PDB-4wcb: Catalytic domain of mouse 2',3'-cyclic nucleotide 3'- phosphodies...

ID or keywords:

Entry

Database: PDB / ID: 4wcb

Title

Catalytic domain of mouse 2',3'-cyclic nucleotide 3'- phosphodiesterase, with mutation H309Q

Components

2',3'-cyclic-nucleotide 3'-phosphodiesterase

Keywords

HYDROLASE / myelin / nervous system

Function / homology

Function and homology information

cyclic nucleotide catabolic process / 2',3'-cyclic-nucleotide 3'-phosphodiesterase / 2',3'-cyclic-nucleotide 3'-phosphodiesterase activity / oligodendrocyte differentiation / axonogenesis / adult locomotory behavior / response to toxic substance / melanosome / myelin sheath / extracellular space ...
Similarity search - Function

Biological species

Mus musculus (house mouse)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.57 Å

Authors

Myllykoski, M. / Raasakka, A. / Kursula, P.

Citation

Journal: Sci Rep / Year: 2015
Title: Determinants of ligand binding and catalytic activity in the myelin enzyme 2',3'-cyclic nucleotide 3'-phosphodiesterase.
Authors: Raasakka, A. / Myllykoski, M. / Laulumaa, S. / Lehtimaki, M. / Hartlein, M. / Moulin, M. / Kursula, I. / Kursula, P.

History

Deposition	Sep 4, 2014	Deposition site: RCSB / Processing site: PDBE
Revision 1.0	Sep 23, 2015	Provider: repository / Type: Initial release
Revision 1.1	Jan 17, 2018	Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2	Jan 10, 2024	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4wcb.cif.gz	143 KB	Display	PDBx/mmCIF format
PDB format	pdb4wcb.ent.gz	112.5 KB	Display	PDB format
PDBx/mmJSON format	4wcb.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	4wcb_validation.pdf.gz	419.7 KB	Display	wwPDB validaton report
Full document	4wcb_full_validation.pdf.gz	420.1 KB	Display
Data in XML	4wcb_validation.xml.gz	13 KB	Display
Data in CIF	4wcb_validation.cif.gz	19.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/wc/4wcb ftp://data.pdbj.org/pub/pdb/validation_reports/wc/4wcb	HTTPS FTP

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Related structure data

Related structure data	4wbiC 4wblC 4wc9C 4wcaC 4wccC 4wdaC 4wdbC 4wddC 4wdeC 4wdfC 4wdgC 4wdhC 4wexC 4wfrC 5ae0C 2xmiS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	3zbr-2 4wcc-d 2ypc-d 4wdd-d 2ydb-d 3zbr-1 3a0d-1 4wdf-d 4wfr-d 4wdg-d 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

Deposited unit

A: 2',3'-cyclic-nucleotide 3'-phosphodiesterase

hetero molecules

24.3 kDa, 1 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)	38.810, 48.270, 108.060
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Details

biological unit is the same as asym.

#1: Protein	2',3'-cyclic-nucleotide 3'-phosphodiesterase / CNPase Mass: 24283.910 Da / Num. of mol.: 1 / Fragment: catalytic domain, UNP residues 179-398 / Mutation: H309Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cnp, Cnp1 / Plasmid: pTH27 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta References: UniProt: P16330, 2',3'-cyclic-nucleotide 3'-phosphodiesterase
#2: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 304 / 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: 2.08 Å³/Da / Density % sol: 40.96 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / Details: Na-acetate, PEG 4000/6000

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

MAX II

/ Beamline: I911-2 / Wavelength: 1.04088 Å

Detector

Type: MAR CCD 165 mm / Detector: CCD / Date: Feb 2, 2012

Radiation

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

Radiation wavelength

Wavelength: 1.04088 Å / Relative weight: 1

Reflection

Resolution: 1.57→30 Å / Num. obs: 29179 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 6.9 % / B_iso Wilson estimate: 15.79 Å² / R_merge F obs: 0.112 / R_merge(I) obs: 0.07 / R_rim(I) all: 0.076 / Χ²: 0.983 / Net I/σ(I): 18.18 / Num. measured all: 200891

Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)	Highest resolution (Å)	R_merge F obs	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. possible	Num. unique obs	R_rim(I) all	% possible all
1.57-1.61		0.79	0.938	2.14	12993	2159	2147	1.032	99.4
1.61-1.65		0.639	0.763	2.61	13522	2035	2035	0.829	100
1.65-1.7		0.506	0.565	3.45	13515	2015	2014	0.613	100
1.7-1.76		0.4	0.473	4.19	13398	1956	1954	0.512	99.9
1.76-1.81		0.324	0.374	5.25	13234	1890	1889	0.404	99.9
1.81-1.88		0.271	0.306	6.48	13144	1867	1867	0.33	100
1.88-1.95		0.189	0.234	8.3	12582	1775	1775	0.252	100
1.95-2.03		0.126	0.164	11.82	12210	1708	1708	0.176	100
2.03-2.12		0.093	0.126	14.98	11716	1648	1647	0.136	99.9
2.12-2.22		0.072	0.099	18.99	11132	1567	1567	0.106	100
2.22-2.34		0.067	0.088	21.87	10706	1509	1508	0.095	99.9
2.34-2.48		0.056	0.074	24.94	10213	1433	1433	0.08	100
2.48-2.65		0.045	0.065	27.73	9631	1350	1350	0.07	100
2.65-2.87		0.039	0.053	31.93	8827	1258	1258	0.058	100
2.87-3.14		0.031	0.044	37.2	8116	1165	1165	0.048	100
3.14-3.51		0.021	0.036	46.61	7297	1078	1075	0.039	99.7
3.51-4.05		0.017	0.03	53.31	6473	945	942	0.032	99.7
4.05-4.96		0.013	0.023	59.11	5588	819	817	0.025	99.8
4.96-7.02		0.016	0.024	54.45	4412	653	653	0.026	100
	7.02	0.015	0.02	53.61	2182	401	375	0.022	93.5

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
XDS	December 31, 2011	data reduction
Coot		model building
PHENIX	(phenix.refine: 1.9_1692)	refinement
PDB_EXTRACT	3.15	data extraction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2xmi

2xmi

Resolution: 1.57→28.868 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 20.56 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.204	1456	5 %
R_work	0.1588	27662	-
obs	0.1611	29118	99.84 %

Solvent computation

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

Displacement parameters

B_iso max: 105.63 Å² / B_iso mean: 24.9192 Å² / B_iso min: 8.05 Å²

Refinement step

Cycle: final / Resolution: 1.57→28.868 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1662	0	1	304	1967
B_iso mean	-	-	19.68	32.88	-
Num. residues	-	-	-	-	214

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	1741
X-RAY DIFFRACTION	f_angle_d	1.083	2349
X-RAY DIFFRACTION	f_chiral_restr	0.042	252
X-RAY DIFFRACTION	f_plane_restr	0.006	302
X-RAY DIFFRACTION	f_dihedral_angle_d	13.812	657

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.5701-1.6263	0.2904	143	0.2559	2738	2881	99
1.6263-1.6914	0.25	143	0.2178	2712	2855	100
1.6914-1.7683	0.2625	144	0.1934	2732	2876	100
1.7683-1.8615	0.232	143	0.1862	2728	2871	100
1.8615-1.9782	0.2057	142	0.1684	2712	2854	100
1.9782-2.1308	0.2103	145	0.1496	2750	2895	100
2.1308-2.3452	0.1916	145	0.1446	2768	2913	100
2.3452-2.6843	0.2063	147	0.1515	2786	2933	100
2.6843-3.3811	0.1902	148	0.1457	2805	2953	100
3.3811-28.8732	0.1836	156	0.1463	2931	3087	99

