PDB-2ghp: Crystal structure of the N-terminal 3 RNA binding domains of the ...

ID or keywords:

Entry

Database: PDB / ID: 2ghp

Title

Crystal structure of the N-terminal 3 RNA binding domains of the yeast splicing factor Prp24

Components

U4/U6 snRNA-associated splicing factor PRP24

Keywords

RNA BINDING PROTEIN / RNA chaperone / RNA binding domain /

RNA recognition motif /

splicing factor /

snRNP /

spliceosome /

Structural Genomics /

Protein Structure Initiative / PSI / Center for Eukaryotic Structural Genomics / CESG

Function / homology

Function and homology information

U6 snRNP /

snRNA binding / spliceosomal complex assembly / spliceosomal tri-snRNP complex assembly /

U6 snRNA binding /

spliceosomal complex /

mRNA splicing, via spliceosome /

ribonucleoprotein complex /

RNA binding /

nucleus
Similarity search - Function

Biological species

Saccharomyces cerevisiae (brewer's yeast)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD /

MAD / Resolution: 2.7 Å

Authors

Bae, E. / Wesenberg, G.E. / Phillips Jr., G.N. / Bitto, E. / Bingman, C.A. / Center for Eukaryotic Structural Genomics (CESG)

Citation

Journal: J.Mol.Biol. / Year: 2007
Title: Structure and interactions of the first three RNA recognition motifs of splicing factor prp24.
Authors: Bae, E. / Reiter, N.J. / Bingman, C.A. / Kwan, S.S. / Lee, D. / Phillips Jr., G.N. / Butcher, S.E. / Brow, D.A.

History

Deposition	Mar 27, 2006	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 25, 2006	Provider: repository / Type: Initial release
Revision 1.1	Jan 15, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.3	Oct 18, 2017	Group: Refinement description / Category: software

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	2ghp.cif.gz	380.2 KB	Display	PDBx/mmCIF format
PDB format	pdb2ghp.ent.gz	321 KB	Display	PDB format
PDBx/mmJSON format	2ghp.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/gh/2ghp ftp://data.pdbj.org/pub/pdb/validation_reports/gh/2ghp	HTTPS FTP

-
Related structure data

Related structure data	2go9C C: citing same article (ref.)
Similar structure data	4db8-d 4b6f-d 4b76-d 3d2f-1 4l0n-d 6ai2-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
Other databases	TargetDB: GO.74368

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#245 - May 2020 Spliceosomes similarity (1)

Deposited unit

A: U4/U6 snRNA-associated splicing factor PRP24

B: U4/U6 snRNA-associated splicing factor PRP24

C: U4/U6 snRNA-associated splicing factor PRP24

D: U4/U6 snRNA-associated splicing factor PRP24

E: U4/U6 snRNA-associated splicing factor PRP24

F: U4/U6 snRNA-associated splicing factor PRP24

G: U4/U6 snRNA-associated splicing factor PRP24

H: U4/U6 snRNA-associated splicing factor PRP24

267 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: U4/U6 snRNA-associated splicing factor PRP24

B: U4/U6 snRNA-associated splicing factor PRP24

C: U4/U6 snRNA-associated splicing factor PRP24

D: U4/U6 snRNA-associated splicing factor PRP24

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

2

E: U4/U6 snRNA-associated splicing factor PRP24

F: U4/U6 snRNA-associated splicing factor PRP24

G: U4/U6 snRNA-associated splicing factor PRP24

H: U4/U6 snRNA-associated splicing factor PRP24

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

Unit cell

Length a, b, c (Å)	114.608, 125.848, 196.542
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Refine code: 2

