PDB-3trt: Crystal structure of stabilised vimentin coil2 fragment

ID or keywords:

Entry

Database: PDB / ID: 3trt

Title

Crystal structure of stabilised vimentin coil2 fragment

Components

Vimentin

Keywords

STRUCTURAL PROTEIN / cytoskeleton / intermediate filament / vimentin / alpha-helix

Function / homology

Function and homology information

keratin filament binding / lens fiber cell development / intermediate filament organization / cellular response to muramyl dipeptide / structural constituent of eye lens / astrocyte development / Striated Muscle Contraction / microtubule organizing center / RHOBTB1 GTPase cycle / intermediate filament cytoskeleton ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 2.3 Å

Authors

Chernyatina, A.A. / Strelkov, S.V.

Citation

Journal: J.Struct.Biol. / Year: 2012
Title: Stabilization of vimentin coil2 fragment via an engineered disulfide.
Authors: Chernyatina, A.A. / Strelkov, S.V.

History

Deposition	Sep 10, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 1, 2012	Provider: repository / Type: Initial release
Revision 1.1	Nov 8, 2017	Group: Refinement description / Category: software
Revision 1.2	Jun 6, 2018	Group: Data collection / Refinement description / Category: software / Item: _software.classification

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3trt.cif.gz	71.9 KB	Display	PDBx/mmCIF format
PDB format	pdb3trt.ent.gz	58.5 KB	Display	PDB format
PDBx/mmJSON format	3trt.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3trt_validation.pdf.gz	457.7 KB	Display	wwPDB validaton report
Full document	3trt_full_validation.pdf.gz	458.2 KB	Display
Data in XML	3trt_validation.xml.gz	8.2 KB	Display
Data in CIF	3trt_validation.cif.gz	10.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/tr/3trt ftp://data.pdbj.org/pub/pdb/validation_reports/tr/3trt	HTTPS FTP

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Related structure data

Related structure data	3klt
Similar structure data	5fiy-2 2vj2-1 5fiy-1 4h22-2 5fiy-4 6dm9-1 3tyy-d 2bez-d 6wsm-1 6dm9-2 1nkn-1 4nkj-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
Related items in Molecule of the Month	#185 - May 2015 Titin similarity (1) #152 - Aug 2012 cAMP-dependent Protein Kinase similarity (1) #56 - Aug 2004 Caspases similarity (1) #135 - Mar 2011 Integrase similarity (1) #19 - Jul 2001 Actin similarity (1)

Deposited unit

A: Vimentin

B: Vimentin

hetero molecules

18.3 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)	53.419, 75.521, 86.859
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	23
Space group name H-M	I222

Components on special symmetry positions

ID	Model	Components
1	1	A-4- SO4
2	1	A-8- NH4

#1: Protein	Vimentin Mass: 8818.362 Da / Num. of mol.: 2 Fragment: first half of vimentin coil2, UNP residues 261-335 Mutation: L265C, L269(MSE), C328(MSE) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: VIM / Plasmid: pPEP-TEV / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P08670
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO₄
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Chemical	ChemComp-NH4 / AMMONIUM ION Mass: 18.038 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H₄N
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 29 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 3

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Sample preparation

Crystal	Density Matthews: 2.48 Å³/Da / Density % sol: 50.47 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 2M ammonium sulphate, 0.1M Tris pH8.5 + protein in 10 mM Tris pH 8, 38 mM NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction

ID	Mean temperature (K)	Crystal-ID
1	100	1
2	100	1
3	100	1

Diffraction source

Source	Site	Beamline	ID	Wavelength (Å)
SYNCHROTRON	SLS	X06DA	1	0.9793
SYNCHROTRON	SLS	X06DA	2	0.9796
SYNCHROTRON	SLS	X06DA	3	0.9793

Detector

Type	ID	Detector	Date
MARMOSAIC 225 mm CCD	1	CCD	Mar 27, 2010
MARMOSAIC 225 mm CCD	2	CCD	Mar 27, 2010
MARMOSAIC 225 mm CCD	3	CCD	Apr 25, 2010

Radiation

ID	Protocol	Monochromatic (M) / Laue (L)	Scattering type	Wavelength-ID
1	SINGLE WAVELENGTH	M	x-ray	1
2	SINGLE WAVELENGTH	M	x-ray	1
3	SINGLE WAVELENGTH	M	x-ray	1

