PDB-6nd9: RHODOCETIN IN COMPLEX WITH THE INTEGRIN ALPHA2-A DOMAIN WITH CALCIUM

ID or keywords:

Entry

Database: PDB / ID: 6nd9

Title

RHODOCETIN IN COMPLEX WITH THE INTEGRIN ALPHA2-A DOMAIN WITH CALCIUM

Components

(Snaclec rhodocetin subunit ...) x 2
Integrin alpha-2

Keywords

CELL ADHESION/TOXIN /

C-TYPE LECTIN /

INTEGRIN /

VENOM /

COAGULATION /

CELL ADHESION / CELL ADHESION-TOXIN complex

Function / homology

Function and homology information

collagen receptor activity / substrate-dependent cell migration / positive regulation of transmission of nerve impulse / positive regulation of cell projection organization / collagen binding involved in cell-matrix adhesion / integrin alpha2-beta1 complex / response to parathyroid hormone / hypotonic response / response to L-ascorbic acid / skin morphogenesis ...

collagen receptor activity / substrate-dependent cell migration / positive regulation of transmission of nerve impulse / positive regulation of cell projection organization / collagen binding involved in cell-matrix adhesion / integrin alpha2-beta1 complex / response to parathyroid hormone / hypotonic response / response to L-ascorbic acid / skin morphogenesis / CHL1 interactions / Laminin interactions / basal part of cell / positive regulation of phagocytosis, engulfment / positive regulation of smooth muscle contraction / collagen-activated signaling pathway / Platelet Adhesion to exposed collagen /

mammary gland development /

heparan sulfate proteoglycan binding / hepatocyte differentiation / mesodermal cell differentiation /

focal adhesion assembly / response to muscle activity /

integrin complex / positive regulation of positive chemotaxis / positive regulation of leukocyte migration / cell adhesion mediated by integrin / MET activates PTK2 signaling / Syndecan interactions / positive regulation of epithelial cell migration / cell-substrate adhesion / positive regulation of smooth muscle cell migration / response to amine / positive regulation of cell adhesion / ECM proteoglycans / positive regulation of collagen biosynthetic process /

laminin binding / Integrin cell surface interactions / detection of mechanical stimulus involved in sensory perception of pain / axon terminus /

collagen binding / cell-matrix adhesion / positive regulation of translation / cellular response to estradiol stimulus / female pregnancy / integrin-mediated signaling pathway / animal organ morphogenesis / positive regulation of smooth muscle cell proliferation /

cell-cell adhesion / cellular response to mechanical stimulus /

blood coagulation /

integrin binding / virus receptor activity /

amyloid-beta binding /

toxin activity / response to hypoxia /

cell adhesion / response to xenobiotic stimulus / external side of plasma membrane /

focal adhesion / protein-containing complex binding / perinuclear region of cytoplasm /

cell surface / extracellular region /

metal ion binding /

plasma membrane
Similarity search - Function

Biological species

Homo sapiens (human)

Calloselasma rhodostoma (Malayan pit viper)

Method

X-RAY DIFFRACTION /

FOURIER SYNTHESIS / Resolution: 2.9 Å

Authors

Stetefeld, J. / McDougall, M.D. / Loewen, P.C.

Citation

Journal: To be published
Title: RHODOCETIN IN COMPLEX WITH THE INTEGRIN ALPHA2-A DOMAIN AND CALCIUM
Authors: Stetefeld, J. / McDougall, M.D. / Loewen, P.C.

History

Deposition	Dec 13, 2018	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 23, 2019	Provider: repository / Type: Initial release
Revision 1.1	Oct 11, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_label_seq_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_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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6nd9.cif.gz	541.5 KB	Display	PDBx/mmCIF format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/nd/6nd9 ftp://data.pdbj.org/pub/pdb/validation_reports/nd/6nd9	HTTPS FTP

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Related structure data

Related structure data	5thpS S: Starting model for refinement
Similar structure data	6nda-2 6ndc-5 6ndf-4 6ndd-2 6ndf-2 6ndf-6 6nd8-4 5thp-5 6ndg-1 6nd8-2 6nd8-3 6ndc-2 6ndh-3 6ndc-6 6ndf-5 6nd8-1 6nda-6 6ndd-6 6ndh-1 6nda-3 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

