PDB-4fmg: Merkel Cell Polyomavirus VP1 Unassembled Pentamer

ID or keywords:

Entry

Database: PDB / ID: 4fmg

Title

Merkel Cell Polyomavirus VP1 Unassembled Pentamer

Components

VP1

Keywords

VIRAL PROTEIN /

viral capsid protein / jelly roll / encapsidation /

receptor binding / sialylated oligosaccharides

Function / homology

Function and homology information

viral capsid / structural molecule activity
Similarity search - Function

Biological species

Merkel cell polyomavirus

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.1 Å

Authors

Neu, U. / Hengel, H. / Stehle, T.

Citation

Journal: Plos Pathog. / Year: 2012
Title: Structures of Merkel Cell Polyomavirus VP1 Complexes Define a Sialic Acid Binding Site Required for Infection.
Authors: Neu, U. / Hengel, H. / Blaum, B.S. / Schowalter, R.M. / Macejak, D. / Gilbert, M. / Wakarchuk, W.W. / Imamura, A. / Ando, H. / Kiso, M. / Arnberg, N. / Garcea, R.L. / Peters, T. / Buck, C.B. / Stehle, T.

History

Deposition	Jun 17, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 5, 2012	Provider: repository / Type: Initial release
Revision 1.1	Feb 28, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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	4fmg.cif.gz	2.1 MB	Display	PDBx/mmCIF format
PDB format	pdb4fmg.ent.gz	1.7 MB	Display	PDB format
PDBx/mmJSON format	4fmg.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

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

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Related structure data

Related structure data	4fmhC 4fmiC 4fmjC C: citing same article (ref.)
Similar structure data	4fmi-2 4fmj-4 4u62-2 4fmh-2 5cpu-d 4u61-2 6hkv-2 4fmh-1 4fmj-2 5cpy-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) 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

4fmhC

4fmiC

4fmjC

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	#47 - Nov 2003 Simian Virus 40 similarity (4) #221 - May 2018 Human Papillomavirus and Vaccines similarity (1) #200 - Aug 2016 Quasisymmetry in Icosahedral Viruses similarity (4)

Deposited unit

A: VP1

B: VP1

C: VP1

D: VP1

E: VP1

F: VP1

G: VP1

H: VP1

I: VP1

J: VP1

K: VP1

L: VP1

M: VP1

N: VP1

O: VP1

P: VP1

Q: VP1

R: VP1

S: VP1

T: VP1

hetero molecules

642 kDa, 20 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: VP1

B: VP1

C: VP1

D: VP1

E: VP1

hetero molecules

defined by author&software
161 kDa, 5 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

F: VP1

G: VP1

H: VP1

I: VP1

J: VP1

hetero molecules

defined by author&software
161 kDa, 5 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

K: VP1

L: VP1

M: VP1

N: VP1

O: VP1

hetero molecules

defined by author&software
160 kDa, 5 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

P: VP1

Q: VP1

R: VP1

S: VP1

T: VP1

hetero molecules

defined by author&software
160 kDa, 5 polymers
Search similar-shape structures of this assembly by Omokage search (details)

5

A: VP1

B: VP1

C: VP1

D: VP1

E: VP1

K: VP1

L: VP1

M: VP1

N: VP1

O: VP1

hetero molecules

defined by software
321 kDa, 10 polymers
Search similar-shape structures of this assembly by Omokage search (details)

