PDB-2vza: Type IV secretion system effector protein BepA

ID or keywords:

Entry

Database: PDB / ID: 2vza

Title

Type IV secretion system effector protein BepA

Components

CELL FILAMENTATION PROTEIN

Keywords

CELL ADHESION / T4SS / OB FOLD / FIC DOMAIN / SUBSTRATE PROTEIN / PROTEIN TRANSLOCATION

Function / homology

Function and homology information

protein adenylylation / AMPylase activity / protein adenylyltransferase / symbiont-mediated suppression of host apoptosis / regulation of cell division / extracellular region / ATP binding
Similarity search - Function

Biological species

BARTONELLA HENSELAE (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.05 Å

Authors

Meury, M. / Schirmer, T.

Citation

Journal: Protein Sci. / Year: 2011
Title: Fic Domain Catalyzed Adenylylation: Insight Provided by the Structural Analysis of the Type Iv Secretion System Effector Bepa.
Authors: Palanivelu, D.V. / Goepfert, A. / Meury, M. / Guye, P. / Dehio, C. / Schirmer, T.

History

Deposition	Jul 31, 2008	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Nov 17, 2009	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Oct 26, 2011	Group: Database references / Other
Revision 1.3	Dec 13, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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	2vza.cif.gz	458.5 KB	Display	PDBx/mmCIF format
PDB format	pdb2vza.ent.gz	376.3 KB	Display	PDB format
PDBx/mmJSON format	2vza.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/vz/2vza ftp://data.pdbj.org/pub/pdb/validation_reports/vz/2vza	HTTPS FTP

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Related structure data

Related structure data	2jk8C 2vy3SC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4fdu-1 5eko-d 1gyr-1 5cx4-2 2vy3-1 4eyj-d 6jfn-d 4hn2-d 3itz-d 3k2i-1 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) 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

2jk8C

2vy3SC

S: Starting model for refinement

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: CELL FILAMENTATION PROTEIN

B: CELL FILAMENTATION PROTEIN

C: CELL FILAMENTATION PROTEIN

D: CELL FILAMENTATION PROTEIN

E: CELL FILAMENTATION PROTEIN

F: CELL FILAMENTATION PROTEIN

G: CELL FILAMENTATION PROTEIN

H: CELL FILAMENTATION PROTEIN

hetero molecules

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

1

A: CELL FILAMENTATION PROTEIN

hetero molecules

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

2

B: CELL FILAMENTATION PROTEIN

hetero molecules

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

3

C: CELL FILAMENTATION PROTEIN

hetero molecules

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

4

D: CELL FILAMENTATION PROTEIN

hetero molecules

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

5

E: CELL FILAMENTATION PROTEIN

hetero molecules

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

6

F: CELL FILAMENTATION PROTEIN

hetero molecules

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

7

G: CELL FILAMENTATION PROTEIN

hetero molecules

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

8

H: CELL FILAMENTATION PROTEIN

hetero molecules

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

Unit cell

Length a, b, c (Å)	229.902, 229.902, 308.994
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	155
Space group name H-M	H32

