PDB-4fmj: Merkel cell polyomavirus VP1 in complex with GD1a oligosaccharide

ID or keywords:

Entry

Database: PDB / ID: 4fmj

Title

Merkel cell polyomavirus VP1 in complex with GD1a oligosaccharide

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: 2.4 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 2.0	Jul 29, 2020	Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details Description: Carbohydrate remediation / Provider: repository / Type: Remediation

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4fmj.cif.gz	2 MB	Display	PDBx/mmCIF format
PDB format	pdb4fmj.ent.gz	1.7 MB	Display	PDB format
PDBx/mmJSON format	4fmj.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/4fmj ftp://data.pdbj.org/pub/pdb/validation_reports/fm/4fmj	HTTPS FTP

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Related structure data

Related structure data	4fmgC 4fmhC 4fmiC C: citing same article (ref.)
Similar structure data	4fmh-2 4fmi-2 4fmh-3 4fmh-1 4fmi-1 4fmi-4 6y5x-1 4fmi-3 6y67-3 4fmg-2 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

4fmgC

4fmhC

4fmiC

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) #113 - May 2009 Influenza Neuraminidase 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

643 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
160 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
160 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
162 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
162 kDa, 5 polymers
Search similar-shape structures of this assembly by Omokage search (details)

5

K: VP1

L: VP1

M: VP1

N: VP1

O: VP1

hetero molecules

A: VP1

B: VP1

C: VP1

D: VP1

E: VP1

hetero molecules

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

6

P: VP1

Q: VP1

R: VP1

S: VP1

T: VP1

hetero molecules

F: VP1

G: VP1

H: VP1

I: VP1

J: VP1

hetero molecules

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

Unit cell

Length a, b, c (Å)	84.660, 130.150, 165.530
Angle α, β, γ (deg.)	98.04, 101.02, 105.81
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	227 - 238
2	9	1	5	B	227 - 238
3	9	1	5	C	227 - 238
4	9	1	5	D	227 - 238
5	9	1	5	E	227 - 238
6	9	1	5	F	227 - 238
7	9	1	5	G	227 - 238
8	9	1	5	H	227 - 238
9	9	1	5	I	227 - 238
10	9	1	5	J	227 - 238
11	9	1	5	K	227 - 238
12	9	1	5	L	227 - 238
13	9	1	5	M	227 - 238
14	9	1	5	N	227 - 238
15	9	1	5	O	227 - 238
16	9	1	5	P	227 - 238
17	9	1	5	Q	227 - 238
18	9	1	5	R	227 - 238
19	9	1	5	S	227 - 238
20	9	1	5	T	227 - 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 - 196
2	13	1	5	B	190 - 196
3	13	1	5	C	190 - 196
4	13	1	5	D	190 - 196
5	13	1	5	E	190 - 196
6	13	1	5	F	190 - 196
7	13	1	5	G	190 - 196
8	13	1	5	H	190 - 196
9	13	1	5	I	190 - 196
10	13	1	5	J	190 - 196
11	13	1	5	K	190 - 196
12	13	1	5	L	190 - 196
13	13	1	5	M	190 - 196
14	13	1	5	N	190 - 196
15	13	1	5	O	190 - 196
16	13	1	5	P	190 - 196
17	13	1	5	Q	190 - 196
18	13	1	5	R	190 - 196
19	13	1	5	S	190 - 196
20	13	1	5	T	190 - 196
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	16	1	5	A	42 - 44
2	16	1	5	B	42 - 44
3	16	1	5	C	42 - 44
4	16	1	5	D	42 - 44
5	16	1	5	E	42 - 44
6	16	1	5	F	42 - 44
7	16	1	5	G	42 - 44
8	16	1	5	H	42 - 44
9	16	1	5	I	42 - 44
10	16	1	5	J	42 - 44
11	16	1	5	K	42 - 44
12	16	1	5	L	42 - 44
13	16	1	5	M	42 - 44
14	16	1	5	N	42 - 44
15	16	1	5	O	42 - 44
16	16	1	5	P	42 - 44
17	16	1	5	Q	42 - 44
18	16	1	5	R	42 - 44
19	16	1	5	S	42 - 44
20	16	1	5	T	42 - 44

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Protein , 1 types, 20 molecules ABCDEFGHIJKLMNOPQRST

#1: Protein	VP1 Mass: 31927.154 Da / Num. of mol.: 20 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

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Sugars , 2 types, 7 molecules

#2: Polysaccharide

N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose

Type: oligosaccharide / Mass: 471.411 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source

Descriptor	Type	Program
DNeup5Aca2-3DGalpb1-ROH	Glycam Condensed Sequence	GMML 1.0
WURCS=2.0/2,2,1/[a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O]/1-2/a3-b2	WURCS	PDB2Glycan 1.1.0
[][b-D-Galp]{[(3+2)][a-D-Neup5Ac]{}}	LINUCS	PDB-CARE