5thpS

S: Starting model for refinement

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#134 - Feb 2011 Integrin similarity (30) #232 - Apr 2019 Proteins and Biominerals similarity (8) #75 - Mar 2006 Tissue Factor similarity (8) #79 - Jul 2006 Amyloid-beta Precursor Protein similarity (1) #189 - Sep 2015 Amyloids similarity (1) #55 - Jul 2004 DNA Ligase similarity (3) #166 - Oct 2013 Proteasome similarity (3) #135 - Mar 2011 Integrase similarity (1) #43 - Jul 2003 Src Tyrosine Kinase similarity (1) #60 - Dec 2004 Ubiquitin similarity (1) #83 - Nov 2006 Fibrin similarity (1) #261 - Sep 2021 DNA-Sequencing Nanopores similarity (1) #69 - Sep 2005 Cholera Toxin similarity (1) #209 - May 2017 Tissue Transglutaminase and Celiac Disease similarity (1) #267 - Mar 2022 Vascular Endothelial Growth Factor (VegF similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#134 - Feb 2011
Integrin
similarity (30)
#232 - Apr 2019
Proteins and Biominerals
similarity (8)
#75 - Mar 2006
Tissue Factor
similarity (8)
#79 - Jul 2006
Amyloid-beta Precursor Protein
similarity (1)
#189 - Sep 2015
Amyloids
similarity (1)
#55 - Jul 2004
DNA Ligase
similarity (3)
#166 - Oct 2013
Proteasome
similarity (3)
#135 - Mar 2011
Integrase
similarity (1)
#43 - Jul 2003
Src Tyrosine Kinase
similarity (1)
#60 - Dec 2004
Ubiquitin
similarity (1)
#83 - Nov 2006
Fibrin
similarity (1)
#261 - Sep 2021
DNA-Sequencing Nanopores
similarity (1)
#69 - Sep 2005
Cholera Toxin
similarity (1)
#209 - May 2017
Tissue Transglutaminase and Celiac Disease
similarity (1)
#267 - Mar 2022
Vascular Endothelial Growth Factor (VegF
similarity (1)

Deposited unit

A: Snaclec rhodocetin subunit gamma

B: Snaclec rhodocetin subunit delta

C: Integrin alpha-2

D: Snaclec rhodocetin subunit gamma

E: Snaclec rhodocetin subunit delta

F: Integrin alpha-2

G: Snaclec rhodocetin subunit gamma

H: Snaclec rhodocetin subunit delta

I: Integrin alpha-2

J: Snaclec rhodocetin subunit gamma

K: Snaclec rhodocetin subunit delta

L: Integrin alpha-2

M: Snaclec rhodocetin subunit gamma

N: Snaclec rhodocetin subunit delta

O: Integrin alpha-2

P: Snaclec rhodocetin subunit gamma

Q: Snaclec rhodocetin subunit delta

R: Integrin alpha-2

hetero molecules

328 kDa, 18 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Snaclec rhodocetin subunit gamma

B: Snaclec rhodocetin subunit delta

C: Integrin alpha-2

hetero molecules

defined by author
Evidence: cross-linking
54.8 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

D: Snaclec rhodocetin subunit gamma

E: Snaclec rhodocetin subunit delta

F: Integrin alpha-2

hetero molecules

defined by author
54.8 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

G: Snaclec rhodocetin subunit gamma

H: Snaclec rhodocetin subunit delta

I: Integrin alpha-2

hetero molecules

defined by author
54.7 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

J: Snaclec rhodocetin subunit gamma

K: Snaclec rhodocetin subunit delta

L: Integrin alpha-2

hetero molecules

defined by author
54.7 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

5

M: Snaclec rhodocetin subunit gamma

N: Snaclec rhodocetin subunit delta

O: Integrin alpha-2

hetero molecules

defined by author
54.6 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

6

P: Snaclec rhodocetin subunit gamma

Q: Snaclec rhodocetin subunit delta

R: Integrin alpha-2

hetero molecules

defined by author
54.7 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	131.044, 131.044, 251.245
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	76
Space group name H-M	P4₁