6

F: VP1

G: VP1

H: VP1

I: VP1

J: VP1

P: VP1

Q: VP1

R: VP1

S: VP1

T: VP1

hetero molecules

defined by software
321 kDa, 10 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	85.270, 85.620, 248.170
Angle α, β, γ (deg.)	92.98, 100.50, 108.05
Int Tables number	1
Space group name H-M	P1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Refine code	Auth asym-ID	Auth seq-ID
1	1	1	5	A	59 - 64
2	1	1	5	B	59 - 64
3	1	1	5	C	59 - 64
4	1	1	5	D	59 - 64
5	1	1	5	E	59 - 64
6	1	1	5	F	59 - 64
7	1	1	5	G	59 - 64
8	1	1	5	H	59 - 64
9	1	1	5	I	59 - 64
10	1	1	5	J	59 - 64
11	1	1	5	K	59 - 64
12	1	1	5	L	59 - 64
13	1	1	5	M	59 - 64
14	1	1	5	N	59 - 64
15	1	1	5	O	59 - 64
16	1	1	5	P	59 - 64
17	1	1	5	Q	59 - 64
18	1	1	5	R	59 - 64
19	1	1	5	S	59 - 64
20	1	1	5	T	59 - 64
1	2	1	5	A	96 - 100
2	2	1	5	B	96 - 100
3	2	1	5	C	96 - 100
4	2	1	5	D	96 - 100
5	2	1	5	E	96 - 100
6	2	1	5	F	96 - 100
7	2	1	5	G	96 - 100
8	2	1	5	H	96 - 100
9	2	1	5	I	96 - 100
10	2	1	5	J	96 - 100
11	2	1	5	K	96 - 100
12	2	1	5	L	96 - 100
13	2	1	5	M	96 - 100
14	2	1	5	N	96 - 100
15	2	1	5	O	96 - 100
16	2	1	5	P	96 - 100
17	2	1	5	Q	96 - 100
18	2	1	5	R	96 - 100
19	2	1	5	S	96 - 100
20	2	1	5	T	96 - 100
1	3	1	5	A	123 - 142
2	3	1	5	B	123 - 142
3	3	1	5	C	123 - 142
4	3	1	5	D	123 - 142
5	3	1	5	E	123 - 142
6	3	1	5	F	123 - 142
7	3	1	5	G	123 - 142
8	3	1	5	H	123 - 142
9	3	1	5	I	123 - 142
10	3	1	5	J	123 - 142
11	3	1	5	K	123 - 142
12	3	1	5	L	123 - 142
13	3	1	5	M	123 - 142
14	3	1	5	N	123 - 142
15	3	1	5	O	123 - 142
16	3	1	5	P	123 - 142
17	3	1	5	Q	123 - 142
18	3	1	5	R	123 - 142
19	3	1	5	S	123 - 142
20	3	1	5	T	123 - 142
1	4	1	5	A	167 - 182
2	4	1	5	B	167 - 182
3	4	1	5	C	167 - 182
4	4	1	5	D	167 - 182
5	4	1	5	E	167 - 182
6	4	1	5	F	167 - 182
7	4	1	5	G	167 - 182
8	4	1	5	H	167 - 182
9	4	1	5	I	167 - 182
10	4	1	5	J	167 - 182
11	4	1	5	K	167 - 182
12	4	1	5	L	167 - 182
13	4	1	5	M	167 - 182
14	4	1	5	N	167 - 182
15	4	1	5	O	167 - 182
16	4	1	5	P	167 - 182
17	4	1	5	Q	167 - 182
18	4	1	5	R	167 - 182
19	4	1	5	S	167 - 182
20	4	1	5	T	167 - 182
1	5	1	5	A	311 - 316
2	5	1	5	B	311 - 316
3	5	1	5	C	311 - 316
4	5	1	5	D	311 - 316
5	5	1	5	E	311 - 316
6	5	1	5	F	311 - 316
7	5	1	5	G	311 - 316
8	5	1	5	H	311 - 316
9	5	1	5	I	311 - 316
10	5	1	5	J	311 - 316
11	5	1	5	K	311 - 316
12	5	1	5	L	311 - 316
13	5	1	5	M	311 - 316
14	5	1	5	N	311 - 316
15	5	1	5	O	311 - 316
16	5	1	5	P	311 - 316
17	5	1	5	Q	311 - 316
18	5	1	5	R	311 - 316
19	5	1	5	S	311 - 316
20	5	1	5	T	311 - 316
1	6	1	5	A	303 - 307
2	6	1	5	B	303 - 307
3	6	1	5	C	303 - 307
4	6	1	5	D	303 - 307
5	6	1	5	E	303 - 307
6	6	1	5	F	303 - 307
7	6	1	5	G	303 - 307
8	6	1	5	H	303 - 307
9	6	1	5	I	303 - 307
10	6	1	5	J	303 - 307
11	6	1	5	K	303 - 307
12	6	1	5	L	303 - 307
13	6	1	5	M	303 - 307
14	6	1	5	N	303 - 307
15	6	1	5	O	303 - 307
16	6	1	5	P	303 - 307
17	6	1	5	Q	303 - 307
18	6	1	5	R	303 - 307
19	6	1	5	S	303 - 307
20	6	1	5	T	303 - 307
1	7	1	5	A	259 - 261
2	7	1	5	B	259 - 261
3	7	1	5	C	259 - 261
4	7	1	5	D	259 - 261
5	7	1	5	E	259 - 261
6	7	1	5	F	259 - 261
7	7	1	5	G	259 - 261
8	7	1	5	H	259 - 261
9	7	1	5	I	259 - 261
10	7	1	5	J	259 - 261
11	7	1	5	K	259 - 261
12	7	1	5	L	259 - 261
13	7	1	5	M	259 - 261
14	7	1	5	N	259 - 261
15	7	1	5	O	259 - 261
16	7	1	5	P	259 - 261
17	7	1	5	Q	259 - 261
18	7	1	5	R	259 - 261
19	7	1	5	S	259 - 261
20	7	1	5	T	259 - 261
1	8	1	5	A	272 - 275
2	8	1	5	B	272 - 275
3	8	1	5	C	272 - 275
4	8	1	5	D	272 - 275
5	8	1	5	E	272 - 275