#5: Sugar

ChemComp-SIA / N-acetyl-alpha-neuraminic acid

Type: D-saccharide, alpha linking / Mass: 309.270 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C₁₁H₁₉NO₉

Identifier	Type	Program
DNeup5Aca	CONDENSED IUPAC CARBOHYDRATE SYMBOL	GMML 1.0
N-acetyl-a-D-neuraminic acid	COMMON NAME	GMML 1.0
a-D-Neup5Ac	IUPAC CARBOHYDRATE SYMBOL	PDB-CARE 1.0
Neu5Ac	SNFG CARBOHYDRATE SYMBOL	GMML 1.0

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Non-polymers , 3 types, 1596 molecules

#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: Cl
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1568 / 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: 2.64 Å³/Da / Density % sol: 53.43 % 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, soaked in 25 mM GD1a oligosaccharide, 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: SLS / Beamline: X06SA / Wavelength: 1 Å
Detector	Type: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 10, 2010
Radiation	Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.4→50 Å / Num. all: 255632 / Num. obs: 248679 / % possible obs: 97.3 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / R_merge(I) obs: 0.101 / Net I/σ(I): 8.74
Reflection shell	Resolution: 2.4→2.46 Å / Redundancy: 3.7 % / R_merge(I) obs: 0.666 / Mean I/σ(I) obs: 2.07 / % possible all: 96.8

-
Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.4→50 Å / Cor.coef. F_o:F_c: 0.959 / Cor.coef. F_o:F_c free: 0.928 / SU B: 17.178 / SU ML: 0.2 / Cross valid method: THROUGHOUT / ESU R: 0.388 / ESU R Free: 0.258 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: THE BINDING SITE IN CHAIN B CONTAINS ONLY VERY WEAK ELECTRON DENSITY FEATURES FOR THE LIGAND. RESIDUES 71 AND 72 ADOPT MULTIPLE CONFORMATIONS IN THE STRUCTURE.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.24623	6193	2.5 %	RANDOM
R_work	0.19162	-	-	-
obs	0.19297	242479	97.33 %	-

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: 38.97 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	2.61 Å²	-1.06 Å²	0.17 Å²
2-	-	-2.22 Å²	-1.14 Å²
3-	-	-	-1.21 Å²

Refinement step

Cycle: LAST / Resolution: 2.4→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	42561	0	281	1568	44410

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.022	43902
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.112	1.979	59833
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.75	5	5417
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.002	25.05	1818
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.917	15	7263
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.605	15	160
X-RAY DIFFRACTION	r_chiral_restr	0.073	0.2	6771
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.021	32939
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	1.105	3	27178
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	2.076	5	44288
X-RAY DIFFRACTION	r_scbond_it	2.755	7	16724
X-RAY DIFFRACTION	r_scangle_it	4.231	9	15534
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	456	medium positional	0.11	0.5
2	B	456	medium positional	0.12	0.5
3	C	456	medium positional	0.13	0.5
4	D	456	medium positional	0.11	0.5
5	E	456	medium positional	0.12	0.5
6	F	456	medium positional	0.12	0.5
7	G	456	medium positional	0.12	0.5
8	H	456	medium positional	0.11	0.5
9	I	456	medium positional	0.14	0.5
10	J	456	medium positional	0.11	0.5
11	K	456	medium positional	0.1	0.5
12	L	456	medium positional	0.1	0.5
13	M	456	medium positional	0.11	0.5
14	N	456	medium positional	0.11	0.5
15	O	456	medium positional	0.11	0.5
16	P	456	medium positional	0.1	0.5
17	Q	456	medium positional	0.12	0.5
18	R	456	medium positional	0.11	0.5
19	S	456	medium positional	0.11	0.5
20	T	456	medium positional	0.11	0.5
1	A	404	loose positional	0.16	5
2	B	404	loose positional	0.18	5
3	C	404	loose positional	0.19	5
4	D	404	loose positional	0.16	5
5	E	404	loose positional	0.17	5
6	F	404	loose positional	0.16	5
7	G	404	loose positional	0.15	5
8	H	404	loose positional	0.2	5
9	I	404	loose positional	0.18	5
10	J	404	loose positional	0.16	5
11	K	404	loose positional	0.16	5
12	L	404	loose positional	0.17	5
13	M	404	loose positional	0.18	5
14	N	404	loose positional	0.15	5
15	O	404	loose positional	0.15	5
16	P	404	loose positional	0.18	5
17	Q	404	loose positional	0.18	5
18	R	404	loose positional	0.16	5
19	S	404	loose positional	0.17	5
20	T	404	loose positional	0.16	5
1	A	456	medium thermal	0.51	2
2	B	456	medium thermal	0.54	2
3	C	456	medium thermal	0.56	2
4	D	456	medium thermal	0.61	2
5	E	456	medium thermal	0.5	2
6	F	456	medium thermal	0.55	2
7	G	456	medium thermal	0.46	2
8	H	456	medium thermal	0.65	2
9	I	456	medium thermal	0.7	2
10	J	456	medium thermal	0.44	2
11	K	456	medium thermal	0.6	2
12	L	456	medium thermal	0.71	2
13	M	456	medium thermal	0.8	2
14	N	456	medium thermal	0.86	2
15	O	456	medium thermal	0.61	2
16	P	456	medium thermal	0.56	2
17	Q	456	medium thermal	0.55	2
18	R	456	medium thermal	0.49	2
19	S	456	medium thermal	0.54	2
20	T	456	medium thermal	0.59	2
1	A	404	loose thermal	0.53	10
2	B	404	loose thermal	0.61	10
3	C	404	loose thermal	0.65	10
4	D	404	loose thermal	0.65	10
5	E	404	loose thermal	0.67	10
6	F	404	loose thermal	0.61	10
7	G	404	loose thermal	0.58	10
8	H	404	loose thermal	0.66	10
9	I	404	loose thermal	0.66	10
10	J	404	loose thermal	0.48	10
11	K	404	loose thermal	0.62	10
12	L	404	loose thermal	0.66	10
13	M	404	loose thermal	0.72	10
14	N	404	loose thermal	0.82	10
15	O	404	loose thermal	0.62	10
16	P	404	loose thermal	0.61	10
17	Q	404	loose thermal	0.63	10
18	R	404	loose thermal	0.54	10
19	S	404	loose thermal	0.58	10
20	T	404	loose thermal	0.64	10