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-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	ASN	ASN	SER	SER	A	A	3 - 133	3 - 133
2	1	ASN	ASN	SER	SER	D	D	3 - 133	3 - 133
1	2	ASN	ASN	SER	SER	A	A	3 - 133	3 - 133
2	2	ASN	ASN	SER	SER	G	G	3 - 133	3 - 133
1	3	ASN	ASN	SER	SER	A	A	3 - 133	3 - 133
2	3	ASN	ASN	SER	SER	J	J	3 - 133	3 - 133
1	4	ASN	ASN	SER	SER	A	A	3 - 133	3 - 133
2	4	ASN	ASN	SER	SER	M	M	3 - 133	3 - 133
1	5	ASN	ASN	SER	SER	A	A	3 - 133	3 - 133
2	5	ASN	ASN	SER	SER	P	P	3 - 133	3 - 133
1	6	CYS	CYS	PHE	PHE	B	B	1 - 122	1 - 122
2	6	CYS	CYS	PHE	PHE	E	E	1 - 122	1 - 122
1	7	CYS	CYS	PHE	PHE	B	B	1 - 122	1 - 122
2	7	CYS	CYS	PHE	PHE	H	H	1 - 122	1 - 122
1	8	CYS	CYS	PHE	PHE	B	B	1 - 122	1 - 122
2	8	CYS	CYS	PHE	PHE	K	K	1 - 122	1 - 122
1	9	CYS	CYS	PHE	PHE	B	B	1 - 122	1 - 122
2	9	CYS	CYS	PHE	PHE	N	N	1 - 122	1 - 122
1	10	CYS	CYS	PHE	PHE	B	B	1 - 122	1 - 122
2	10	CYS	CYS	PHE	PHE	Q	Q	1 - 122	1 - 122
1	11	LEU	LEU	PHE	PHE	C	C	172 - 362	23 - 213
2	11	LEU	LEU	PHE	PHE	F	F	172 - 362	23 - 213
1	12	LEU	LEU	PHE	PHE	C	C	172 - 362	23 - 213
2	12	LEU	LEU	PHE	PHE	I	I	172 - 362	23 - 213
1	13	LEU	LEU	PHE	PHE	C	C	172 - 362	23 - 213
2	13	LEU	LEU	PHE	PHE	L	L	172 - 362	23 - 213
1	14	LEU	LEU	PHE	PHE	C	C	172 - 362	23 - 213
2	14	LEU	LEU	PHE	PHE	O	O	172 - 362	23 - 213
1	15	LEU	LEU	PHE	PHE	C	C	172 - 362	23 - 213
2	15	LEU	LEU	PHE	PHE	R	R	172 - 362	23 - 213
1	16	ASN	ASN	SER	SER	D	D	3 - 133	3 - 133
2	16	ASN	ASN	SER	SER	G	G	3 - 133	3 - 133
1	17	ASN	ASN	SER	SER	D	D	3 - 133	3 - 133
2	17	ASN	ASN	SER	SER	J	J	3 - 133	3 - 133
1	18	ASN	ASN	SER	SER	D	D	3 - 133	3 - 133
2	18	ASN	ASN	SER	SER	M	M	3 - 133	3 - 133
1	19	ASN	ASN	SER	SER	D	D	3 - 133	3 - 133
2	19	ASN	ASN	SER	SER	P	P	3 - 133	3 - 133
1	20	CYS	CYS	PHE	PHE	E	E	1 - 122	1 - 122
2	20	CYS	CYS	PHE	PHE	H	H	1 - 122	1 - 122
1	21	CYS	CYS	PHE	PHE	E	E	1 - 122	1 - 122
2	21	CYS	CYS	PHE	PHE	K	K	1 - 122	1 - 122
1	22	CYS	CYS	PHE	PHE	E	E	1 - 122	1 - 122
2	22	CYS	CYS	PHE	PHE	N	N	1 - 122	1 - 122