6	8	1	5	F	272 - 275
7	8	1	5	G	272 - 275
8	8	1	5	H	272 - 275
9	8	1	5	I	272 - 275
10	8	1	5	J	272 - 275
11	8	1	5	K	272 - 275
12	8	1	5	L	272 - 275
13	8	1	5	M	272 - 275
14	8	1	5	N	272 - 275
15	8	1	5	O	272 - 275
16	8	1	5	P	272 - 275
17	8	1	5	Q	272 - 275
18	8	1	5	R	272 - 275
19	8	1	5	S	272 - 275
20	8	1	5	T	272 - 275
1	9	1	5	A	224 - 238
2	9	1	5	B	224 - 238
3	9	1	5	C	224 - 238
4	9	1	5	D	224 - 238
5	9	1	5	E	224 - 238
6	9	1	5	F	224 - 238
7	9	1	5	G	224 - 238
8	9	1	5	H	224 - 238
9	9	1	5	I	224 - 238
10	9	1	5	J	224 - 238
11	9	1	5	K	224 - 238
12	9	1	5	L	224 - 238
13	9	1	5	M	224 - 238
14	9	1	5	N	224 - 238
15	9	1	5	O	224 - 238
16	9	1	5	P	224 - 238
17	9	1	5	Q	224 - 238
18	9	1	5	R	224 - 238
19	9	1	5	S	224 - 238
20	9	1	5	T	224 - 238
1	10	1	5	A	243 - 248
2	10	1	5	B	243 - 248
3	10	1	5	C	243 - 248
4	10	1	5	D	243 - 248
5	10	1	5	E	243 - 248
6	10	1	5	F	243 - 248
7	10	1	5	G	243 - 248
8	10	1	5	H	243 - 248
9	10	1	5	I	243 - 248
10	10	1	5	J	243 - 248
11	10	1	5	K	243 - 248
12	10	1	5	L	243 - 248
13	10	1	5	M	243 - 248
14	10	1	5	N	243 - 248
15	10	1	5	O	243 - 248
16	10	1	5	P	243 - 248
17	10	1	5	Q	243 - 248
18	10	1	5	R	243 - 248
19	10	1	5	S	243 - 248
20	10	1	5	T	243 - 248
1	11	1	5	A	284 - 294
2	11	1	5	B	284 - 294
3	11	1	5	C	284 - 294
4	11	1	5	D	284 - 294
5	11	1	5	E	284 - 294
6	11	1	5	F	284 - 294
7	11	1	5	G	284 - 294
8	11	1	5	H	284 - 294
9	11	1	5	I	284 - 294
10	11	1	5	J	284 - 294
11	11	1	5	K	284 - 294
12	11	1	5	L	284 - 294
13	11	1	5	M	284 - 294
14	11	1	5	N	284 - 294
15	11	1	5	O	284 - 294
16	11	1	5	P	284 - 294
17	11	1	5	Q	284 - 294
18	11	1	5	R	284 - 294
19	11	1	5	S	284 - 294
20	11	1	5	T	284 - 294
1	12	1	5	A	153 - 156
2	12	1	5	B	153 - 156
3	12	1	5	C	153 - 156
4	12	1	5	D	153 - 156
5	12	1	5	E	153 - 156
6	12	1	5	F	153 - 156
7	12	1	5	G	153 - 156
8	12	1	5	H	153 - 156
9	12	1	5	I	153 - 156
10	12	1	5	J	153 - 156
11	12	1	5	K	153 - 156
12	12	1	5	L	153 - 156
13	12	1	5	M	153 - 156
14	12	1	5	N	153 - 156
15	12	1	5	O	153 - 156
16	12	1	5	P	153 - 156
17	12	1	5	Q	153 - 156
18	12	1	5	R	153 - 156
19	12	1	5	S	153 - 156
20	12	1	5	T	153 - 156
1	13	1	5	A	190 - 192
2	13	1	5	B	190 - 192
3	13	1	5	C	190 - 192
4	13	1	5	D	190 - 192
5	13	1	5	E	190 - 192
6	13	1	5	F	190 - 192
7	13	1	5	G	190 - 192
8	13	1	5	H	190 - 192
9	13	1	5	I	190 - 192
10	13	1	5	J	190 - 192
11	13	1	5	K	190 - 192
12	13	1	5	L	190 - 192
13	13	1	5	M	190 - 192
14	13	1	5	N	190 - 192
15	13	1	5	O	190 - 192
16	13	1	5	P	190 - 192
17	13	1	5	Q	190 - 192
18	13	1	5	R	190 - 192
19	13	1	5	S	190 - 192
20	13	1	5	T	190 - 192
1	14	1	5	A	254 - 257
2	14	1	5	B	254 - 257
3	14	1	5	C	254 - 257
4	14	1	5	D	254 - 257
5	14	1	5	E	254 - 257
6	14	1	5	F	254 - 257
7	14	1	5	G	254 - 257
8	14	1	5	H	254 - 257
9	14	1	5	I	254 - 257
10	14	1	5	J	254 - 257
11	14	1	5	K	254 - 257
12	14	1	5	L	254 - 257
13	14	1	5	M	254 - 257
14	14	1	5	N	254 - 257
15	14	1	5	O	254 - 257
16	14	1	5	P	254 - 257
17	14	1	5	Q	254 - 257
18	14	1	5	R	254 - 257
19	14	1	5	S	254 - 257
20	14	1	5	T	254 - 257
1	15	1	5	A	264 - 269
2	15	1	5	B	264 - 269
3	15	1	5	C	264 - 269
4	15	1	5	D	264 - 269
5	15	1	5	E	264 - 269
6	15	1	5	F	264 - 269
7	15	1	5	G	264 - 269
8	15	1	5	H	264 - 269
9	15	1	5	I	264 - 269
10	15	1	5	J	264 - 269
11	15	1	5	K	264 - 269
12	15	1	5	L	264 - 269
13	15	1	5	M	264 - 269
14	15	1	5	N	264 - 269
15	15	1	5	O	264 - 269
16	15	1	5	P	264 - 269
17	15	1	5	Q	264 - 269
18	15	1	5	R	264 - 269
19	15	1	5	S	264 - 269
20	15	1	5	T	264 - 269