Dom-ID	Component-ID	Ens-ID	Beg label comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	1	THR	VAL	A	A	42 - 103	43 - 104
2	1	1	THR	VAL	E	E	42 - 103	43 - 104
3	2	1	GLU	LEU	A	A	108 - 149	109 - 150
4	2	1	GLU	LEU	E	E	108 - 149	109 - 150
5	3	1	PHE	PRO	A	A	160 - 195	161 - 196
6	3	1	PHE	PRO	E	E	160 - 195	161 - 196
7	4	1	LEU	PRO	A	A	207 - 243	208 - 244
8	4	1	LEU	PRO	E	E	207 - 243	208 - 244
9	5	1	CYS	ASP	A	A	254 - 288	255 - 289
10	5	1	CYS	ASP	E	E	254 - 288	255 - 289
1	1	2	THR	VAL	B	B	42 - 103	43 - 104
2	1	2	THR	VAL	F	F	42 - 103	43 - 104
3	2	2	GLU	LEU	B	B	108 - 149	109 - 150
4	2	2	GLU	LEU	F	F	108 - 149	109 - 150
5	3	2	PHE	PRO	B	B	160 - 195	161 - 196
6	3	2	PHE	PRO	F	F	160 - 195	161 - 196
7	4	2	LEU	PRO	B	B	207 - 243	208 - 244
8	4	2	LEU	PRO	F	F	207 - 243	208 - 244
9	5	2	CYS	ASP	B	B	254 - 288	255 - 289
10	5	2	CYS	ASP	F	F	254 - 288	255 - 289
1	1	3	THR	VAL	C	C	42 - 103	43 - 104
2	1	3	THR	VAL	G	G	42 - 103	43 - 104
3	2	3	GLU	LEU	C	C	108 - 149	109 - 150
4	2	3	GLU	LEU	G	G	108 - 149	109 - 150
5	3	3	PHE	PRO	C	C	160 - 195	161 - 196
6	3	3	PHE	PRO	G	G	160 - 195	161 - 196
7	4	3	LEU	PRO	C	C	207 - 243	208 - 244
8	4	3	LEU	PRO	G	G	207 - 243	208 - 244
9	5	3	CYS	ASP	C	C	254 - 288	255 - 289
10	5	3	CYS	ASP	G	G	254 - 288	255 - 289
1	1	4	THR	VAL	D	D	42 - 103	43 - 104
2	1	4	THR	VAL	H	H	42 - 103	43 - 104
3	2	4	GLU	LEU	D	D	108 - 149	109 - 150
4	2	4	GLU	LEU	H	H	108 - 149	109 - 150
5	3	4	PHE	PRO	D	D	160 - 195	161 - 196
6	3	4	PHE	PRO	H	H	160 - 195	161 - 196
7	4	4	LEU	PRO	D	D	207 - 243	208 - 244
8	4	4	LEU	PRO	H	H	207 - 243	208 - 244
9	5	4	CYS	ASP	D	D	254 - 288	255 - 289
10	5	4	CYS	ASP	H	H	254 - 288	255 - 289

NCS ensembles :

ID
1
2
3
4

Details

The biological unit is a tetramer. There are 2 biological units in the asymmetric unit (chains A, B, C & D and chains E, F, G & H).

#1: Protein	U4/U6 snRNA-associated splicing factor PRP24 / U4/U6 snRNP protein Mass: 33401.359 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: PRP24 / Plasmid: PVP 16 / Production host: Escherichia coli (E. coli) / Strain (production host): B834 P(RARE2) / References: UniProt: P49960
#2: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 193 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

U4/U6 snRNA-associated splicing factor PRP24 / U4/U6 snRNP protein

Mass: 33401.359 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Saccharomyces cerevisiae (brewer's yeast)
Gene: PRP24 / Plasmid: PVP 16 / Production host:

Escherichia coli (E. coli) / Strain (production host): B834 P(RARE2) / References: UniProt: P49960

#2: Water

ChemComp-HOH / water /

Water

Mass: 18.015 Da / Num. of mol.: 193 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.65 Å³/Da / Density % sol: 53.61 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, hanging drop Details: PROTEIN SOLUTION (10 MG/ML PROTEIN, 0.050 M SODIUM CHLORIDE, 0.0003 M TCEP, 0.005 TRIS PH 8.0) MIXED IN A 1:1 RATIO WITH THE WELL SOLUTION (14% MEPEG 5000, 0.20 M TETRAMETHYL AMMONIUM ...Details: PROTEIN SOLUTION (10 MG/ML PROTEIN, 0.050 M SODIUM CHLORIDE, 0.0003 M TCEP, 0.005 TRIS PH 8.0) MIXED IN A 1:1 RATIO WITH THE WELL SOLUTION (14% MEPEG 5000, 0.20 M TETRAMETHYL AMMONIUM CHLORIDE, 0.10 M SODIUM SUCCINATE PH 4.0) Crystals cryo-protected with the well solution supplemented with 30% ethylene glycol., VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal

Density Matthews: 2.65 Å³/Da / Density % sol: 53.61 %

Crystal grow

Temperature: 277 K / Method: vapor diffusion, hanging drop
Details: PROTEIN SOLUTION (10 MG/ML PROTEIN, 0.050 M SODIUM CHLORIDE, 0.0003 M TCEP, 0.005 TRIS PH 8.0) MIXED IN A 1:1 RATIO WITH THE WELL SOLUTION (14% MEPEG 5000, 0.20 M TETRAMETHYL AMMONIUM ...