LS refinement shell

Resolution: 2.4→2.462 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.333	476	-
R_work	0.272	17730	-
obs	-	-	96.79 %

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	0.0952	0.1563	0.0976	0.7219	0.2072	0.1987	-0.1105	0.0439	-0.0299	-0.426	0.167	-0.1367	-0.1051	0.0656	-0.0566	0.281	-0.0864	0.1004	0.0745	-0.0343	0.0987	72.656	50.143	33.303
2	0.0602	-0.0146	0.053	0.7472	0.2594	0.3526	-0.0595	-0.017	-0.0063	-0.3769	0.0167	0.1997	-0.127	-0.0334	0.0428	0.2908	-0.0127	-0.103	0.0491	0.0118	0.0994	44.362	59.036	34.166
3	0.0875	0.0254	0.0465	0.7031	0.175	0.3473	-0.0106	-0.0119	0.0231	0.0366	-0.0688	0.2502	0.0236	-0.0823	0.0795	0.0065	-0.0124	0.0251	0.0984	-0.0341	0.239	33.269	50.835	60.833
4	0.244	0.123	0.0633	0.8664	0.2007	0.3789	0.0108	-0.0019	0.0221	0.2099	-0.0306	0.0204	0.1537	-0.0347	0.0197	0.0973	-0.0059	0.0271	0.056	0.0095	0.092	55.209	37.226	75.647
5	0.1276	0.1642	0.0729	0.8816	0.1086	0.354	-0.02	0.0195	-0.0534	-0.0287	0.1122	-0.2179	0.0522	0.0614	-0.0923	0.0409	0.0308	0.0287	0.0736	-0.0445	0.1613	79.365	37.12	58.845
6	0.1317	-0.0015	0.0076	0.388	0.2821	0.5626	-0.0399	0.0338	-0.0348	0.1076	0.1487	-0.1285	0.1809	0.1528	-0.1088	0.1945	0.0612	0.0021	0.0843	-0.0381	0.1192	106.066	20.613	139.668
7	0.1253	0.0566	-0.0497	0.4847	0.2157	0.4512	-0.1059	0.0255	-0.0379	-0.22	0.1424	-0.0739	-0.0989	0.0771	-0.0365	0.1756	-0.0506	0.057	0.0895	-0.0406	0.085	100.445	33.097	113.524
8	0.0505	0.1192	0.0937	0.4769	0.3165	0.7333	-0.0678	-0.0113	0.0165	-0.1733	-0.0617	0.1778	-0.1781	-0.1256	0.1295	0.1595	0.0155	-0.0618	0.092	-0.0237	0.1183	72.213	42.204	113.258
9	0.0558	0.0311	-0.0996	0.4736	0.3814	0.7288	-0.0062	0.0153	0.0261	0.2118	-0.1728	0.22	0.1597	-0.2889	0.1789	0.1264	-0.0477	0.088	0.1633	-0.081	0.212	60.401	33.877	139.185
10	0.1471	0.0695	0.0736	0.4938	0.2281	0.5355	-0.0341	-0.0116	0.0095	0.3041	-0.0415	0.0328	0.2912	-0.0586	0.0755	0.3527	-0.0284	0.0771	0.0353	-0.0092	0.0789	81.14	20.969	155.382
11	0.2592	0.0727	-0.0186	0.604	0.2596	0.3523	0.0064	-0.0091	-0.005	0.1691	0.0473	-0.1062	0.0814	0.0642	-0.0536	0.0539	0.0327	-0.043	0.1159	-0.0061	0.0868	45.08	-28.774	92.361
12	0.1579	0.0663	0.0496	0.488	0.0764	0.4167	0.0264	-0.0044	0.0138	0.1931	-0.0324	0.0878	0.0549	0.0196	0.0059	0.0889	0.0075	0.0259	0.0779	0.0002	0.0709	17.387	-24.099	101.701