#1: Protein	VP1 Mass: 31927.154 Da / Num. of mol.: 20 / Fragment: UNP residues 37-319 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Merkel cell polyomavirus / Strain: W162 / Gene: VP1 / Production host: Escherichia coli (E. coli) / References: UniProt: C0JPK1
#2: Chemical	... ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 32 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Chemical	ChemComp-CL / CHLORIDE ION / Chloride Mass: 35.453 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: Cl
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 3274 / 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: 2.63 Å³/Da / Density % sol: 53.32 % Description: THE CRYSTAL SUFFERED FROM RADIATION DAMAGE DURING DATA COLLECTION.
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1 M sodium cacodylate, pH 6.5, 6% w/v PEG3350, 0.3 M magnesium chloride, cryoprotection: 25% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction	Mean temperature: 93 K
Diffraction source	Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
Detector	Type: RAYONIX MX-225 / Detector: CCD / Date: Nov 11, 2009
Radiation	Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9184 Å / Relative weight: 1
Reflection	Resolution: 2.1→50 Å / Num. all: 380544 / Num. obs: 351188 / % possible obs: 92.3 % / Observed criterion σ(I): -3 / Redundancy: 2.8 % / R_merge(I) obs: 0.113 / Net I/σ(I): 8.98
Reflection shell	Resolution: 2.1→2.15 Å / Redundancy: 2.7 % / R_merge(I) obs: 0.569 / Mean I/σ(I) obs: 1.95 / % possible all: 64.7

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Processing

Software

Name	Version	Classification
MxCuBE		data collection
PHASER		phasing
REFMAC	5.5.0109	refinement
XDS		data reduction
XSCALE		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.1→50 Å / Cor.coef. F_o:F_c: 0.95 / Cor.coef. F_o:F_c free: 0.923 / SU B: 9.293 / SU ML: 0.132 / Cross valid method: THROUGHOUT / ESU R: 0.211 / ESU R Free: 0.179 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: RESIDUES 71 AND 72 ADOPT MULTIPLE CONFORMATIONS IN THE STRUCTURE.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.22699	3543	1 %	RANDOM
R_work	0.18232	-	-	-
obs	0.18277	347623	92.31 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 24.932 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.78 Å²	0.55 Å²	0.05 Å²
2-	-	1.13 Å²	0.09 Å²
3-	-	-	-1.54 Å²

Refinement step

Cycle: LAST / Resolution: 2.1→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	42369	0	212	3274	45855

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.022	44145
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.104	1.976	60203
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.119	5	5516
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.413	25.008	1811
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.805	15	7318
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.522	15	162
X-RAY DIFFRACTION	r_chiral_restr	0.074	0.2	6759
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.021	33314
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	1.002	3	27449
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.817	5	44835
X-RAY DIFFRACTION	r_scbond_it	2.751	7	16696
X-RAY DIFFRACTION	r_scangle_it	3.978	9	15363
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