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Refine code: 1

Dom-ID	Component-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	1	THR	THR	PRO	PRO	A	A	11 - 16	3 - 8
2	1	1	THR	THR	PRO	PRO	B	B	11 - 16	3 - 8
3	1	1	THR	THR	PRO	PRO	C	C	11 - 16	3 - 8
4	1	1	THR	THR	PRO	PRO	D	D	11 - 16	3 - 8
5	1	1	THR	THR	PRO	PRO	E	E	11 - 16	3 - 8
6	1	1	THR	THR	PRO	PRO	F	F	11 - 16	3 - 8
7	1	1	THR	THR	PRO	PRO	G	G	11 - 16	3 - 8
8	1	1	THR	THR	PRO	PRO	H	H	11 - 16	3 - 8
1	2	1	HIS	HIS	ASN	ASN	A	A	18 - 37	10 - 29
2	2	1	HIS	HIS	ASN	ASN	B	B	18 - 37	10 - 29
3	2	1	HIS	HIS	ASN	ASN	C	C	18 - 37	10 - 29
4	2	1	HIS	HIS	ASN	ASN	D	D	18 - 37	10 - 29
5	2	1	HIS	HIS	ASN	ASN	E	E	18 - 37	10 - 29
6	2	1	HIS	HIS	ASN	ASN	F	F	18 - 37	10 - 29
7	2	1	HIS	HIS	ASN	ASN	G	G	18 - 37	10 - 29
8	2	1	HIS	HIS	ASN	ASN	H	H	18 - 37	10 - 29
1	3	1	LEU	LEU	LYS	LYS	A	A	75 - 105	67 - 97
2	3	1	LEU	LEU	LYS	LYS	B	B	75 - 105	67 - 97
3	3	1	LEU	LEU	LYS	LYS	C	C	75 - 105	67 - 97
4	3	1	LEU	LEU	LYS	LYS	D	D	75 - 105	67 - 97
5	3	1	LEU	LEU	LYS	LYS	E	E	75 - 105	67 - 97
6	3	1	LEU	LEU	LYS	LYS	F	F	75 - 105	67 - 97
7	3	1	LEU	LEU	LYS	LYS	G	G	75 - 105	67 - 97
8	3	1	LEU	LEU	LYS	LYS	H	H	75 - 105	67 - 97
1	1	2	ALA	ALA	GLN	GLN	A	A	38 - 74	30 - 66
2	1	2	ALA	ALA	GLN	GLN	B	B	38 - 74	30 - 66
3	1	2	ALA	ALA	GLN	GLN	C	C	38 - 74	30 - 66
4	1	2	ALA	ALA	GLN	GLN	D	D	38 - 74	30 - 66
5	1	2	ALA	ALA	GLN	GLN	E	E	38 - 74	30 - 66
6	1	2	ALA	ALA	GLN	GLN	F	F	38 - 74	30 - 66
7	1	2	ALA	ALA	GLN	GLN	G	G	38 - 74	30 - 66
8	1	2	ALA	ALA	GLN	GLN	H	H	38 - 74	30 - 66
1	1	3	ALA	ALA	PRO	PRO	A	A	112 - 160	104 - 152
2	1	3	ALA	ALA	PRO	PRO	B	B	112 - 160	104 - 152
3	1	3	ALA	ALA	PRO	PRO	C	C	112 - 160	104 - 152
4	1	3	ALA	ALA	PRO	PRO	D	D	112 - 160	104 - 152
5	1	3	ALA	ALA	PRO	PRO	E	E	112 - 160	104 - 152
6	1	3	ALA	ALA	PRO	PRO	F	F	112 - 160	104 - 152
7	1	3	ALA	ALA	PRO	PRO	G	G	112 - 160	104 - 152
8	1	3	ALA	ALA	PRO	PRO	H	H	112 - 160	104 - 152
1	2	3	PHE	PHE	GLY	GLY	A	A	161 - 166	153 - 158
2	2	3	PHE	PHE	GLY	GLY	B	B	161 - 166	153 - 158
3	2	3	PHE	PHE	GLY	GLY	C	C	161 - 166	153 - 158
4	2	3	PHE	PHE	GLY	GLY	D	D	161 - 166	153 - 158
5	2	3	PHE	PHE	GLY	GLY	E	E	161 - 166	153 - 158
6	2	3	PHE	PHE	GLY	GLY	F	F	161 - 166	153 - 158
7	2	3	PHE	PHE	GLY	GLY	G	G	161 - 166	153 - 158
8	2	3	PHE	PHE	GLY	GLY	H	H	161 - 166	153 - 158
1	3	3	THR	THR	HIS	HIS	A	A	168 - 182	160 - 174
2	3	3	THR	THR	HIS	HIS	B	B	168 - 182	160 - 174
3	3	3	THR	THR	HIS	HIS	C	C	168 - 182	160 - 174
4	3	3	THR	THR	HIS	HIS	D	D	168 - 182	160 - 174
5	3	3	THR	THR	HIS	HIS	E	E	168 - 182	160 - 174
6	3	3	THR	THR	HIS	HIS	F	F	168 - 182	160 - 174
7	3	3	THR	THR	HIS	HIS	G	G	168 - 182	160 - 174
8	3	3	THR	THR	HIS	HIS	H	H	168 - 182	160 - 174
1	4	3	GLN	GLN	MET	MET	A	A	183 - 233	175 - 225
2	4	3	GLN	GLN	MET	MET	B	B	183 - 233	175 - 225
3	4	3	GLN	GLN	MET	MET	C	C	183 - 233	175 - 225
4	4	3	GLN	GLN	MET	MET	D	D	183 - 233	175 - 225
5	4	3	GLN	GLN	MET	MET	E	E	183 - 233	175 - 225
6	4	3	GLN	GLN	MET	MET	F	F	183 - 233	175 - 225
7	4	3	GLN	GLN	MET	MET	G	G	183 - 233	175 - 225
8	4	3	GLN	GLN	MET	MET	H	H	183 - 233	175 - 225
1	1	4	VAL	VAL	VAL	VAL	A	A	240 - 247	232 - 239
2	1	4	VAL	VAL	VAL	VAL	B	B	240 - 247	232 - 239
3	1	4	VAL	VAL	VAL	VAL	C	C	240 - 247	232 - 239
4	1	4	VAL	VAL	VAL	VAL	D	D	240 - 247	232 - 239
5	1	4	VAL	VAL	VAL	VAL	E	E	240 - 247	232 - 239
6	1	4	VAL	VAL	VAL	VAL	F	F	240 - 247	232 - 239
7	1	4	VAL	VAL	VAL	VAL	G	G	240 - 247	232 - 239
8	1	4	VAL	VAL	VAL	VAL	H	H	240 - 247	232 - 239
1	2	4	ALA	ALA	HIS	HIS	A	A	248 - 306	240 - 298
2	2	4	ALA	ALA	HIS	HIS	B	B	248 - 306	240 - 298
3	2	4	ALA	ALA	HIS	HIS	C	C	248 - 306	240 - 298
4	2	4	ALA	ALA	HIS	HIS	D	D	248 - 306	240 - 298
5	2	4	ALA	ALA	HIS	HIS	E	E	248 - 306	240 - 298
6	2	4	ALA	ALA	HIS	HIS	F	F	248 - 306	240 - 298
7	2	4	ALA	ALA	HIS	HIS	G	G	248 - 306	240 - 298
8	2	4	ALA	ALA	HIS	HIS	H	H	248 - 306	240 - 298