1	23	CYS	CYS	PHE	PHE	E	E	1 - 122	1 - 122
2	23	CYS	CYS	PHE	PHE	Q	Q	1 - 122	1 - 122
1	24	LEU	LEU	PHE	PHE	F	F	172 - 362	23 - 213
2	24	LEU	LEU	PHE	PHE	I	I	172 - 362	23 - 213
1	25	LEU	LEU	PHE	PHE	F	F	172 - 362	23 - 213
2	25	LEU	LEU	PHE	PHE	L	L	172 - 362	23 - 213
1	26	LEU	LEU	PHE	PHE	F	F	172 - 362	23 - 213
2	26	LEU	LEU	PHE	PHE	O	O	172 - 362	23 - 213
1	27	LEU	LEU	PHE	PHE	F	F	172 - 362	23 - 213
2	27	LEU	LEU	PHE	PHE	R	R	172 - 362	23 - 213
1	28	ASN	ASN	SER	SER	G	G	3 - 133	3 - 133
2	28	ASN	ASN	SER	SER	J	J	3 - 133	3 - 133
1	29	ASN	ASN	SER	SER	G	G	3 - 133	3 - 133
2	29	ASN	ASN	SER	SER	M	M	3 - 133	3 - 133
1	30	ASN	ASN	SER	SER	G	G	3 - 133	3 - 133
2	30	ASN	ASN	SER	SER	P	P	3 - 133	3 - 133
1	31	CYS	CYS	PHE	PHE	H	H	1 - 122	1 - 122
2	31	CYS	CYS	PHE	PHE	K	K	1 - 122	1 - 122
1	32	CYS	CYS	PHE	PHE	H	H	1 - 122	1 - 122
2	32	CYS	CYS	PHE	PHE	N	N	1 - 122	1 - 122
1	33	CYS	CYS	PHE	PHE	H	H	1 - 122	1 - 122
2	33	CYS	CYS	PHE	PHE	Q	Q	1 - 122	1 - 122
1	34	LEU	LEU	PHE	PHE	I	I	172 - 362	23 - 213
2	34	LEU	LEU	PHE	PHE	L	L	172 - 362	23 - 213
1	35	LEU	LEU	PHE	PHE	I	I	172 - 362	23 - 213
2	35	LEU	LEU	PHE	PHE	O	O	172 - 362	23 - 213
1	36	LEU	LEU	PHE	PHE	I	I	172 - 362	23 - 213
2	36	LEU	LEU	PHE	PHE	R	R	172 - 362	23 - 213
1	37	ASN	ASN	SER	SER	J	J	3 - 133	3 - 133
2	37	ASN	ASN	SER	SER	M	M	3 - 133	3 - 133
1	38	ASN	ASN	SER	SER	J	J	3 - 133	3 - 133
2	38	ASN	ASN	SER	SER	P	P	3 - 133	3 - 133
1	39	CYS	CYS	PHE	PHE	K	K	1 - 122	1 - 122
2	39	CYS	CYS	PHE	PHE	N	N	1 - 122	1 - 122
1	40	CYS	CYS	PHE	PHE	K	K	1 - 122	1 - 122
2	40	CYS	CYS	PHE	PHE	Q	Q	1 - 122	1 - 122
1	41	LEU	LEU	PHE	PHE	L	L	172 - 362	23 - 213
2	41	LEU	LEU	PHE	PHE	O	O	172 - 362	23 - 213
1	42	LEU	LEU	PHE	PHE	L	L	172 - 362	23 - 213
2	42	LEU	LEU	PHE	PHE	R	R	172 - 362	23 - 213
1	43	ASN	ASN	SER	SER	M	M	3 - 133	3 - 133
2	43	ASN	ASN	SER	SER	P	P	3 - 133	3 - 133
1	44	CYS	CYS	PHE	PHE	N	N	1 - 122	1 - 122
2	44	CYS	CYS	PHE	PHE	Q	Q	1 - 122	1 - 122
1	45	LEU	LEU	PHE	PHE	O	O	172 - 362	23 - 213
2	45	LEU	LEU	PHE	PHE	R	R	172 - 362	23 - 213