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

Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	A	444	medium positional	0.07	0.5
2	B	444	medium positional	0.08	0.5
3	C	444	medium positional	0.1	0.5
4	D	444	medium positional	0.07	0.5
5	E	444	medium positional	0.08	0.5
6	F	444	medium positional	0.1	0.5
7	G	444	medium positional	0.08	0.5
8	H	444	medium positional	0.08	0.5
9	I	444	medium positional	0.09	0.5
10	J	444	medium positional	0.08	0.5
11	K	444	medium positional	0.09	0.5
12	L	444	medium positional	0.08	0.5
13	M	444	medium positional	0.09	0.5
14	N	444	medium positional	0.1	0.5
15	O	444	medium positional	0.09	0.5
16	P	444	medium positional	0.07	0.5
17	Q	444	medium positional	0.08	0.5
18	R	444	medium positional	0.08	0.5
19	S	444	medium positional	0.08	0.5
20	T	444	medium positional	0.07	0.5
1	A	397	loose positional	0.14	5
2	B	397	loose positional	0.14	5
3	C	397	loose positional	0.17	5
4	D	397	loose positional	0.13	5
5	E	397	loose positional	0.15	5
6	F	397	loose positional	0.15	5
7	G	397	loose positional	0.16	5
8	H	397	loose positional	0.15	5
9	I	397	loose positional	0.15	5
10	J	397	loose positional	0.16	5
11	K	397	loose positional	0.16	5
12	L	397	loose positional	0.15	5
13	M	397	loose positional	0.14	5
14	N	397	loose positional	0.15	5
15	O	397	loose positional	0.15	5
16	P	397	loose positional	0.16	5
17	Q	397	loose positional	0.15	5
18	R	397	loose positional	0.2	5
19	S	397	loose positional	0.14	5
20	T	397	loose positional	0.13	5
1	A	444	medium thermal	0.54	2
2	B	444	medium thermal	0.55	2
3	C	444	medium thermal	0.62	2
4	D	444	medium thermal	0.75	2
5	E	444	medium thermal	0.59	2
6	F	444	medium thermal	0.64	2
7	G	444	medium thermal	0.55	2
8	H	444	medium thermal	0.53	2
9	I	444	medium thermal	0.57	2
10	J	444	medium thermal	0.61	2
11	K	444	medium thermal	0.75	2
12	L	444	medium thermal	0.55	2
13	M	444	medium thermal	0.62	2
14	N	444	medium thermal	0.53	2
15	O	444	medium thermal	0.81	2
16	P	444	medium thermal	0.55	2
17	Q	444	medium thermal	0.59	2
18	R	444	medium thermal	0.71	2
19	S	444	medium thermal	0.57	2
20	T	444	medium thermal	0.59	2
1	A	397	loose thermal	0.62	10
2	B	397	loose thermal	0.61	10
3	C	397	loose thermal	0.68	10
4	D	397	loose thermal	0.82	10
5	E	397	loose thermal	0.7	10
6	F	397	loose thermal	0.66	10
7	G	397	loose thermal	0.65	10
8	H	397	loose thermal	0.65	10
9	I	397	loose thermal	0.68	10
10	J	397	loose thermal	0.71	10
11	K	397	loose thermal	0.78	10
12	L	397	loose thermal	0.69	10
13	M	397	loose thermal	0.67	10
14	N	397	loose thermal	0.63	10
15	O	397	loose thermal	0.75	10
16	P	397	loose thermal	0.68	10
17	Q	397	loose thermal	0.62	10
18	R	397	loose thermal	0.76	10
19	S	397	loose thermal	0.66	10
20	T	397	loose thermal	0.65	10

LS refinement shell

Resolution: 2.1→2.154 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.291	175	-
R_work	0.259	17988	-
obs	-	-	64.67 %