NCS ensembles :

ID
1
2
3
4

NCS oper:

ID	Code	Matrix	Vector
1	given	(0.992557, 0.117928, 0.030391), (0.118415, -0.992854, -0.014775), (0.028432, 0.018264, -0.999429)	-9.287, 133.6263, 127.9978
2	given	(0.188564, -0.899338, 0.394506), (-0.07614, -0.413892, -0.907136), (0.979105, 0.141015, -0.14652)	29.9693, 177.3464, 60.7275
3	given	(-0.382974, -0.527779, -0.758143), (-0.855425, -0.107166, 0.506719), (-0.348683, 0.842594, -0.410433)	107.0033, 11.6916, 46.1396
4	given	(-0.433856, -0.535946, -0.724245), (-0.825809, -0.0849, 0.557523), (-0.360291, 0.839973, -0.405755)	102.3143, 7.3174, -32.6353
5	given	(-0.475725, -0.496042, -0.726381), (0.804219, 0.089183, -0.587605), (0.356257, -0.863707, 0.356499)	93.7869, 129.9321, 89.1448
6	given	(0.536022, 0.368222, -0.759666), (0.728413, -0.656591, 0.19571), (-0.426725, -0.658256, -0.620166)	54.0723, 124.9574, 76.8873
7	given	(0.893915, -0.29754, 0.33524), (0.170868, 0.917633, 0.358822), (-0.414391, -0.263475, 0.871126)	49.5209, 19.6665, -63.02
8	given	(0.430365, 0.516969, 0.739969), (-0.468906, -0.572424, 0.672631), (0.771305, -0.636453, -0.003941)	-108.2985, 35.0402, 85.6203
9	given	(-0.661802, -0.187728, 0.72578), (0.43061, -0.88769, 0.16303), (0.613672, 0.420433, 0.668332)	-59.0241, 114.0452, -38.248
10	given	(0.047474, -0.995898, 0.077008), (-0.78411, -0.084927, -0.614799), (0.618803, -0.031212, -0.784917)	63.8723, 116.2178, 149.058
11	given	(-0.000795, -0.999415, 0.034157), (-0.768033, -0.021276, -0.640071), (0.64041, -0.026758, -0.767558)	65.799, 115.5365, 69.8431
12	given	(-0.011463, -0.998076, -0.060951), (0.788112, -0.046522, 0.613783), (-0.615424, -0.040984, 0.787119)	66.4337, 25.1714, -16.7258
13	given	(0.951711, -0.210971, 0.223031), (-0.211934, 0.074071, 0.974472), (-0.222104, -0.974681, 0.025759)	2.6308, -7.278, 37.3313
14	given	(0.032279, 0.40756, 0.912617), (0.445432, 0.811525, -0.37815), (-0.894733, 0.418713, -0.155352)	-62.4614, 100.1076, -11.8853
15	given	(0.998856, 0.036647, -0.030712), (0.036538, -0.999324, -0.004087), (-0.030841, 0.00296, -0.99952)	1.4753, 133.3349, 129.015
16	given	(0.236282, -0.907146, 0.34822), (-0.148819, -0.387924, -0.909598), (0.960221, 0.1631, -0.22666)	32.2195, 175.4079, 66.1615
17	given	(-0.388821, -0.614238, -0.68668), (-0.837997, -0.073941, 0.540641), (-0.382856, 0.785649, -0.48598)	104.9416, 7.4133, 56.4789
18	given	(-0.41591, -0.629445, -0.656367), (-0.840175, -0.010259, 0.542219), (-0.348031, 0.776977, -0.524577)	101.0774, 3.7226, -16.5922
19	given	(-0.479438, -0.593995, -0.645994), (0.794426, 0.018993, -0.607064), (0.372863, -0.804244, 0.462779)	91.0253, 132.5449, 74.6117
20	given	(0.489207, 0.206401, -0.847393), (0.711408, -0.656507, 0.250795), (-0.504555, -0.725532, -0.468003)	67.7663, 116.4881, 66.2752
21	given	(0.913462, -0.325948, 0.243608), (0.278317, 0.937177, 0.210331), (-0.296861, -0.124329, 0.946793)	50.6918, 36.6986, -71.0233