-
Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 22-ID / Wavelength: 0.97911 Å

Detector

Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 11, 2005
Details: HORIZONTAL SAGITALLY FOCUSING 2ND BENT MONOCHROMATOR CRYSTAL, VERTICAL BENT FOCUSING MIRROR

Radiation

Monochromator: CRYOGENICALLY COOLED SI (220) DOUBLE BOUNCE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97911 Å / Relative weight: 1

Reflection

Resolution: 2.7→49.503 Å / Num. obs: 74236 / % possible obs: 94.2 % / Redundancy: 7 % / R_merge(I) obs: 0.122 / Χ²: 1.105 / Net I/σ(I): 7.416

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique all	Χ²	% possible all
2.7-2.8	5.4	0.489	2.39	5801	0.977	74.3
2.8-2.91	6	0.396		6195	0.993	80.2
2.91-3.04	6.3	0.332		6999	1.026	89.6
3.04-3.2	6.7	0.272		7631	1.116	97.9
3.2-3.4	7.3	0.222		7822	1.163	100
3.4-3.66	7.6	0.159		7806	1.158	100
3.66-4.03	7.6	0.121		7868	1.163	100
4.03-4.62	7.6	0.09		7898	1.119	100
4.62-5.82	7.5	0.092		7966	1.093	100
5.82-49.5	7.2	0.084		8250	1.115	99.7

-
Phasing

Phasing

Method:

MAD

Phasing MAD set

R cullis centric: 0 / Highest resolution: 4 Å / Lowest resolution: 48.1 Å / Power centric: 0

ID	R cullis acentric	Power acentric	Reflection acentric	Reflection centric
ISO_1	0	0	21701	2960
ANO_1	0.682	1.653	21700	0

Phasing MAD set shell

R cullis centric: 0 / Power centric: 0

ID	Resolution (Å)	R cullis acentric	Power acentric	Reflection acentric	Reflection centric
ISO_1	16.82-48.1	0	0	229	139
ISO_1	12.27-16.82	0	0	414	147
ISO_1	10.13-12.27	0	0	554	148
ISO_1	8.82-10.13	0	0	662	148
ISO_1	7.92-8.82	0	0	753	142
ISO_1	7.24-7.92	0	0	838	150
ISO_1	6.72-7.24	0	0	919	147
ISO_1	6.29-6.72	0	0	981	148
ISO_1	5.94-6.29	0	0	1060	149
ISO_1	5.64-5.94	0	0	1123	155
ISO_1	5.38-5.64	0	0	1183	149
ISO_1	5.15-5.38	0	0	1237	145
ISO_1	4.95-5.15	0	0	1294	145
ISO_1	4.77-4.95	0	0	1352	148
ISO_1	4.61-4.77	0	0	1397	150
ISO_1	4.47-4.61	0	0	1445	147
ISO_1	4.34-4.47	0	0	1502	152
ISO_1	4.21-4.34	0	0	1542	143
ISO_1	4.1-4.21	0	0	1588	148
ISO_1	4-4.1	0	0	1628	160
ANO_1	16.82-48.1	0.778	1.392	228	0
ANO_1	12.27-16.82	0.659	1.804	414	0
ANO_1	10.13-12.27	0.67	1.793	554	0
ANO_1	8.82-10.13	0.656	1.778	662	0
ANO_1	7.92-8.82	0.581	2.164	753	0
ANO_1	7.24-7.92	0.604	2.072	838	0
ANO_1	6.72-7.24	0.571	2.209	919	0
ANO_1	6.29-6.72	0.566	2.274	981	0
ANO_1	5.94-6.29	0.617	2.043	1060	0
ANO_1	5.64-5.94	0.566	2.186	1123	0
ANO_1	5.38-5.64	0.627	1.941	1183	0
ANO_1	5.15-5.38	0.66	1.707	1237	0
ANO_1	4.95-5.15	0.7	1.545	1294	0
ANO_1	4.77-4.95	0.735	1.496	1352	0
ANO_1	4.61-4.77	0.762	1.328	1397	0
ANO_1	4.47-4.61	0.729	1.324	1445	0
ANO_1	4.34-4.47	0.771	1.211	1502	0
ANO_1	4.21-4.34	0.754	1.292	1542	0
ANO_1	4.1-4.21	0.781	1.165	1588	0
ANO_1	4-4.1	0.822	1.091	1628	0