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	2.4628	-1.2913	2.3476	1.6562	-1.9589	5.7791	-0.0935	0.1978	0.1752	-0.0618	-0.1093	-0.1546	-0.23	0.5734	0.2028	0.1006	-0.0982	0.0193	0.1269	-0.0048	0.1474	20.579	23.113	-7.507
2	0.3822	-0.0376	-0.0063	0.3968	0.0431	0.5807	-0.0045	-0.0001	0.0801	-0.0202	-0.0196	-0.0113	-0.1715	0.1236	0.0242	0.0568	-0.0559	-0.0018	0.1134	-0.0111	0.0657	12.035	20.445	1.741
3	1.4693	-0.3303	1.1259	3.405	-2.2363	6.3025	0.0198	0.0833	-0.0269	-0.4153	-0.0785	-0.2156	0.712	0.0954	0.0586	0.1109	0.0087	0.0513	0.1677	-0.0281	0.0975	23.404	-10.955	-19.742
4	0.5006	0.0632	0.064	0.4514	-0.0259	0.2811	-0.0061	0.0344	0.0208	-0.0485	0.0123	-0.0748	0.0152	0.193	-0.0063	0.0216	0.0089	0.0131	0.1542	-0.0085	0.0596	22.747	-4.451	-6.858
5	4.3848	0.2138	-3.3524	1.966	-1.6798	15.9944	-0.0649	0.5244	-0.0884	-0.1133	0.1047	0.0533	0.2195	-1.1207	-0.0398	0.1064	0.0044	-0.0253	0.1081	-0.0191	0.0469	-10.189	-21.851	-31.652
6	0.3897	0.0294	-0.0513	0.3911	0.0022	0.584	-0.0017	0.0147	-0.0903	-0.0363	-0.0085	-0.0545	0.1992	0.0744	0.0102	0.09	0.0193	0.0075	0.0569	0.0087	0.0657	1.029	-23.981	-5.389
7	0.6908	0.6515	-0.8821	3.2601	3.4898	12.6151	0.0383	0.0846	0.0498	-0.4912	-0.2286	0.2614	-0.8193	-0.7913	0.1903	0.1099	0.0716	-0.0479	0.2074	-0.0097	0.1318	-34.394	-1.001	-18.471
8	0.3428	0.0072	-0.0735	0.4873	-0.0018	0.6539	0.0174	-0.0129	-0.04	-0.0191	-0.0325	0.0476	0.0814	-0.1243	0.0152	0.0288	-0.0263	0.0125	0.0794	-0.0031	0.0539	-21.812	-9.793	4.415
9	2.2849	0.0923	3.0226	0.7007	-0.5481	6.8594	-0.1716	0.0002	0.2581	0.0013	-0.0793	0.0681	-0.495	0.0149	0.2508	0.0847	0.0141	0.0131	0.0448	-0.0381	0.0969	-13.823	28.156	3.664
10	0.5498	0.0481	0.1003	0.4124	0.0056	0.586	-0.0188	-0.034	0.0759	0.0162	-0.0054	0.0734	-0.0765	-0.0815	0.0243	0.0412	-0.0041	0.0083	0.072	-0.0287	0.0451	-15.066	16.643	8.386
11	7.2137	1.8802	4.8196	2.2629	2.3721	11.2811	-0.3976	0.8567	0.1142	-0.1684	0.3709	-0.0036	-0.8459	0.1617	0.0267	0.2476	0.0353	-0.0077	0.1669	0.0301	0.085	15.248	5.289	-137.947
12	0.4694	-0.0385	0.1386	0.4423	-0.0695	0.5525	-0.0489	-0.0618	0.0459	0.0825	0.0221	0.0858	-0.158	-0.1255	0.0267	0.1111	0.0382	0.0233	0.0566	-0.015	0.0323	21.641	-5.253	-112.85
13	2.0078	-0.8713	2.3974	1.0141	-1.2608	4.0275	-0.0415	0.2909	0.1655	-0.121	-0.112	-0.092	0.0196	0.3988	0.1535	0.0979	-0.0612	-0.003	0.1217	0.0377	0.0856	54.268	-0.006	-134.586
14	0.4422	-0.0704	0.0804	0.4975	0.0034	0.5002	-0.0351	0.0063	0.0742	0.0427	-0.0077	-0.0184	-0.1736	0.0766	0.0427	0.1226	-0.03	-0.0153	0.0656	0.0017	0.0533	48.727	-2.972	-120.192
15	2.9686	-0.2698	-0.0722	4.3163	-4.1516	7.1229	-0.1442	0.3822	-0.0632	-0.4609	0.0922	-0.2129	0.5104	0.1737	0.0521	0.159	-0.0213	0.018	0.1876	-0.0505	0.0543	54.063	-30.103	-155.478
16	0.5901	0.088	0.0532	0.5368	-0.021	0.4935	-0.0164	0.0674	-0.0193	-0.0201	0.0094	-0.0744	0.0261	0.202	0.007	0.0684	0.0191	-0.002	0.1103	0.0024	0.0752	59.061	-29.139	-127.247
17	3.0266	1.0257	-1.9676	1.5991	-2.1647	14.1766	-0.2201	0.5676	-0.057	-0.1311	0.1433	0.1157	0.2683	-0.9177	0.0768	0.1223	-0.0215	-0.015	0.146	-0.0261	0.0902	25.487	-47.822	-149.397
18	0.4512	0.0223	0.0479	0.4143	0.0131	0.5848	0.0045	0.0271	-0.0983	0.0009	0.0142	-0.0216	0.1883	0.0507	-0.0186	0.1322	0.0028	0.0056	0.035	0.0177	0.0751	36.808	-47.443	-123.671
19	1.5265	0.3184	-0.5187	2.557	5.2314	12.2765	-0.1357	0.0535	0.1842	-0.4342	-0.2296	0.3142	-0.7822	-0.7132	0.3653	0.1226	0.069	-0.0501	0.1971	0.0153	0.1199	1.134	-25.387	-140.382
20	0.4519	0.0595	0.0122	0.5636	0.0097	0.7841	-0.0041	-0.04	-0.058	0.0505	-0.0015	0.0809	0.078	-0.2159	0.0057	0.0536	-0.0049	0.039	0.0832	0.0228	0.0571	13.758	-32.922	-115.452