#1: Protein	CELL FILAMENTATION PROTEIN / BEPA PROTEIN / BEPA Mass: 34010.574 Da / Num. of mol.: 8 / Fragment: RESIDUES 10-303 Source method: isolated from a genetically manipulated source Details: C-TERMINAL (HIS)6-TAG / Source: (gene. exp.) BARTONELLA HENSELAE (bacteria) / Plasmid: PRUN / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: Q6G2A9
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO₄
Nonpolymer details	SULPHATES 310 OF CHAINS A TO H ARE BOUND TO THE PUTATIVE ACTIVE SITE AT THE N-TERMINUS OF ALPHA- ...SULPHATES 310 OF CHAINS A TO H ARE BOUND TO THE PUTATIVE ACTIVE SITE AT THE N-TERMINUS OF ALPHA-HELIX 5 OF EACH CHAIN. THEY OCCUPY TWO ALTERNATIVE, MUTUALLY EXCLUSIVE POSITIONS. AN OCCUPANCY OF 0.5 IS ASSIGNED TO EACH POSITION. SULPHATE B 311 MEDIATES CRYSTAL CONTACT BETWEEN CHAINS A AND B SULPHATE F 311 MEDIATES CRYSTAL CONTACT BETWEEN CHAINS E AND F

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.86 Å³/Da / Density % sol: 56.94 % / Description: NONE
Crystal grow	pH: 8.25 Details: 30 MG/ML PROTEIN IN 20 MM TRIS_HCL (PH 8.0), 500 MM NACL AND 2 MM BETA-MERCAPTOETHANOL MIXED WITH 1.5 M AMMONIUM SULFATE, 10 MM TRIS-HCL (PH 8.25) AND 0.1 M LITHIUM SULFATE

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.0001
Detector	Type: MARRESEARCH / Detector: CCD / Date: Mar 16, 2007
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.0001 Å / Relative weight: 1
Reflection	Resolution: 2.95→83.62 Å / Num. obs: 55048 / % possible obs: 92.6 % / Observed criterion σ(I): 0 / Redundancy: 2.91 % / R_merge(I) obs: 0.11 / Net I/σ(I): 5.34
Reflection shell	Resolution: 3.05→3.21 Å / Redundancy: 1.84 % / R_merge(I) obs: 0.45 / Mean I/σ(I) obs: 1.61 / % possible all: 75.4

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0019	refinement
MOSFLM		data reduction
SCALA		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VY3

2vy3

Resolution: 3.05→30 Å / Cor.coef. F_o:F_c: 0.913 / Cor.coef. F_o:F_c free: 0.882 / SU B: 53.121 / SU ML: 0.424 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.517 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.277	2796	5.1 %	RANDOM
R_work	0.244	-	-	-
obs	0.246	52197	92.1 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 60.65 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.27 Å²	0.13 Å²	0 Å²
2-	-	0.27 Å²	0 Å²
3-	-	-	-0.4 Å²

Refinement step

Cycle: LAST / Resolution: 3.05→30 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	19008	0	50	0	19058

