PDB-4a1h: Human myelin P2 protein, K45S mutant

ID or keywords:

Entry

Database: PDB / ID: 4a1h

Title

Human myelin P2 protein, K45S mutant

Components

MYELIN P2 PROTEIN

Keywords

TRANSPORT / LIPID-BINDING

Function / homology

Function and homology information

membrane organization / cholesterol binding / fatty acid transport / fatty acid binding / myelin sheath / extracellular exosome / nucleus / cytosol
Similarity search - Function

Biological species

HOMO SAPIENS (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.201 Å

Authors

Lehtimaki, M. / Kursula, P.

Citation

Journal: To be Published
Title: Structure-Function Relationships in the Myelin Peripheral Membrane Protein P2
Authors: Lehtimaki, M. / Kursula, P.

History

Deposition	Sep 15, 2011	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Sep 26, 2012	Provider: repository / Type: Initial release
Revision 1.1	Jul 17, 2019	Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2	Apr 8, 2020	Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_sf
Revision 1.3	Dec 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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Download

PDBx/mmCIF format	4a1h.cif.gz	177.4 KB	Display	PDBx/mmCIF format
PDB format	pdb4a1h.ent.gz	143.9 KB	Display	PDB format
PDBx/mmJSON format	4a1h.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4a1h_validation.pdf.gz	1.1 MB	Display	wwPDB validaton report
Full document	4a1h_full_validation.pdf.gz	1.1 MB	Display
Data in XML	4a1h_validation.xml.gz	20 KB	Display
Data in CIF	4a1h_validation.cif.gz	27.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/a1/4a1h ftp://data.pdbj.org/pub/pdb/validation_reports/a1/4a1h	HTTPS FTP

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Related structure data

Related structure data	4a1yC 4a8zC 2wutS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4a1y-4 5n4q-d 1lif-d 6ew5-1 1lie-d 3fr2-d 3fr4-d 2q9s-d 5ur9-1 6ew5-3 Search similar-shape structures by Omokage search (details) 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

Related structure data

4a1yC

4a8zC

2wutS

S: Starting model for refinement

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#193 - Jan 2016 Siderocalin similarity (3) #147 - Mar 2012 Rhodopsin similarity (1) #100 - Apr 2008 Adrenergic Receptors similarity (1) #164 - Aug 2013 Serotonin Receptor similarity (1) #171 - Mar 2014 Neurotransmitter Transporters similarity (1) #27 - Mar 2002 Bacteriorhodopsin similarity (1) #78 - Jun 2006 Luciferase similarity (1)

Deposited unit

A: MYELIN P2 PROTEIN

B: MYELIN P2 PROTEIN

C: MYELIN P2 PROTEIN

hetero molecules

45.8 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: MYELIN P2 PROTEIN

hetero molecules

defined by author&software
15.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: MYELIN P2 PROTEIN

hetero molecules

defined by author&software
15.2 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: MYELIN P2 PROTEIN

hetero molecules

defined by author&software
15.2 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	120.130, 63.610, 84.470
Angle α, β, γ (deg.)	90.00, 130.10, 90.00
Int Tables number	5
Space group name H-M	C121

#1: Protein	MYELIN P2 PROTEIN / PERIPHERAL MYELIN PROTEIN 2 Mass: 14949.368 Da / Num. of mol.: 3 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PTH27 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA / References: UniProt: P02689
#2: Chemical	ChemComp-PLM / PALMITIC ACID Mass: 256.424 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₁₆H₃₂O₂
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 205 / Source method: isolated from a natural source / Formula: H₂O
Compound details	ENGINEERED RESIDUE IN CHAIN A, LYS 46 TO SER ENGINEERED RESIDUE IN CHAIN B, LYS 46 TO SER ...ENGINEERED RESIDUE IN CHAIN A, LYS 46 TO SER ENGINEERED RESIDUE IN CHAIN B, LYS 46 TO SER ENGINEERED RESIDUE IN CHAIN C, LYS 46 TO SER

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.75 Å³/Da / Density % sol: 55.31 % / Description: NONE
Crystal grow	pH: 4.5 / Details: pH 4.5

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 1.0332
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 1, 2010
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.0332 Å / Relative weight: 1
Reflection	Resolution: 2.2→20 Å / Num. obs: 22007 / % possible obs: 88 % / Observed criterion σ(I): -3 / Redundancy: 3.4 % / B_iso Wilson estimate: 33.29 Å² / R_merge(I) obs: 0.08 / Net I/σ(I): 11
Reflection shell	Resolution: 2.2→2.26 Å / Redundancy: 2.8 % / R_merge(I) obs: 0.62 / Mean I/σ(I) obs: 1.6 / % possible all: 49.2