21	5.2441	0.9021	6.3138	4.3926	4.2182	13.8521	0.1925	-0.1312	-0.2083	0.5305	0.0475	-0.0538	0.6608	-0.4474	-0.24	0.1341	0.005	0.0536	0.1495	-0.0026	0.0684	-37.25	19.313	-31.165
22	0.3411	0.0193	0.0416	0.5037	0.1025	0.8326	0.0208	-0.0634	0.0586	-0.0218	-0.0545	0.0607	-0.2421	-0.2858	0.0338	0.1164	0.082	-0.0051	0.1076	-0.0288	0.0517	-38.825	27.665	-58.745
23	1.3658	0.837	-0.4484	1.1383	2.4537	12.6058	0.0724	-0.0626	-0.1545	0.0895	0.0403	-0.136	0.4577	0.137	-0.1127	0.2755	-0.056	0.01	0.1458	0.0462	0.1132	-30.575	-12.496	-42.092
24	0.3936	-0.0426	0.036	0.3792	0.0753	0.6898	0.0009	-0.0549	-0.0141	-0.0118	-0.023	0.0721	0.06	-0.2335	0.0221	0.0783	-0.015	-0.0045	0.0938	-0.0194	0.0514	-37.134	-0.015	-66.046
25	3.9444	1.4135	1.5374	2.9867	-3.5032	10.7811	0.1541	-0.4417	-0.012	0.2408	-0.6444	-0.247	0.1189	1.1666	0.4904	0.1524	0.0252	0.0153	0.2382	0.0546	0.0847	3.173	-12.7	-51.741
26	0.3171	0.0209	0.0004	0.4326	0.0809	0.5434	0.0127	-0.0038	-0.047	-0.068	-0.0272	-0.0459	0.143	0.0287	0.0146	0.1235	0.0089	0.0246	0.0382	-0.0029	0.0478	-10.626	-5.324	-74.958
27	1.5735	-0.9433	1.9923	2.4441	-2.1935	5.3297	-0.0682	-0.0424	0.1696	-0.0251	-0.1229	-0.3088	-0.3585	0.4102	0.191	0.1188	-0.072	0.0656	0.1473	-0.0085	0.1842	11.166	25.632	-66.226
28	0.3693	-0.0571	-0.0774	0.4893	-0.0083	0.8002	0.0078	-0.0097	-0.0212	-0.0826	-0.0167	-0.1257	-0.0862	0.1912	0.0089	0.1116	-0.0313	0.0448	0.077	0.0085	0.0813	3.921	17.928	-72.739
29	8.8128	-2.5638	4.0214	2.886	-3.0086	5.8989	-0.2471	-0.9229	-0.2291	0.139	0.2627	-0.0029	-0.3032	-0.569	-0.0157	0.1934	0.0001	0.0027	0.1341	-0.0077	0.0504	-9.512	38.451	-35.637
30	0.4829	-0.0322	0.032	0.5021	0.0643	0.8425	0.0143	-0.0532	0.0571	-0.1029	-0.0245	-0.0574	-0.3515	0.0401	0.0101	0.2273	-0.0061	0.0354	0.0114	0.0011	0.0253	-12.768	39.594	-63.165
31	0.7003	-0.3875	0.6467	0.7996	0.195	6.1111	0.0694	-0.0758	-0.0764	0.0874	-0.0366	0.0454	0.4836	-0.1579	-0.0328	0.1324	-0.0801	0.0208	0.1582	0.0279	0.1868	0.724	-38.886	-180.79
32	0.4662	-0.071	0.0261	0.4507	0.0622	0.3999	-0.0008	-0.0367	-0.0411	0.0564	0.0048	0.0851	0.0736	-0.116	-0.004	0.0366	-0.0356	-0.0037	0.1125	0.0025	0.0828	-1.535	-27.375	-185.549
33	3.2953	1.055	-4.9873	3.136	-3.1726	14.2044	0.1373	-0.1808	-0.0455	0.2674	-0.1053	-0.2337	0.0888	0.8182	-0.0319	0.1564	0.0149	-0.0295	0.1494	0.0334	0.1264	39.057	-40.654	-169.846
34	0.4379	0.1176	0.0289	0.5358	-0.0242	0.5394	0.0172	-0.0122	-0.0959	-0.0222	-0.0221	-0.0218	0.1406	0.0335	0.0049	0.0545	0.0048	-0.0009	0.0998	-0.0074	0.0617	25.275	-34.583	-194.967
35	0.8722	-0.5017	0.9605	1.5669	-1.5416	3.9176	-0.0782	-0.0362	0.0513	0.1203	-0.0761	-0.1425	-0.221	0.2458	0.1543	0.0476	-0.0427	0.0107	0.1864	0.0137	0.1383	47.105	-3.135	-188.453
36	0.3252	-0.0329	0.0451	0.5021	-0.0612	0.5619	0.0041	0.0266	-0.0234	-0.0114	-0.0128	-0.0858	0.0442	0.1384	0.0087	0.0294	-0.02	0.0161	0.1327	0.0152	0.0735	39.981	-11.356	-194.413
37	10.6053	-2.2444	6.2464	3.202	-2.4601	8.5241	-0.2925	-1.0572	0.0024	0.2907	0.2517	0.1095	-0.6031	-0.5672	0.0407	0.2025	-0.0077	0.034	0.118	-0.0207	0.0831	27.496	12.011	-158.156
38	0.4747	0.0407	0.0475	0.3337	-0.0927	0.4718	-0.0172	0.0021	0.0693	0.0102	-0.0039	-0.0202	-0.1398	0.0559	0.0211	0.062	-0.0201	0.0001	0.0563	0.0204	0.0574	22.868	11.178	-186.958
39	2.0093	0.9628	4.3544	4.0398	2.9569	10.357	0.312	-0.4055	-0.1385	0.5214	-0.2284	-0.1303	0.893	-0.5781	-0.0835	0.1422	-0.0457	0.0594	0.2742	0.0714	0.1554	-1.997	-7.004	-154.362
40	0.3097	-0.0106	0.0526	0.5056	0.0513	0.6194	0.0022	-0.0273	0.0587	0.0519	-0.0214	0.0776	-0.0841	-0.1374	0.0193	0.0198	0.015	0.0088	0.1024	0.0153	0.0742	-2.884	0.029	-181.318