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.021	18285
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	12029
X-RAY DIFFRACTION	r_angle_refined_deg	1.017	1.945	24769
X-RAY DIFFRACTION	r_angle_other_deg	0.821	3	29200
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.198	5	2290
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	29.771	24.75	880
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.492	15	2882
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	12.73	15	66
X-RAY DIFFRACTION	r_chiral_restr	0.057	0.2	2657
X-RAY DIFFRACTION	r_gen_planes_refined	0.003	0.02	20700
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	3692
X-RAY DIFFRACTION	r_nbd_refined	0.223	0.2	4464
X-RAY DIFFRACTION	r_nbd_other	0.167	0.2	11897
X-RAY DIFFRACTION	r_nbtor_refined	0.18	0.2	9133
X-RAY DIFFRACTION	r_nbtor_other	0.087	0.2	9200
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.142	0.2	383
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	0.232	0.2	86
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.235	0.2	137
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.158	0.2	10
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	0.228	1.5	14600
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	0.277	2	18122
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	0.448	3	7919
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	0.709	4.5	6647
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-ID	Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	1	A	775	tight positional	0.07	0.05
1	2	B	775	tight positional	0.07	0.05
1	3	C	775	tight positional	0.07	0.05
1	4	D	775	tight positional	0.07	0.05
1	5	E	775	tight positional	0.08	0.05
1	6	F	775	tight positional	0.06	0.05
1	7	G	775	tight positional	0.07	0.05
1	8	H	775	tight positional	0.06	0.05
2	1	A	501	tight positional	0.05	0.05
2	2	B	501	tight positional	0.05	0.05
2	3	C	501	tight positional	0.06	0.05
2	4	D	501	tight positional	0.05	0.05
2	5	E	501	tight positional	0.05	0.05
2	6	F	501	tight positional	0.05	0.05
2	7	G	501	tight positional	0.06	0.05
2	8	H	501	tight positional	0.05	0.05
3	1	A	1525	tight positional	0.06	0.05
3	2	B	1525	tight positional	0.06	0.05
3	3	C	1525	tight positional	0.06	0.05
3	4	D	1525	tight positional	0.07	0.05
3	5	E	1525	tight positional	0.06	0.05
3	6	F	1525	tight positional	0.07	0.05
3	7	G	1525	tight positional	0.07	0.05
3	8	H	1525	tight positional	0.05	0.05
4	1	A	803	tight positional	0.05	0.05
4	2	B	803	tight positional	0.06	0.05
4	3	C	803	tight positional	0.04	0.05
4	4	D	803	tight positional	0.05	0.05
4	5	E	803	tight positional	0.04	0.05
4	6	F	803	tight positional	0.06	0.05
4	7	G	803	tight positional	0.05	0.05
4	8	H	803	tight positional	0.04	0.05
1	1	A	775	tight thermal	0.1	0.5
1	2	B	775	tight thermal	0.09	0.5
1	3	C	775	tight thermal	0.1	0.5
1	4	D	775	tight thermal	0.1	0.5
1	5	E	775	tight thermal	0.09	0.5
1	6	F	775	tight thermal	0.08	0.5
1	7	G	775	tight thermal	0.1	0.5
1	8	H	775	tight thermal	0.09	0.5
2	1	A	501	tight thermal	0.09	0.5
2	2	B	501	tight thermal	0.09	0.5
2	3	C	501	tight thermal	0.09	0.5
2	4	D	501	tight thermal	0.07	0.5
2	5	E	501	tight thermal	0.08	0.5
2	6	F	501	tight thermal	0.08	0.5
2	7	G	501	tight thermal	0.09	0.5
2	8	H	501	tight thermal	0.06	0.5
3	1	A	1525	tight thermal	0.09	0.5
3	2	B	1525	tight thermal	0.08	0.5
3	3	C	1525	tight thermal	0.09	0.5
3	4	D	1525	tight thermal	0.08	0.5
3	5	E	1525	tight thermal	0.08	0.5
3	6	F	1525	tight thermal	0.08	0.5
3	7	G	1525	tight thermal	0.1	0.5
3	8	H	1525	tight thermal	0.07	0.5
4	1	A	803	tight thermal	0.08	0.5
4	2	B	803	tight thermal	0.08	0.5
4	3	C	803	tight thermal	0.07	0.5
4	4	D	803	tight thermal	0.07	0.5
4	5	E	803	tight thermal	0.06	0.5
4	6	F	803	tight thermal	0.09	0.5
4	7	G	803	tight thermal	0.07	0.5
4	8	H	803	tight thermal	0.06	0.5