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Processing

Software

Name	Version	Classification
PHENIX	(PHENIX.REFINE)	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WUT

2wut

Resolution: 2.201→19.945 Å / SU ML: 0.63 / σ(F): 1.99 / Phase error: 31.07 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2518	1101	5 %
R_work	0.1943	-	-
obs	0.1973	22001	88.63 %

Solvent computation

Shrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 44.099 Å² / k_sol: 0.343 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-9.5794 Å²	0 Å²	-3.4755 Å²
2-	-	15.4309 Å²	0 Å²
3-	-	-	-5.8515 Å²

Refinement step

Cycle: LAST / Resolution: 2.201→19.945 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3135	0	63	205	3403

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	3224
X-RAY DIFFRACTION	f_angle_d	0.766	4295
X-RAY DIFFRACTION	f_dihedral_angle_d	15.52	1265
X-RAY DIFFRACTION	f_chiral_restr	0.048	495
X-RAY DIFFRACTION	f_plane_restr	0.002	528

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 (%)
2.2014-2.3015	0.3522	81	0.2971	1537	X-RAY DIFFRACTION	53
2.3015-2.4226	0.3374	111	0.273	2097	X-RAY DIFFRACTION	71
2.4226-2.5741	0.3198	144	0.2441	2744	X-RAY DIFFRACTION	94
2.5741-2.7724	0.3071	151	0.2433	2877	X-RAY DIFFRACTION	98
2.7724-3.0505	0.3441	152	0.2353	2885	X-RAY DIFFRACTION	98
3.0505-3.4899	0.2579	152	0.2044	2892	X-RAY DIFFRACTION	98
3.4899-4.3892	0.2145	154	0.1607	2908	X-RAY DIFFRACTION	98
4.3892-19.9463	0.1955	156	0.153	2960	X-RAY DIFFRACTION	98