NCS ensembles :

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Snaclec rhodocetin subunit ... , 2 types, 12 molecules ADGJMPBEHKNQ

#1: Protein	Snaclec rhodocetin subunit gamma Mass: 15741.510 Da / Num. of mol.: 6 / Source method: isolated from a natural source Source: (natural) Calloselasma rhodostoma (Malayan pit viper) References: UniProt: D2YW39
#2: Protein	Snaclec rhodocetin subunit delta Mass: 14875.982 Da / Num. of mol.: 6 / Source method: isolated from a natural source Source: (natural) Calloselasma rhodostoma (Malayan pit viper) References: UniProt: D2YW40

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Protein , 1 types, 6 molecules CFILOR

#3: Protein	Integrin alpha-2 / CD49 antigen-like family member B / Collagen receptor / Platelet membrane glycoprotein Ia / GPIa / ...CD49 antigen-like family member B / Collagen receptor / Platelet membrane glycoprotein Ia / GPIa / VLA-2 subunit alpha Mass: 23737.738 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ITGA2, CD49B / Production host: Escherichia coli (E. coli) / References: UniProt: P17301

#3: Protein

Integrin alpha-2 / CD49 antigen-like family member B / Collagen receptor / Platelet membrane glycoprotein Ia / GPIa / ...

Mass: 23737.738 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Homo sapiens (human) / Gene: ITGA2, CD49B / Production host:

Escherichia coli (E. coli) / References: UniProt: P17301

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Non-polymers , 7 types, 43 molecules

#4: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: SO₄
#5: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#6: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na
#7: Chemical	ChemComp-NH4 / AMMONIUM ION / Ammonium Mass: 18.038 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H₄N
#8: Chemical	ChemComp-CL / CHLORIDE ION / Chloride Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#9: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C₃H₈O₃
#10: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 10 / 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: 3.54 Å³/Da / Density % sol: 65.23 % / Mosaicity: 0.14 °
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.1 M TRIS, 2.65 M AMMONIUM SULPHATE

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å

Detector

Type: RIGAKU / Detector: IMAGE PLATE / Date: Jun 27, 2010 / Details: mirrors

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1.54 Å / Relative weight: 1

Reflection

Resolution: 2.9→131.044 Å / Num. obs: 93403 / % possible obs: 100 % / Redundancy: 6.4 % / R_pim(I) all: 0.049 / R_rim(I) all: 0.124 / R_sym value: 0.114 / Net I/av σ(I): 6.5 / Net I/σ(I): 14.4

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique obs	R_pim(I) all	R_rim(I) all	R_sym value	% possible all
2.9-3.06	6.4	0.6	1.3	13623	0.258	0.654	0.6	100
3.06-3.24	6.4	0.376	2.1	12889	0.161	0.409	0.376	100
3.24-3.47	6.4	0.235	3.3	12112	0.101	0.256	0.235	100
3.47-3.74	6.4	0.148	5.2	11283	0.063	0.161	0.148	100
3.74-4.1	6.4	0.105	7.3	10403	0.045	0.114	0.105	100
4.1-4.59	6.4	0.074	10	9386	0.032	0.08	0.074	100
4.59-5.29	6.4	0.066	11.1	8285	0.028	0.072	0.066	100
5.29-6.48	6.5	0.073	10	7022	0.031	0.08	0.073	100
6.48-9.17	6.5	0.045	14.5	5424	0.019	0.049	0.045	99.9
9.17-48.016	6.3	0.029	21	2976	0.012	0.032	0.029	99.1

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0238	refinement
SCALA	3.3.22	data scaling
PDB_EXTRACT	3.24	data extraction
XDS		data reduction
REFMAC	5.8.0238	phasing

Refinement

Method to determine structure:

FOURIER SYNTHESIS
Starting model: 5THP

5thp

Resolution: 2.9→48.06 Å / Cor.coef. F_o:F_c: 0.907 / Cor.coef. F_o:F_c free: 0.873 / SU B: 17.424 / SU ML: 0.324 / SU R Cruickshank DPI: 2.0364 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 2.036 / ESU R Free: 0.396 / Details: MOLECULAR REPLACEMENT