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.9793	1
2	0.9796	1

Reflection

Redundancy: 5.3 % / Av σ(I) over netI: 18.92 / Number: 35451 / R_merge(I) obs: 0.099 / Χ²: 1.78 / D res high: 3 Å / D res low: 28 Å / Num. obs: 6742 / % possible obs: 99.4

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	% possible obs (%)	ID	R_merge(I) obs	Chi squared	Redundancy
8.08	28	100	1	0.031	1.583	5.3
6.44	8.08	100	1	0.053	1.426	5.4
5.63	6.44	100	1	0.083	1.449	5.5
5.12	5.63	100	1	0.085	1.345	5.5
4.76	5.12	100	1	0.067	1.724	5.5
4.48	4.76	100	1	0.07	1.765	5.4
4.25	4.48	100	1	0.082	1.88	5.4
4.07	4.25	100	1	0.076	1.956	5.5
3.91	4.07	100	1	0.092	2.11	5.1
3.78	3.91	99.7	1	0.117	2.555	5.1
3.66	3.78	99.4	1	0.122	3.068	4.8
3.56	3.66	99.4	1	0.199	1.982	5.1
3.46	3.56	100	1	0.152	2.383	5.4
3.38	3.46	99.7	1	0.189	2.452	5.1
3.3	3.38	100	1	0.165	1.499	5.5
3.23	3.3	100	1	0.176	1.421	5.4
3.17	3.23	100	1	0.205	1.388	5.3
3.11	3.17	98.9	1	0.22	1.323	5.1
3.05	3.11	96.4	1	0.192	1.204	5
3	3.05	94.3	1	0.18	1.173	4.9

Reflection

Resolution: 2.3→28 Å / Num. all: 14768 / Num. obs: 14768 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / B_iso Wilson estimate: 37.6 Å² / R_sym value: 0.088 / Χ²: 1.718 / Net I/σ(I): 10.7

Reflection shell

Diffraction-ID: 1,2,3

Resolution (Å)	Redundancy (%)	Mean I/σ(I) obs	Num. unique all	R_sym value	Χ²	% possible all
2.3-2.34	2.5	2	695	0.352	1.07	87.1
2.34-2.39	2.7		718	0.37	1.138	92.3
2.39-2.44	2.9		741	0.341	1.201	91.4
2.44-2.49	3		727	0.297	1.088	95.2
2.49-2.55	3.1		795	0.266	1.18	96.7
2.55-2.61	3.2		760	0.248	1.24	98.2
2.61-2.68	3.3		796	0.228	1.241	99
2.68-2.76	3.5		820	0.21	1.147	99.5
2.76-2.85	3.6		753	0.193	1.285	99.9
2.85-2.95	3.7		780	0.157	1.361	100
2.95-3.07	3.7		814	0.121	1.377	100
3.07-3.21	3.7		812	0.107	1.524	100
3.21-3.38	3.7		785	0.088	1.809	100
3.38-3.59	3.7		792	0.075	1.986	100
3.59-3.86	3.6		786	0.065	2.287	100
3.86-4.25	3.6		815	0.058	2.742	99.9
4.25-4.86	3.6		795	0.059	2.95	99.9
4.86-6.12	3.7		782	0.051	2.278	100
6.12-28	3.6		802	0.044	2.529	99.4

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Phasing

Phasing	Method: MAD

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
SHELX		phasing
SHELX		model building
PHENIX	dev_780	refinement
PDB_EXTRACT	3.1	data extraction
go.com		data collection
SHELXCD		phasing
SHELXE		model building

Refinement

Method to determine structure:

MAD / Resolution: 2.3→27.034 Å / Occupancy max: 1 / Occupancy min: 0.19 / SU ML: 0.98 / σ(F): 1.06 / Phase error: 31.05 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2984	1870	12.67 %	random
R_work	0.2246	-	-	-
all	0.2336	14755	-	-
obs	0.2336	14755	97.3 %	-

Solvent computation

Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 43.28 Å² / k_sol: 0.382 e/Å³

Displacement parameters

B_iso max: 179.52 Å² / B_iso mean: 40.835 Å² / B_iso min: 18.86 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	16.9221 Å²	0 Å²	-0 Å²
2-	-	-0.5955 Å²	-0 Å²
3-	-	-	-16.3266 Å²

Refinement step

Cycle: LAST / Resolution: 2.3→27.034 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1192	0	39	29	1260