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	8.4102	-3.2227	6.7816	9.8794	-1.4056	8.3483	0.4921	0.0537	-1.2291	-0.3055	0.3128	0.3696	0.235	0.9508	-0.7167	0.4276	-0.0042	-0.0472	0.4307	-0.0697	0.3091	-19.5383	11.2692	27.5169
2	5.499	3.2259	-3.6332	6.9079	-3.8343	5.4657	0.2864	-0.4914	0.3672	0.3484	-0.8465	-0.0326	-0.5304	-0.2735	0.4908	0.2119	-0.0094	-0.0965	0.3794	-0.1181	0.3728	-21.9539	27.2489	25.0367
3	7.2762	-1.2274	-1.5366	4.6112	2.5343	6.9104	-0.1891	0.8168	0.9283	-0.1396	0.4661	-0.11	-0.7304	-0.363	-0.1888	0.2981	-0.1065	-0.0393	0.4965	0.1412	0.2492	-9.3618	34.4618	17.0247
4	3.9375	-1.1567	-0.3431	5.7692	-1.2024	2.9323	0.1143	0.5899	0.5454	0.0906	-0.5473	-0.0771	-0.362	0.3634	0.2962	0.2961	-0.106	-0.1639	0.4797	0.0557	0.2841	-19.2759	29.1506	15.3407
5	4.4993	-2.3231	0.0894	4.1832	0.7006	2.2502	0.2056	0.2985	-0.0701	-0.2164	-0.3104	0.4798	0.2682	0.332	0.0343	0.2569	0.0719	-0.0788	0.2896	-0.1642	0.2985	-20.4068	17.846	13.6692
6	3.2791	-1.7266	0.4784	4.5663	-2.6081	2.6795	0.1774	0.5716	0.0238	-0.205	-0.4003	-0.1566	0.1094	0.9231	0.1701	0.1456	0.064	-0.0521	0.578	-0.0355	0.1609	-9.2816	16.7617	14.134
7	5.165	1.5608	-1.7524	8.2255	0.2269	1.2788	0.1551	0.3778	-0.0083	-1.0366	-0.2733	-0.5891	0.441	0.8026	0.2476	0.2351	0.0768	0.0296	0.5856	0.0334	0.2279	-5.4493	20.3759	14.3909
8	0.5838	0.4686	-1.9505	3.2341	-2.6461	7.9599	0.0959	-0.3171	0.0311	-0.0883	-0.2841	-0.287	0.0868	1.3508	0.3091	0.249	-0.0783	-0.0241	0.5608	-0.011	0.1716	-9.0823	22.018	22.312
9	2.3774	1.912	-2.306	3.4587	-3.3635	3.8347	0.2762	-0.654	-0.614	0.1446	-0.8342	-0.4947	-0.4452	1.0795	0.5003	0.2213	-0.0055	-0.0394	0.5701	0.0219	0.2186	-13.0808	24.8506	26.7123
10	3.0809	0.0699	0.9954	3.0928	-0.055	2.7189	-0.2716	0.0104	-0.0903	-0.1548	-0.1743	-0.0326	-0.0913	0.2225	0.2748	0.1433	-0.0364	0.0021	0.4954	-0.0478	0.3157	-15.5924	27.8148	24.6659
11	0.0988	-0.581	-0.2133	3.4159	1.2544	0.4607	0.0185	0.1394	0.1397	0.3126	-0.4701	-1.1564	-0.3718	1.8894	0.5256	0.3783	-0.1269	-0.0875	0.9425	0.2464	0.3975	8.0159	27.6855	53.5927
12	3.6225	-0.4063	-0.5731	1.5892	-0.4039	0.7337	0.2568	-0.585	-0.1772	0.4619	-0.4244	-0.1677	0.0766	0.0126	-0.0762	0.3247	-0.2767	-0.0471	0.6369	0.0971	0.2408	-7.6664	26.4633	50.8929
13	6.8843	2.1158	0.4001	4.1574	-5.0627	7.6909	-0.0355	-0.7086	0.3007	0.745	-0.0478	0.3736	-0.8601	-0.9355	0.1262	0.3139	0.0101	-0.0335	0.7056	-0.2529	0.4555	-14.6207	38.7261	42.756
14	4.5093	-0.767	1.3309	2.3414	0.1157	2.1657	0.216	-0.1329	-0.4224	0.03	-0.4709	0.232	-0.0133	-0.1374	0.1596	0.2093	-0.0498	-0.0341	0.5799	-0.0049	0.2156	-9.716	29.3857	40.7839
15	7.6808	-0.8688	1.7417	1.9818	0.9734	2.6687	0.2044	0.0647	-0.715	-0.0894	-0.1695	-0.5954	0.0357	0.0903	-0.1054	0.2515	-0.0984	-0.1141	0.4799	0.1509	0.4509	5.5507	26.2894	41.8124
16	9.4473	7.7009	0.7902	8.7014	1.2311	4.0541	-0.5	0.3405	-0.078	-0.4981	0.281	0.0238	0.4459	0.0754	0.2175	0.2908	-0.0874	0.0372	0.4746	-0.0479	0.2066	-2.3584	26.7726	37.2819
17	6.2503	1.2401	3.2358	4.1456	0.4299	4.131	0.0593	0.4048	-0.1574	-0.0638	-0.1975	0.2211	0.107	0.1409	0.1791	0.2377	-0.1204	-0.0024	0.276	-0.039	0.1901	3.3766	36.1829	36.1651
18	5.8563	-1.1385	5.9641	2.4401	-2.213	8.9084	0.1836	-0.5426	0.0263	0.3852	-0.3577	-0.1318	-0.418	0.2542	0.2193	0.2423	-0.2066	-0.0028	0.4872	-0.0018	0.2404	3.5326	40.0473	43.431
19	2.2117	0.0909	1.5894	6.324	-4.6989	8.0714	0.056	-0.4914	0.2135	0.2209	-0.2649	0.3127	-0.3739	-0.1704	0.1318	0.2506	-0.1525	-0.016	0.698	-0.1212	0.3461	-1.882	39.978	45.8074
20	3.1377	1.4453	0.0619	2.5629	0.2008	2.2896	0.2708	-0.7996	-0.0137	0.7316	-0.6268	0.1536	-0.2378	-0.0203	-0.11	0.3139	-0.303	0.0434	0.7442	-0.0781	0.2843	-6.6669	33.9109	51.1392
21	4.9489	-2.2275	0.0984	4.7372	0.2103	5.3518	-0.6796	-1.5107	0.086	0.1687	0.4268	-0.1264	-0.0864	-0.5047	0.3026	0.3037	-0.0173	-0.1399	0.421	0.1129	0.3574	-24.197	9.9884	67.5142
22	2.3423	-1.2145	-0.5372	3.5339	-0.5801	1.0857	-0.3631	-0.1871	-0.0572	-0.1978	-0.228	-1.0825	0.5067	0.7719	0.4178	0.3441	0.2458	0.1276	0.8346	0.1981	0.4433	-6.8972	6.027	55.0557
23	1.6348	-1.532	-1.2839	3.4644	-1.2828	4.0536	0.1021	-0.0982	0.4824	0.1238	-0.0496	-0.1551	-0.0507	0.0195	-0.0916	0.259	-0.1001	-0.0451	0.2533	0.1668	0.2849	-25.4486	11.9874	59.017
24	2.5573	0.1592	-0.272	4.6673	1.4983	5.7237	0.2804	0.4058	0.1573	0.3719	-0.096	-0.8828	-0.1318	0.7641	0.0381	0.3253	-0.0812	-0.1315	0.4053	0.1924	0.3617	-21.9927	12.9621	53.2266
25	7.2241	1.0944	-2.817	4.3997	-3.728	6.9991	0.1232	0.4148	-0.5641	-0.9575	-0.0746	0.0313	1.8569	-0.0851	0.2178	0.7772	-0.0308	-0.1512	0.3066	0.0595	0.3247	-25.4873	0.251	52.0433
26	5.2497	-0.318	-0.8584	3.9413	2.8193	7.1327	0.205	0.0277	-0.4764	-0.5958	-0.1473	-0.1816	1.1832	0.268	0.0117	0.6541	0.1229	-0.1	0.2383	0.0263	0.3081	-20.452	-0.67	61.6471
27	6.296	-4.0556	-0.9501	3.8738	1.4086	7.2825	-0.2197	-0.2541	0.1945	0.3157	-0.0528	-0.8059	0.5481	0.8016	0.1938	0.2488	-0.0027	-0.0824	0.3598	0.1745	0.3795	-15.7629	6.5167	65.8585