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	40 - 77
2	X-RAY DIFFRACTION	2	A	78 - 319
3	X-RAY DIFFRACTION	3	B	41 - 73
4	X-RAY DIFFRACTION	4	B	74 - 319
5	X-RAY DIFFRACTION	5	C	40 - 56
6	X-RAY DIFFRACTION	6	C	57 - 319
7	X-RAY DIFFRACTION	7	D	40 - 57
8	X-RAY DIFFRACTION	8	D	58 - 319
9	X-RAY DIFFRACTION	9	E	40 - 77
10	X-RAY DIFFRACTION	10	E	78 - 319
11	X-RAY DIFFRACTION	11	F	40 - 57
12	X-RAY DIFFRACTION	12	F	58 - 319
13	X-RAY DIFFRACTION	13	G	41 - 70
14	X-RAY DIFFRACTION	14	G	71 - 319
15	X-RAY DIFFRACTION	15	H	40 - 56
16	X-RAY DIFFRACTION	16	H	57 - 319
17	X-RAY DIFFRACTION	17	I	40 - 57
18	X-RAY DIFFRACTION	18	I	58 - 319
19	X-RAY DIFFRACTION	19	J	41 - 56
20	X-RAY DIFFRACTION	20	J	57 - 319
21	X-RAY DIFFRACTION	21	K	40 - 56
22	X-RAY DIFFRACTION	22	K	57 - 319
23	X-RAY DIFFRACTION	23	L	40 - 57
24	X-RAY DIFFRACTION	24	L	58 - 319
25	X-RAY DIFFRACTION	25	M	41 - 57
26	X-RAY DIFFRACTION	26	M	58 - 319
27	X-RAY DIFFRACTION	27	N	40 - 78
28	X-RAY DIFFRACTION	28	N	79 - 319
29	X-RAY DIFFRACTION	29	O	41 - 57
30	X-RAY DIFFRACTION	30	O	58 - 319
31	X-RAY DIFFRACTION	31	P	40 - 77
32	X-RAY DIFFRACTION	32	P	78 - 319
33	X-RAY DIFFRACTION	33	Q	41 - 56
34	X-RAY DIFFRACTION	34	Q	57 - 319
35	X-RAY DIFFRACTION	35	R	40 - 78
36	X-RAY DIFFRACTION	36	R	79 - 319
37	X-RAY DIFFRACTION	37	S	40 - 56
38	X-RAY DIFFRACTION	38	S	57 - 319
39	X-RAY DIFFRACTION	39	T	41 - 57
40	X-RAY DIFFRACTION	40	T	58 - 319

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Yorodumi