13	0.2176	0.0697	-0.0626	0.4412	0.1475	0.5367	0.0178	0.0179	0.015	0.0048	-0.0278	0.0946	-0.047	-0.0535	0.01	0.0172	0.0327	-0.0064	0.0789	-0.0021	0.1186	2.804	-10.108	80.277
14	0.1698	0.0386	0.0386	0.4733	0.1219	0.3853	0.0078	0.0202	0.0028	-0.1864	0.026	-0.0232	-0.1064	0.025	-0.0338	0.1072	0.0147	0.0041	0.0555	0.0179	0.0705	20.834	-6.608	57.143
15	0.1881	0.1644	-0.0406	0.4351	0.1275	0.3802	-0.0051	-0.0106	-0.0028	-0.0822	0.0491	-0.1311	0.0158	0.0851	-0.044	0.034	-0.0059	0.0427	0.1032	-0.0123	0.1253	47.39	-17.737	64.945
16	0.1248	-0.0291	0.0869	0.483	0.2648	0.7777	0.0103	0.004	0.0017	0.1293	-0.0442	0.0802	0.0849	-0.0245	0.0338	0.0948	-0.0032	0.0208	0.0728	-0.0111	0.0751	-10.167	-7.09	21.96
17	0.188	0.0472	-0.0655	0.5922	0.3019	0.5388	0.0479	0.0036	-0.0253	-0.1556	-0.143	0.156	-0.1923	-0.1266	0.095	0.0925	0.0683	-0.0325	0.0989	-0.054	0.1316	-23.925	6.521	-0.268
18	0.1482	0.1133	0.0953	0.4899	0.2184	0.6111	0.0333	0.0191	-0.0062	-0.2816	0.0153	0.0008	-0.2688	0.0382	-0.0486	0.3304	0.0211	0.0048	0.0391	0.0061	0.0438	-4.885	9.969	-22.652
19	0.1606	0.0769	-0.0734	0.2436	0.2141	0.476	-0.006	-0.0204	-0.0331	-0.1531	0.12	-0.1259	-0.1034	0.215	-0.114	0.1565	-0.0491	0.0798	0.1511	-0.0493	0.117	21.243	-0.784	-13.488
20	0.1774	0.0975	-0.0108	0.6514	0.2445	0.7611	0.0006	-0.0049	0.0102	0.1247	0.1037	-0.1026	0.1598	0.2094	-0.1042	0.0455	0.062	-0.0359	0.1538	-0.0383	0.092	17.752	-11.635	13.728

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	41 - 319
2	X-RAY DIFFRACTION	2	B	40 - 319
3	X-RAY DIFFRACTION	3	C	41 - 319
4	X-RAY DIFFRACTION	4	D	40 - 319
5	X-RAY DIFFRACTION	5	E	40 - 319
6	X-RAY DIFFRACTION	6	F	40 - 319
7	X-RAY DIFFRACTION	7	G	41 - 319
8	X-RAY DIFFRACTION	8	H	40 - 319
9	X-RAY DIFFRACTION	9	I	40 - 319
10	X-RAY DIFFRACTION	10	J	41 - 319
11	X-RAY DIFFRACTION	11	K	40 - 319
12	X-RAY DIFFRACTION	12	L	40 - 319
13	X-RAY DIFFRACTION	13	M	40 - 319
14	X-RAY DIFFRACTION	14	N	40 - 320
15	X-RAY DIFFRACTION	15	O	40 - 319
16	X-RAY DIFFRACTION	16	P	40 - 319
17	X-RAY DIFFRACTION	17	Q	40 - 319
18	X-RAY DIFFRACTION	18	R	41 - 319
19	X-RAY DIFFRACTION	19	S	41 - 319
20	X-RAY DIFFRACTION	20	T	40 - 319

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