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN A AND (RESSEQ -1:5)
2	X-RAY DIFFRACTION	2	CHAIN A AND (RESSEQ 6:14)
3	X-RAY DIFFRACTION	3	CHAIN A AND (RESSEQ 15:23)
4	X-RAY DIFFRACTION	4	CHAIN A AND (RESSEQ 24:45)
5	X-RAY DIFFRACTION	5	CHAIN A AND (RESSEQ 46:65)
6	X-RAY DIFFRACTION	6	CHAIN A AND (RESSEQ 66:90)
7	X-RAY DIFFRACTION	7	CHAIN A AND (RESSEQ 91:99)
8	X-RAY DIFFRACTION	8	CHAIN A AND (RESSEQ 100:109)
9	X-RAY DIFFRACTION	9	CHAIN A AND (RESSEQ 110:119)
10	X-RAY DIFFRACTION	10	CHAIN A AND (RESSEQ 120:131)
11	X-RAY DIFFRACTION	11	CHAIN B AND (RESSEQ -1:5)
12	X-RAY DIFFRACTION	12	CHAIN B AND (RESSEQ 6:14)
13	X-RAY DIFFRACTION	13	CHAIN B AND (RESSEQ 15:22)
14	X-RAY DIFFRACTION	14	CHAIN B AND (RESSEQ 23:45)
15	X-RAY DIFFRACTION	15	CHAIN B AND (RESSEQ 46:54)
16	X-RAY DIFFRACTION	16	CHAIN B AND (RESSEQ 55:64)
17	X-RAY DIFFRACTION	17	CHAIN B AND (RESSEQ 65:78)
18	X-RAY DIFFRACTION	18	CHAIN B AND (RESSEQ 79:97)
19	X-RAY DIFFRACTION	19	CHAIN B AND (RESSEQ 98:109)
20	X-RAY DIFFRACTION	20	CHAIN B AND (RESSEQ 110:131)
21	X-RAY DIFFRACTION	21	CHAIN C AND (RESSEQ -1:14)
22	X-RAY DIFFRACTION	22	CHAIN C AND (RESSEQ 15:33)
23	X-RAY DIFFRACTION	23	CHAIN C AND (RESSEQ 34:54)
24	X-RAY DIFFRACTION	24	CHAIN C AND (RESSEQ 55:64)
25	X-RAY DIFFRACTION	25	CHAIN C AND (RESSEQ 65:87)
26	X-RAY DIFFRACTION	26	CHAIN C AND (RESSEQ 88:119)
27	X-RAY DIFFRACTION	27	CHAIN C AND (RESSEQ 120:131)

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-Yorodumi

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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

-
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