Phasing MAD set site

ID	Cartn x (Å)	Cartn y (Å)	Cartn z (Å)	Atom type symbol	B iso	Occupancy
1	-5.231	-109.79	-2.42	SE	58.01	2.33
2	15.908	-156.671	14.473	SE	56.77	2.45
3	41.072	-144.78	10.255	SE	42.49	2.12
4	-17.616	-133.706	-6.427	SE	74.35	2.53
5	-8.409	-146.278	-9.385	SE	61.1	2.33
6	20.208	-105.24	9.339	SE	61.58	2.25
7	-12.816	-93.459	14.576	SE	61.56	2.44
8	-7.318	-137.722	-12.667	SE	62.4	2.21
9	9.005	-73.924	6.55	SE	59.89	2.25
10	10.999	-117.788	6.392	SE	56.83	2.25
11	-33.734	-141.498	2.568	SE	68.63	2.3
12	10.111	-112.583	-6.362	SE	86.92	2.43
13	12.397	-81.717	10.288	SE	52.85	2.1
14	-13.918	-90.387	23.324	SE	71.51	2.35
15	21.289	-113.821	12.682	SE	73.01	2.26
16	-30.474	-139.186	10.687	SE	79.61	2.54
17	-11.499	-92.575	-4.013	SE	55.26	1.85
18	-2.8	-76.988	9.649	SE	93.45	2.96
19	-40.024	-158.745	4.162	SE	57.93	1.88
20	25.159	-146.186	22.015	SE	61.18	1.99
21	37.667	-137.178	6.514	SE	68.79	2.3
22	47.45	-155.213	-3.921	SE	45.47	1.85
23	-18.407	-138.845	6.373	SE	87.13	2.46
24	25.9	-140.226	9.726	SE	92.23	3.04
25	15.212	-94.466	23.49	SE	64.8	1.88
26	-3.55	-82.798	22.005	SE	75.08	2.05
27	14.819	-153.68	23.271	SE	59.75	2.11
28	18.702	-92.046	-3.906	SE	45.08	1.81
29	-13.407	-157.042	-23.6	SE	52.7	1.79
30	-7.968	-111.471	16.043	SE	65.53	1.93
31	20.797	-174.805	15.982	SE	63.56	1.91
32	-1.901	-112.296	-10.575	SE	85.9	2.61

Phasing dm

FOM : 0.53 / FOM acentric: 0.53 / FOM centric: 0.49 / Reflection: 74149 / Reflection acentric: 67967 / Reflection centric: 6182

Phasing dm shell

Resolution (Å)	FOM	FOM acentric	FOM centric	Reflection	Reflection acentric	Reflection centric
7.7-48.099	0.75	0.78	0.62	3596	2828	768
4.8-7.7	0.72	0.74	0.57	10644	9390	1254
3.9-4.8	0.73	0.75	0.62	13191	12035	1156
3.4-3.9	0.63	0.64	0.5	13240	12247	993
2.9-3.4	0.39	0.4	0.34	22330	20938	1392
2.7-2.9	0.19	0.19	0.21	11148	10529	619

-
Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
SHARP		phasing
RESOLVE	2.1	phasing
REFMAC	5.2.0005	refinement
PDB_EXTRACT	1.701	data extraction
PHENIX		phasing
SHELXD		phasing
ARP/wARP		model building

Refinement

Method to determine structure:

SAD / Resolution: 2.7→49.503 Å / Cor.coef. F_o:F_c: 0.952 / Cor.coef. F_o:F_c free: 0.924 / WR_factor R_free: 0.27 / WR_factor R_work: 0.218 / SU B: 26.293 / SU ML: 0.255 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.754 / ESU R Free: 0.344
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE ELECTRON DENSITY MAP INDICATES SOME DISORDER IN THE RRM1 DOMAIN (Residues 41 to 117) OF CHAINS D and H.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2642	3738	5.041 %	random
R_work	0.213	-	-	-
all	0.216	-	-	-
obs	-	74155	94.218 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK

Displacement parameters

B_iso mean: 56.783 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-2.223 Å²	0 Å²	0 Å²
2-	-	5.883 Å²	0 Å²
3-	-	-	-3.66 Å²

Refinement step

Cycle: LAST / Resolution: 2.7→49.503 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	15026	0	0	193	15219

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.022	15262
X-RAY DIFFRACTION	r_angle_refined_deg	1.38	1.968	20562
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.966	5	1840
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.723	23.9	718
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	20.165	15	2860
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.817	15	122
X-RAY DIFFRACTION	r_chiral_restr	0.096	0.2	2354
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	11280
X-RAY DIFFRACTION	r_nbd_refined	0.213	0.2	6413
X-RAY DIFFRACTION	r_nbtor_refined	0.312	0.2	10393
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.138	0.2	525
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.238	0.2	49
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.157	0.2	4
X-RAY DIFFRACTION	r_mcbond_it	0.884	2	9539
X-RAY DIFFRACTION	r_mcangle_it	1.681	4	15096
X-RAY DIFFRACTION	r_scbond_it	3.112	6	6314
X-RAY DIFFRACTION	r_scangle_it	4.851	8	5466

Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	A	848	tight positional	0.032	0.05
1	A	857	medium positional	0.276	0.5
1	A	848	tight thermal	0.083	0.5
1	A	857	medium thermal	0.63	2
2	B	848	tight positional	0.03	0.05
2	B	857	medium positional	0.221	0.5
2	B	848	tight thermal	0.076	0.5
2	B	857	medium thermal	0.641	2
3	C	848	tight positional	0.031	0.05
3	C	857	medium positional	0.239	0.5
3	C	848	tight thermal	0.054	0.5
3	C	857	medium thermal	0.587	2
4	D	848	tight positional	0.031	0.05
4	D	857	medium positional	0.319	0.5
4	D	848	tight thermal	0.058	0.5
4	D	857	medium thermal	0.575	2

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	% reflection obs (%)
2.7-2.77	0.408	209	0.351	3998	0.354	5736	73.344
2.77-2.846	0.335	231	0.315	4163	0.316	5632	78.018
2.846-2.928	0.319	199	0.284	4273	0.285	5444	82.145
2.928-3.018	0.336	223	0.281	4508	0.284	5286	89.501
3.018-3.117	0.311	241	0.275	4702	0.277	5139	96.186
3.117-3.226	0.301	258	0.248	4688	0.251	4982	99.277
3.226-3.348	0.257	241	0.224	4569	0.226	4811	99.979
3.348-3.485	0.267	237	0.216	4394	0.219	4632	99.978
3.485-3.639	0.262	241	0.205	4223	0.208	4464	100
3.639-3.817	0.244	239	0.208	4031	0.21	4270	100
3.817-4.023	0.252	206	0.195	3836	0.198	4042	100
4.023-4.267	0.246	178	0.189	3675	0.191	3853	100
4.267-4.561	0.228	199	0.167	3426	0.17	3625	100
4.561-4.925	0.179	180	0.156	3211	0.157	3391	100
4.925-5.394	0.235	153	0.185	2971	0.188	3124	100
5.394-6.029	0.282	144	0.206	2719	0.209	2863	100
6.029-6.958	0.304	129	0.208	2385	0.212	2514	100
6.958-8.513	0.262	104	0.198	2066	0.201	2170	100
8.513-12	0.232	79	0.182	1627	0.184	1706	100
12-106	0.348	47	0.267	952	0.271	1022	97.75