LS refinement shell

Resolution: 3.05→3.13 Å / Total num. of bins used: 20 /

	R_factor	Num. reflection
R_free	0.367	147
R_work	0.36	2677

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	4.5741	0.5396	-1.4276	6.3337	1.371	6.9113	0.0729	-0.2053	-0.3481	0.4171	-0.5021	-0.735	0.4584	0.4353	0.4291	-0.4625	-0.1278	-0.0436	-0.6012	-0.0433	-0.0055	20.876	80.502	79.464
2	5.3044	0.0706	-5.6753	7.6518	-2.0083	6.5603	0.3886	-0.176	-0.1815	-0.425	-0.5608	-0.2682	-0.0786	-0.0065	0.1722	-0.4217	-0.0593	-0.0644	-0.6847	-0.1083	-0.1345	17.626	87.127	75.452
3	3.4239	0.3364	2.5001	8.0755	-4.2169	8.8523	0.3184	-0.2123	0.6588	1.02	-0.3141	1.5277	-0.227	-0.7988	-0.0042	-0.178	-0.3218	0.1579	-0.2247	-0.3296	-0.0492	-0.672	79.047	84.641
4	2.6835	4.1937	-0.0211	10.1681	-2.3443	2.5211	0.777	-0.1089	-0.2034	0.9296	-0.9168	-0.5209	0.1656	0.3126	0.1398	0.0057	-0.3353	0.0511	-0.3201	-0.0465	-0.3206	7.424	64.283	83.78
5	5.6081	7.2484	0.8774	13.89	2.8126	5.2751	0.6636	-0.1515	-0.8624	0.2465	-0.4449	-1.2978	0.3025	0.1467	-0.2187	-0.0195	-0.2864	-0.051	-0.4282	0.0534	-0.2817	3.216	43.921	83.292
6	5.9311	-0.2739	0.7602	4.9918	2.4953	8.6949	0.4447	0.3349	0.3238	-0.2702	-0.2735	-0.9692	-0.658	0.8538	-0.1712	-0.3075	0.0661	0.1518	-0.5145	0.0541	0.0486	23.368	54.992	50.643
7	6.1968	0.1474	1.9664	11.1059	-1.8703	3.9791	0.2088	-0.0011	0.2677	0.2901	0.0354	-0.4517	-0.3392	-0.3452	-0.2442	-0.1859	0.0764	0.1304	-0.4409	-0.0083	-0.2297	20.78	48.165	54.656
8	3.941	-1.6148	-1.7776	6.8485	-1.8501	4.2335	0.6421	0.5028	-0.6994	-0.7985	-0.4983	0.9577	0.0978	-0.9199	-0.1438	-0.1416	0.3042	0.0151	-0.0818	-0.1155	-0.1596	2.012	54.049	44.793
9	2.3355	-4.4455	-1.2906	10.3924	0.4367	2.8264	0.7949	0.2311	0.3658	-0.6264	-0.657	-0.8189	-0.8408	-0.109	-0.138	0.0707	0.3624	0.1057	-0.1286	0.1775	-0.3211	8.891	69.379	45.428
10	6.4894	-5.8507	0.582	16.0922	3.6488	8.2776	0.4401	-0.2178	1.8313	-0.6283	-0.8905	-1.421	-0.521	0.0697	0.4504	0.2526	0.6338	0.1323	-0.1802	0.2463	-0.1281	3.736	89.146	45.584
11	6.0537	-3.5511	1.9086	9.442	-0.4798	7.8565	-0.3173	-0.6189	0.4759	0.3599	-0.0069	0.2941	-0.2105	-1.2086	0.3242	-0.5697	-0.1869	-0.0947	-0.231	-0.2502	-0.3428	4.062	107.263	83.076
12	6.8203	-1.4187	2.5112	4.2482	-5.4173	6.9857	-0.2299	-0.1966	0.6774	-0.1968	-0.1543	-0.4507	0.0859	-0.614	0.3842	-0.587	-0.093	-0.0832	-0.5617	-0.1835	-0.1536	11.518	106.752	78.916
13	9.6781	-4.3213	2.4278	5.8595	1.4044	7.0597	-0.3368	0.4167	1.7641	-0.7699	-0.4113	-0.8084	-0.8279	-0.4525	0.7481	-0.2904	0.1269	-0.0427	-0.1167	0.0907	-0.0734	-2.094	115.044	63.161
14	9.7548	-0.9803	3.6889	2.0042	1.0551	4.3957	-0.1308	-1.6627	-0.1299	0.3636	-0.125	0.2041	-0.0778	-1.8131	0.2557	-0.365	0.2211	-0.0449	0.6434	-0.0587	-0.3111	-13.821	106.857	72.053
15	17.3892	-3.6203	2.4307	12.6312	-8.2761	13.1327	-0.0417	-3.5992	-2.0574	1.7383	0.1246	0.4373	-0.8844	-0.5432	-0.0829	-0.1204	0.0166	0.0647	1.4507	0.3581	-0.1474	-32.804	98.944	70.165
16	5.2132	2.267	0.4024	11.4081	-2.2308	6.6917	-0.1156	0.8303	-0.3889	-0.2693	0.4727	0.9808	0.5771	-0.4772	-0.357	-0.4117	0.1942	0.1535	-0.3175	-0.177	-0.2066	9.125	26.969	47.081
17	2.3411	0.2462	-0.9919	0.7617	-1.8589	4.6043	0.1462	0.0905	-0.2071	0.4119	-0.3176	0.059	-0.108	-0.2708	0.1714	-0.3267	0.0815	0.0352	-0.4612	-0.1479	-0.204	15.184	30.325	53.76
18	12.8931	5.5674	-0.6636	5.6006	0.3158	4.9606	0.2785	-1.019	-1.5213	0.2957	-0.522	-0.606	0.3332	0.2129	0.2435	-0.038	-0.0172	0.0089	-0.3121	0.0828	-0.1221	2.741	21.167	67.042
19	8.4789	-0.1617	-2.7581	1.9521	-0.9379	1.7407	-0.2521	1.0273	0.0567	-0.7992	0.2999	0.099	0.0947	-0.7826	-0.0477	-0.1413	-0.2811	-0.02	0.0028	0.0292	-0.2366	-8.957	26.943	56.788
