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 40 through 107 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 108 through 161 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 162 through 227 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 228 through 278 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 279 through 302 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 303 through 353 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 354 through 381 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 382 through 416 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 417 through 437 )

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