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	1236
X-RAY DIFFRACTION	f_angle_d	1.034	1654
X-RAY DIFFRACTION	f_chiral_restr	0.063	171
X-RAY DIFFRACTION	f_plane_restr	0.003	218
X-RAY DIFFRACTION	f_dihedral_angle_d	15.718	477

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2.3-2.3592	0.4059	109	0.2846	870	979	83
2.3592-2.4286	0.3825	172	0.2754	921	1093	92
2.4286-2.507	0.304	144	0.2722	947	1091	95
2.507-2.5965	0.3036	156	0.2677	985	1141	97
2.5965-2.7004	0.2945	150	0.2671	987	1137	99
2.7004-2.8231	0.3856	126	0.2605	1051	1177	100
2.8231-2.9718	0.3535	147	0.2407	1016	1163	100
2.9718-3.1577	0.2944	168	0.2557	1001	1169	100
3.1577-3.4011	0.3538	141	0.228	1012	1153	100
3.4011-3.7426	0.2456	140	0.1954	1041	1181	100
3.7426-4.2823	0.2259	134	0.1502	1023	1157	100
4.2823-5.3882	0.2375	151	0.1891	1008	1159	100
5.3882-27.0362	0.3317	132	0.2551	1023	1155	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	1.1969	-0.5259	-1.9699	0.8933	0.1492	6.0828	-0.1072	0.0446	-0.2382	-0.1664	0.2765	-0.1282	0.7649	0.0408	0.0232	0.4828	-0.0806	-0.0168	0.36	0.0083	0.384	6.4686	4.3409	93.3498
2	1.9195	1.3807	0.5361	0.9127	0.3644	1.8201	0.0663	0.14	0.0238	0.0479	-0.0107	0.3209	0.1558	-0.5418	-0.0349	0.2842	0.0661	-0.0067	0.2906	-0.0092	0.2996	6.1567	10.5237	63.2438
3	0.3608	0.5436	0.383	0.2895	-0.0487	0.5208	0.0215	-0.2878	0.3277	0.0333	0.0921	0.0578	0.1053	-0.1727	0.044	0.357	0.0088	0.0305	0.4269	-0.0003	0.3378	4.5677	12.5322	29.2723
4	7.7796	-0.3707	-5.0746	1.3779	0.4128	4.6487	-0.6896	0.4337	-0.4447	-0.4742	-0.1541	0.241	0.6025	0.2146	-2.6928	0.3065	-0.0242	-0.0578	0.2916	-0.0381	0.3331	7.3544	16.7449	4.3998
5	5.0613	3.3865	-3.4874	3.126	-1.3396	7.2176	-0.6308	0.6116	-0.1212	0.269	-0.0122	0.366	-0.9531	-1.634	-0.7992	0.5641	0.0482	0.0376	0.3359	-0.0043	0.3609	12.7075	8.488	100.095
6	0.0737	-0.4966	-0.181	0.8529	0.826	0.4652	0.0276	-0.0445	0.0272	0.127	-0.0034	-0.2995	-0.16	0.4672	-0.0013	0.4235	-0.0588	-0.0297	0.358	0.0215	0.3548	15.3934	4.754	78.9062
7	-0.3749	-0.8501	0.4939	0.1605	-1.1891	0.8591	-0.0238	0.1019	0.0357	-0.16	-0.1115	-0.0615	0.3679	0.2604	-0	0.404	-0.0473	-0.0309	0.3466	0.0305	0.3553	13.0574	10.1972	40.9723
8	5.6429	1.1427	5.701	0.4553	1.2198	8.4232	-0.5354	0.1594	0.2415	-0.045	0.0576	0.3733	-1.5632	0.51	-1.0072	0.3401	-0.0401	0.0094	0.3386	-0.005	0.3794	8.2733	24.8448	11.0696

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	(chain A and resid 261:278)	A	261 - 278
2	X-RAY DIFFRACTION	2	(chain A and resid 279:300)	A	279 - 300
3	X-RAY DIFFRACTION	3	(chain A and resid 301:323)	A	301 - 323
4	X-RAY DIFFRACTION	4	(chain A and resid 324:335)	A	324 - 335
5	X-RAY DIFFRACTION	5	(chain B and resid 262:269)	B	262 - 269
6	X-RAY DIFFRACTION	6	(chain B and resid 270:289)	B	270 - 289
7	X-RAY DIFFRACTION	7	(chain B and resid 290:320)	B	290 - 320
8	X-RAY DIFFRACTION	8	(chain B and resid 321:334)	B	321 - 334

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