20	12.3766	0.3144	-2.579	10.5511	-0.3974	8.1794	0.0591	2.0534	1.6657	-0.1241	0.1616	0.4965	-1.1797	-0.6464	-0.2206	-0.2034	-0.1001	-0.112	0.3782	0.3774	0.0005	-28.156	34.182	56.933
21	6.0162	-1.1107	-2.1877	4.6524	0.141	6.5489	-0.4045	-0.2045	-0.2675	0.19	0.0434	-0.6776	0.3156	0.1652	0.3612	-0.3987	0.1357	-0.1358	-0.3337	-0.2551	-0.049	20.507	80.911	1.355
22	8.1733	3.5578	-2.5941	5.9976	-0.8694	0.8385	-0.1908	-0.1706	0.2621	-0.2386	0.1085	-0.3528	0.0397	0.0608	0.0824	-0.3059	0.1345	-0.1485	-0.4249	-0.2361	-0.1439	17.649	87.67	-2.576
23	5.2812	1.6359	-0.1275	8.864	-5.9437	7.9413	-0.2765	-0.6844	0.3655	0.7921	0.5124	0.7908	-0.4247	-0.6068	-0.236	-0.2808	0.2478	-0.0082	-0.0051	-0.1034	-0.3072	-1.239	80.827	6.647
24	2.0113	2.5209	1.0415	7.8206	-2.3524	3.4101	-0.3299	-0.4377	-0.5047	-0.2578	0.3593	-0.6666	1.0504	-0.18	-0.0294	0.0175	0.1219	0.1416	0.0806	0.0063	-0.2055	5.886	65.567	6.201
25	2.3425	0.2599	0.8707	11.268	0.5272	10.6014	-0.723	-0.697	-1.1555	-1.0145	0.5266	-1.0417	0.7751	0.7041	0.1964	0.5405	-0.0772	0.328	-0.1115	0.2757	0.2239	0.467	45.49	6.496
26	5.7119	1.0105	3.8022	7.0331	2.722	6.8412	-0.236	0.0197	0.1799	0.2379	-0.0565	0.0039	-0.0079	0.538	0.2925	-0.4358	0.1014	0.0953	-0.3269	-0.2202	-0.0844	20.219	57.148	-28.49
27	4.0442	0.2018	4.0044	10.1062	-2.5116	4.6931	0.0626	-0.2581	-0.1509	1.1314	-0.2873	0.8328	0.1859	0.015	0.2246	-0.0775	0.0527	0.1951	-0.3787	-0.1716	-0.0885	17.001	50.296	-24.781
28	4.5038	2.6575	0.9339	8.8766	-2.5254	6.7004	0.0189	-0.5107	-0.1963	-0.0828	-0.0338	1.7922	0.6439	-0.7342	0.0148	-0.3493	0.0373	0.0654	-0.1977	-0.5108	0.4806	-1.267	57.673	-34.914
29	1.4666	-3.3807	-0.8858	10.3245	0.0427	2.4683	0.1716	0.108	-0.1979	0.2034	-0.3886	0.2588	0.0573	0.3893	0.2169	-0.2996	0.0554	-0.0073	-0.171	-0.2401	-0.0679	5.721	72.805	-33.054
30	7.6973	-4.2712	0.1172	9.6939	2.4583	8.2512	0.0692	0.2156	0.5027	-0.1976	-0.1107	-0.4134	-0.3973	-0.0833	0.0414	-0.356	0.1225	0.0368	-0.3999	-0.1394	-0.2027	0.212	92.668	-31.824
31	6.3359	-1.0022	1.9493	7.9488	-3.5793	7.58	-0.162	-0.3746	-0.1319	0.4261	0.5018	0.6342	-0.5059	-0.1693	-0.3398	-0.5087	-0.0506	-0.154	-0.4801	-0.2174	-0.3572	4.497	107.849	5.482
32	2.1022	-0.8341	1.7461	1.2707	-2.2444	4.0122	-0.2297	0.271	0.1236	-0.0059	0.4209	-0.251	0.2306	0.3171	-0.1912	-0.5257	0.0188	-0.1341	-0.2317	-0.154	-0.1815	10.884	105.46	-1.051
33	13.613	-4.3586	2.384	5.6296	1.4349	5.7992	0.1395	0.9351	1.3409	-0.6897	-0.2679	-0.4994	-0.626	0.2627	0.1284	-0.3463	0.0089	-0.045	-0.3324	0.0387	-0.281	-2.009	114.177	-14.271
34	7.5725	-0.2402	3.291	1.4323	0.1812	4.8637	-0.1563	-1.0033	-0.1817	0.6083	0.0351	-0.1339	0.1495	-0.9347	0.1211	-0.459	0.152	-0.0223	-0.0609	-0.0079	-0.3188	-13.67	107.079	-4.755
35	14.8938	2.7732	3.4518	8.0212	1.4078	8.9946	0.0898	-2.2048	-1.6703	0.2184	-0.1457	0.429	0.9171	-1.5893	0.0559	-0.5809	-0.0795	0.0559	0.6793	0.2379	-0.1963	-32.614	98.834	-6.234
36	7.114	1.8745	-2.0808	10.3018	-1.8752	5.3361	-0.1794	0.1533	-0.3091	0.1285	0.1767	0.9551	0.5442	-0.1853	0.0027	-0.197	0.143	0.2517	-0.3412	-0.1245	-0.2542	4.095	30.216	-32.875
37	4.2902	-1.546	0.487	2.2318	-3.1228	5.2426	-0.2538	-0.3073	-0.4159	0.9656	0.2072	0.3151	0.2033	-0.1775	0.0467	-0.0363	0.0859	0.129	-0.3315	-0.0365	-0.1213	11.37	30.732	-28.547
38	6.0222	1.9946	1.3816	8.6226	-0.8907	7.3462	-0.3474	-0.8592	-1.318	0.3212	0.1316	-0.2414	0.6228	0.1574	0.2158	0.4162	0.1164	0.4277	-0.0879	0.126	0.1288	-2.207	22.221	-12.826
39	9.4687	1.7307	-0.2003	1.0725	0.7343	1.1632	-0.3512	0.0039	-0.2407	-0.0953	-0.086	0.5349	0.0037	-0.6991	0.4372	0.4181	-0.0147	0.5343	0.0436	-0.0003	0.1877	-14.159	30.305	-21.575
40	9.5414	4.9901	1.5315	10.7572	-0.1933	5.2166	-0.6284	0.0532	0.4162	-0.9892	0.8835	-0.3416	-0.545	-0.0824	-0.2551	0.2416	0.1182	0.4077	0.2765	-0.0443	-0.0089	-33.368	37.781	-19.483