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	4.5746	1.3972	1.5847	5.2359	1.2091	7.6077	0.2125	-0.3446	-0.5103	0.2285	-0.0082	-0.4289	0.5866	0.4223	-0.2043	-0.3548	0.0373	-0.0531	0.0428	0.0916	-0.3149	-6.3109	-38.3165	27.4299
2	4.2736	0.5241	-0.2828	2.6738	0.4025	5.346	-0.0412	-0.2049	-0.2652	-0.0999	-0.1595	-0.1215	-0.0571	0.5448	0.2007	-0.2132	0.0492	0.0048	-0.1294	0.032	-0.1426	-11.0639	-33.8474	5.7342
3	4.4959	0.0732	-0.6516	4.8861	-0.373	6.6218	-0.0451	0.2257	-0.6406	-0.5317	0.0106	0.1718	0.8793	-0.0827	0.0345	0.0068	-0.0293	-0.0432	-0.3568	-0.0288	0.0589	-23.063	-49.7818	-8.9902
4	3.1358	-0.1511	-0.6866	3.4906	-0.7156	9.1978	-0.0069	0.5049	-0.1787	0.0025	-0.0345	-0.3273	-0.2752	0.774	0.0415	-0.2881	-0.0226	0.0186	0.0818	-0.0892	-0.3778	-12.6765	-27.5605	-47.2101
5	3.9065	0.4347	0.6989	1.2484	0.5684	4.4266	-0.0145	0.3655	-0.0353	-0.1039	-0.0287	-0.0871	0.346	0.4897	0.0431	-0.083	-0.0118	0.0128	-0.0962	-0.0596	-0.1806	-12.8715	-29.9292	-24.8006
6	5.2881	0.3839	1.2544	3.029	-1.082	7.1063	0.0993	-0.131	0.5813	0.1257	-0.0624	0.0128	-0.4439	0.2792	-0.0369	-0.0832	-0.092	0.0333	-0.4535	-0.0801	-0.0358	-10.4777	-11.5426	-9.2465
7	5.8637	2.8366	-0.7579	8.6515	-1.0186	5.5817	0.3301	-1.7276	-0.6202	0.9256	-0.4092	0.3449	0.3364	0.1537	0.0791	-0.2081	-0.0071	0.0382	0.3116	0.3058	-0.0627	-43.9499	-46.8095	23.4992
8	3.4581	1.3127	-1.8506	3.3467	-0.4323	1.5715	0.0107	-0.0956	0.0885	-0.1273	0.1776	0.3666	0.0024	-0.7681	-0.1883	-0.1381	0.0416	-0.0509	0.0525	0.0272	0.0046	-38.7692	-34.2124	5.5928
9	5.0837	-0.9115	0.451	4.869	-0.8109	5.4978	-0.2023	-0.4123	0.656	0.2311	0.1408	0.0394	-0.9965	0.0651	0.0614	0.0111	0.0714	-0.0105	-0.1912	-0.1606	0.0043	-26.7845	-12.637	7.7099
10	10.3446	-0.7736	4.1186	8.2571	-0.839	11.4149	0.1888	1.1793	1.619	-1.4168	-0.0748	0.1129	-1.1285	-1.1678	-0.114	0.5275	0.3468	-0.0552	0.1048	0.4187	0.2756	-36.7617	1.4709	-34.3218
11	4.4325	-0.4242	1.833	4.1792	-1.1334	4.3081	-0.1373	0.2111	0.4506	0.1031	0.4378	0.2687	-0.6965	-0.8808	-0.3005	0.0088	0.1414	-0.0182	-0.1257	0.0587	0.029	-35.4237	-13.5622	-17.7644
12	6.1203	0.9897	-0.8722	3.4342	-2.4635	6.1998	0.0138	0.4701	-0.6192	-0.172	0.155	0.0358	0.5884	-0.2209	-0.1688	-0.1599	-0.0592	-0.0942	-0.1273	-0.0731	-0.0976	-39.2911	-37.8676	-21.1465
13	4.3339	1.2183	0.3118	5.0851	1.0497	8.6194	0.132	-0.3897	-0.4911	0.2207	0.0127	-0.4168	0.6379	0.5285	-0.1447	-0.3427	0.0966	-0.066	0.0596	0.0804	-0.3235	-35.0781	-101.4975	27.4346
14	4.1219	0.1977	0.2379	2.7846	0.4231	7.0052	-0.0613	-0.153	-0.2367	-0.1692	-0.1941	-0.1071	-0.0502	0.6679	0.2553	-0.2022	0.0916	0.0113	-0.0562	0.0287	-0.1553	-39.8185	-97.0612	5.7914
15	5.0028	-0.068	0.3634	4.8311	-0.6495	8.9916	-0.024	0.2974	-0.7873	-0.449	0	0.13	1.0494	0.1123	0.024	-0.0074	0.0807	0.0233	-0.3415	-0.1082	0.0676	-51.8262	-113.0009	-9.0191
16	3.7514	-0.2604	-0.4512	3.8444	-1.0292	9.38	-0.0751	0.4565	-0.1531	-0.0015	-0.0897	-0.3346	-0.4012	1.0801	0.1649	-0.3047	-0.0737	0.0376	0.2019	-0.0987	-0.3871	-41.3943	-90.8198	-47.2406
17	4.215	0.3467	0.5836	0.8429	1.0647	4.8822	-0.0222	0.4265	-0.0711	-0.054	-0.0889	-0.071	0.1971	0.9134	0.1111	-0.1196	-0.0132	0.0135	0.083	-0.0439	-0.1519	-41.5787	-93.159	-24.8434
18	5.2941	0.8851	1.2601	3.6377	-2.0468	6.3605	-0.0594	-0.1152	0.6465	0.2327	-0.0276	0.0383	-0.7211	0.5423	0.0871	0.0126	-0.1257	-0.0409	-0.1531	-0.0452	-0.0382	-39.2279	-74.7481	-9.2546
19	5.7468	3.3859	-1.325	8.8163	-0.5352	6.6858	0.4581	-1.8652	-0.7456	1.033	-0.6606	0.1372	0.3504	0.0019	0.2024	-0.1857	-0.013	0.0456	0.4362	0.286	-0.0676	-72.7738	-110.0817	23.411
20	3.0797	0.8553	-1.3965	2.661	-0.0033	1.1087	0.001	-0.1266	0.0259	-0.0258	0.0852	0.3313	-0.0114	-0.5967	-0.0862	-0.1183	0.0948	-0.0268	0.0651	-0.0104	-0.0018	-67.5528	-97.5364	5.5062
21	4.9943	-0.9751	0.5055	5.2689	-1.2043	7.5522	-0.2095	-0.617	0.6632	0.1652	-0.0755	0.162	-1.3591	0.0442	0.285	0.1078	0.1383	-0.0825	-0.2541	-0.2015	-0.0153	-55.5479	-75.9734	7.5765
22	7.031	-0.7853	3.1398	10.5366	-2.8347	12.043	0.0005	1.3252	1.3571	-1.2779	0.204	0.2083	-1.3681	-0.7972	-0.2044	0.6301	0.1589	-0.2051	0.2376	0.4146	0.2543	-65.4767	-61.9214	-34.4588
23	4.9308	0.4928	1.7113	4.4123	0.0411	5.3179	-0.2388	0.2331	0.6158	0.0849	0.2155	0.1946	-0.8195	-0.6293	0.0233	0.0538	0.1648	-0.0781	-0.2533	-0.0174	0.0029	-64.1573	-76.9519	-17.8633
24	5.3054	0.9241	0.5646	3.3493	-2.0442	6.1392	-0.0347	0.2784	-0.635	-0.1473	0.0815	-0.0035	0.5798	-0.1344	-0.0468	-0.1843	0.0229	-0.025	-0.154	-0.1242	-0.0962	-68.0483	-101.2049	-21.2064