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	0.0136	-0.013	-0.0193	0.0592	0.0008	0.0308	-0.144	0.1155	0.106	-0.0305	0.0475	0.0859	-0.0532	-0.0335	-0.0009	0.071	-0.0133	-0.0264	0.1336	-0.0001	0.1243	-10.121	14.7807	-28.9649
2	0.0272	-0.0057	-0.0154	0.0087	0.0104	0.0113	-0.0138	0.0654	0.1073	0.0247	-0.0449	-0.081	0.0181	0.1085	-0.0023	0.1236	0.0073	-0.0572	0.1485	0.0187	0.1802	9.7671	9.147	-14.1015
3	0.298	0.0482	0.0838	0.125	-0.1064	0.2501	-0.014	-0.0102	-0.211	0.07	-0.0104	-0.0246	0.1699	0.1818	-0.0358	0.2477	0.0542	-0.1	0.1279	0.0577	0.2113	9.9724	-9.3475	-7.7663
4	0.031	0.0161	-0.0015	0.0538	-0.0654	0.0421	-0.0708	0.0137	0.002	0.0167	0.0305	0.0402	0.0765	0.0428	-0.0097	0.0943	0.0149	0.0004	0.1095	-0.0109	0.1164	-3.6767	5.6424	-24.5698
5	0.0147	-0.01	0.0142	0.0075	-0.0207	0.0499	-0.0033	0.0359	0.0036	-0.0652	0.037	0.1672	-0.1386	-0.0914	0.0165	0.0936	0.0212	-0.0113	0.1062	0.0041	0.1369	-18.0271	20.3257	-25.3855
6	0.0897	0.0278	-0.0449	0.0094	-0.0182	0.0422	-0.049	-0.0474	0.0025	0.0635	0.002	0.0143	-0.0602	0.0185	-0.0067	0.1482	0.0092	-0.0177	0.1187	-0.0106	0.0962	-2.0913	8.9981	-12.4311
7	0.0655	-0.0075	0.0039	0.0192	-0.0104	0.037	0.0771	-0.0367	-0.1243	0.2331	0.0796	0.062	-0.0236	-0.0994	0.0516	0.1144	0.0183	0.0139	0.1426	-0.0121	0.132	-15.4516	13.4515	-15.1853
8	0.0324	0.0104	0.0009	0.1027	-0.0546	0.0714	0.0719	0.0788	-0.0625	0.0233	-0.0311	0.0901	0.0185	-0.0858	0.0227	0.1026	0.0004	-0.0001	0.1298	-0.0082	0.1098	-8.2607	3.2722	-15.0864
9	-0.0001	-0.0003	0.0017	0.0237	-0.004	0.0042	-0.0359	-0.0453	-0.0847	0.0235	0.0204	0.0895	0.0096	-0.014	-0	0.114	0.0029	0.016	0.1386	0.0036	0.1165	-8.5284	0.534	-10.1707
10	0.062	0.0048	0.0472	0.0266	-0.0166	0.0387	-0.0296	-0.0964	0.0396	0.1157	-0.027	0.0116	-0.0617	-0.1043	-0.0704	0.3928	-0.0501	-0.1407	0.1797	0.0293	-0.014	2.753	2.6818	0.9827
11	0.1289	-0.0112	-0.0222	0.0259	-0.0289	0.0252	-0.0508	-0.0056	0.0505	0.0812	0.031	-0.1157	-0.0228	-0.0381	0.0181	0.1474	-0.0017	-0.0294	0.1021	-0.0103	0.1003	-1.5687	11.5658	-13.7662

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 162 through 174 )	A
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 175 through 194 )	A
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 195 through 216 )	A
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 217 through 243 )	A
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 244 through 259 )	A
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 260 through 279 )	A
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 280 through 296 )	A
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 297 through 319 )	A
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 320 through 335 )	A
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 336 through 355 )	A
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 356 through 378 )	A

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