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	11 - 74
2	X-RAY DIFFRACTION	2	A	75 - 109
3	X-RAY DIFFRACTION	3	A	110 - 160
4	X-RAY DIFFRACTION	4	A	161 - 247
5	X-RAY DIFFRACTION	5	A	248 - 302
6	X-RAY DIFFRACTION	6	B	11 - 74
7	X-RAY DIFFRACTION	7	B	75 - 109
8	X-RAY DIFFRACTION	8	B	110 - 160
9	X-RAY DIFFRACTION	9	B	161 - 247
10	X-RAY DIFFRACTION	10	B	248 - 302
11	X-RAY DIFFRACTION	11	C	11 - 74
12	X-RAY DIFFRACTION	12	C	75 - 109
13	X-RAY DIFFRACTION	13	C	110 - 160
14	X-RAY DIFFRACTION	14	C	161 - 247
15	X-RAY DIFFRACTION	15	C	248 - 302
16	X-RAY DIFFRACTION	16	D	11 - 74
17	X-RAY DIFFRACTION	17	D	75 - 109
18	X-RAY DIFFRACTION	18	D	110 - 160
19	X-RAY DIFFRACTION	19	D	161 - 247
20	X-RAY DIFFRACTION	20	D	248 - 302
21	X-RAY DIFFRACTION	21	E	11 - 74
22	X-RAY DIFFRACTION	22	E	75 - 109
23	X-RAY DIFFRACTION	23	E	110 - 160
24	X-RAY DIFFRACTION	24	E	161 - 247
25	X-RAY DIFFRACTION	25	E	248 - 302
26	X-RAY DIFFRACTION	26	F	11 - 74
27	X-RAY DIFFRACTION	27	F	75 - 109
28	X-RAY DIFFRACTION	28	F	110 - 160
29	X-RAY DIFFRACTION	29	F	161 - 247
30	X-RAY DIFFRACTION	30	F	248 - 302
31	X-RAY DIFFRACTION	31	G	11 - 74
32	X-RAY DIFFRACTION	32	G	75 - 109
33	X-RAY DIFFRACTION	33	G	110 - 160
34	X-RAY DIFFRACTION	34	G	161 - 247
35	X-RAY DIFFRACTION	35	G	248 - 302
36	X-RAY DIFFRACTION	36	H	11 - 74
37	X-RAY DIFFRACTION	37	H	75 - 109
38	X-RAY DIFFRACTION	38	H	110 - 160
39	X-RAY DIFFRACTION	39	H	161 - 247
40	X-RAY DIFFRACTION	40	H	248 - 302

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+About Yorodumi

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-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

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Movie

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Structure viewers

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Viewer log

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This page

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This web site

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Options

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Open data

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Basic information

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Structure visualization

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Downloads & links

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Download

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Validation report

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Related structure data

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Links

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Assembly

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Components

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Experimental details

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Experiment

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Sample preparation

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Data collection

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Processing

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About Yorodumi

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News

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

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Aug 12, 2020. Covid-19 info

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Mar 5, 2020. Novel coronavirus structure data

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Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

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Jul 12, 2017. Major update of PDB

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Yorodumi