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	A	A	41 - 117	42 - 118
2	2	A	A	118 - 196	119 - 197
3	3	A	A	206 - 291	207 - 292
4	4	B	B	41 - 117	42 - 118
5	5	B	B	118 - 196	119 - 197
6	6	B	B	206 - 291	207 - 292
7	7	C	C	41 - 117	42 - 118
8	8	C	C	118 - 196	119 - 197
9	9	C	C	206 - 291	207 - 292
10	10	D	D	41 - 117	42 - 118
11	11	D	D	118 - 196	119 - 197
12	12	D	D	206 - 291	207 - 292
13	13	E	E	41 - 117	42 - 118
14	14	E	E	118 - 196	119 - 197
15	15	E	E	206 - 291	207 - 292
16	16	F	F	41 - 117	42 - 118
17	17	F	F	118 - 196	119 - 197
18	18	F	F	206 - 291	207 - 292
19	19	G	G	41 - 117	42 - 118
20	20	G	G	118 - 196	119 - 197
21	21	G	G	206 - 291	207 - 292
22	22	H	H	41 - 117	42 - 118
23	23	H	H	118 - 196	119 - 197
24	24	H	H	206 - 291	207 - 292

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
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

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
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

-
Phasing

-
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

-
Yorodumi

-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

-Phasing

-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

-Yorodumi

-
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

-
Phasing

-
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

-
Yorodumi