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.272	4578	4.9 %	RANDOM
R_work	0.2292	-	-	-
obs	0.2313	88792	99.95 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å

Displacement parameters

B_iso max: 178.73 Å² / B_iso mean: 49.621 Å² / B_iso min: 15.21 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.47 Å²	0 Å²	0 Å²
2-	-	0.47 Å²	0 Å²
3-	-	-	-0.94 Å²

Refinement step

Cycle: final / Resolution: 2.9→48.06 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	21486	0	107	10	21603
B_iso mean	-	-	73.43	22.92	-
Num. residues	-	-	-	-	2664

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.013	22142
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.018	19680
X-RAY DIFFRACTION	r_angle_refined_deg	1.39	1.637	30010
X-RAY DIFFRACTION	r_angle_other_deg	1.207	1.579	45646
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	8.586	5	2646
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.012	22.463	1218
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.951	15	3708
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.253	15	132
X-RAY DIFFRACTION	r_chiral_restr	0.052	0.2	2766
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	24744
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	5028

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	A	4104	0.08
1	2	D	4104	0.08
2	1	A	4095	0.08
2	2	G	4095	0.08
3	1	A	4110	0.08
3	2	J	4110	0.08
4	1	A	3965	0.11
4	2	M	3965	0.11
5	1	A	4003	0.1
5	2	P	4003	0.1
6	1	B	3717	0.1
6	2	E	3717	0.1
7	1	B	3749	0.09
7	2	H	3749	0.09
8	1	B	3820	0.09
8	2	K	3820	0.09
9	1	B	3785	0.09
9	2	N	3785	0.09
10	1	B	3758	0.1
10	2	Q	3758	0.1
11	1	C	5930	0.1
11	2	F	5930	0.1
12	1	C	5951	0.09
12	2	I	5951	0.09
13	1	C	6111	0.06
13	2	L	6111	0.06
14	1	C	5982	0.09
14	2	O	5982	0.09
15	1	C	5966	0.09
15	2	R	5966	0.09
16	1	D	4161	0.07
16	2	G	4161	0.07
17	1	D	4057	0.09
17	2	J	4057	0.09
18	1	D	3983	0.11
18	2	M	3983	0.11
19	1	D	4001	0.11
19	2	P	4001	0.11
20	1	E	3837	0.08
20	2	H	3837	0.08
21	1	E	3694	0.11
21	2	K	3694	0.11
22	1	E	3721	0.1
22	2	N	3721	0.1
23	1	E	3726	0.11
23	2	Q	3726	0.11
24	1	F	6069	0.07
24	2	I	6069	0.07
25	1	F	5913	0.09
25	2	L	5913	0.09
26	1	F	5904	0.1
26	2	O	5904	0.1
27	1	F	5893	0.1
27	2	R	5893	0.1
28	1	G	4079	0.08
28	2	J	4079	0.08
29	1	G	3969	0.1
29	2	M	3969	0.1
30	1	G	3993	0.1
30	2	P	3993	0.1
31	1	H	3728	0.1
31	2	K	3728	0.1
32	1	H	3722	0.11
32	2	N	3722	0.11
33	1	H	3696	0.11
33	2	Q	3696	0.11
34	1	I	5974	0.09
34	2	L	5974	0.09
35	1	I	5935	0.1
35	2	O	5935	0.1
36	1	I	5912	0.1
36	2	R	5912	0.1
37	1	J	3920	0.11
37	2	M	3920	0.11
38	1	J	3942	0.11
38	2	P	3942	0.11
39	1	K	3794	0.1
39	2	N	3794	0.1
40	1	K	3769	0.1
40	2	Q	3769	0.1
41	1	L	5978	0.08
41	2	O	5978	0.08
42	1	L	5961	0.09
42	2	R	5961	0.09
43	1	M	4051	0.09
43	2	P	4051	0.09
44	1	N	3880	0.07
44	2	Q	3880	0.07
45	1	O	6152	0.06
45	2	R	6152	0.06

LS refinement shell

Resolution: 2.9→2.975 Å / R_factor R_free error: 0 / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.345	315	-
R_work	0.31	6580	-
all	-	6895	-
obs	-	-	100 %

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