PDB-5hlg: Structure of reduced AbfR bound to DNA

ID or keywords:

Entry

Database: PDB / ID: 5hlg

Title

Structure of reduced AbfR bound to DNA

Components

DNA (5'-D(*TP*AP*AP*CP*TP*CP*AP*AP*TP*CP*GP*CP*GP*CP*GP*CP*GP*AP*TP*TP*GP*AP*GP*T)-3')
MarR family transcriptional regulator

Keywords

TRANSCRIPTION REGULATOR/DNA / TRANSCRIPTION REGULATOR-DNA complex

Function / homology

Function and homology information

response to stress / DNA-binding transcription factor activity
Similarity search - Function

Biological species

Staphylococcus epidermidis (bacteria)
synthetic construct (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3 Å

Authors

Liu, G. / Liu, X. / Gan, J. / Yang, C.G.

Citation

Journal: J. Am. Chem. Soc. / Year: 2017
Title: Structural Insights into the Redox-Sensing Mechanism of MarR-Type Regulator AbfR.
Authors: Liu, G. / Liu, X. / Xu, H. / Liu, X. / Zhou, H. / Huang, Z. / Gan, J. / Chen, H. / Lan, L. / Yang, C.G.

History

Deposition	Jan 15, 2016	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Jan 25, 2017	Provider: repository / Type: Initial release
Revision 1.1	Apr 5, 2017	Group: Database references
Revision 1.2	Nov 8, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

-
Download

PDBx/mmCIF format	5hlg.cif.gz	335.6 KB	Display	PDBx/mmCIF format
PDB format	pdb5hlg.ent.gz	264.5 KB	Display	PDB format
PDBx/mmJSON format	5hlg.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	5hlg_validation.pdf.gz	521.1 KB	Display	wwPDB validaton report
Full document	5hlg_full_validation.pdf.gz	530.7 KB	Display
Data in XML	5hlg_validation.xml.gz	40.9 KB	Display
Data in CIF	5hlg_validation.cif.gz	57.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/hl/5hlg ftp://data.pdbj.org/pub/pdb/validation_reports/hl/5hlg	HTTPS FTP

-
Related structure data

Related structure data	5hlhC 5hliC 4hblS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	5hlh-2 5hlh-1 2ja3-2 5hlh-4 5hlh-3 5nzm-d 5nzh-1 3kw2-d 5o4p-1 3q5f-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) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

5hlhC

5hliC

4hblS

C: citing same article (ref.)

S: Starting model for refinement

Similar structure data

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#67 - Jul 2005 TATA-Binding Protein similarity (1) #91 - Jul 2007 Thymine Dimers similarity (1) #255 - Mar 2021 Cisplatin and DNA similarity (1) #168 - Dec 2013 DNA Helicase similarity (1) #253 - Jan 2021 Expressome similarity (1) #172 - Apr 2014 RecA and Rad51 similarity (1) #122 - Feb 2010 Enhanceosome similarity (1) #181 - Jan 2015 Cascade and CRISPR similarity (1) #84 - Dec 2006 Transposase similarity (1) #48 - Dec 2003 Catabolite Activator Protein similarity (1) #227 - Nov 2018 Telomerase similarity (1) #112 - Apr 2009 Oct and Sox Transcription Factors similarity (1) #150 - Jun 2012 Sliding Clamps similarity (1) #180 - Dec 2014 TAL Effectors similarity (1) #135 - Mar 2011 Integrase similarity (1) #40 - Apr 2003 RNA Polymerase similarity (1) #155 - Nov 2012 Vitamin D Receptor similarity (1) #87 - Mar 2007 Zinc Fingers similarity (1) #73 - Jan 2006 Topoisomerase similarity (1) #3 - Mar 2000 DNA Polymerase similarity (1) #139 - Jul 2011 DNA Methyltransferase similarity (1) #125 - May 2010 Parvoviruses similarity (1) #131 - Nov 2010 Inteins similarity (1) #8 - Aug 2000 Restriction Enzymes similarity (1) #7 - Jul 2000 Nucleosome similarity (1) #55 - Jul 2004 DNA Ligase similarity (1) #45 - Sep 2003 Estrogen Receptor similarity (1) #33 - Sep 2002 HIV Reverse Transcriptase similarity (1) #39 - Mar 2003 lac Repressor similarity (1) #160 - Apr 2013 Actinomycin similarity (1) #31 - Jul 2002 p53 Tumor Suppressor similarity (1) #258 - Jun 2021 Glucocorticoid Receptor and Dexamethasone similarity (1) #257 - May 2021 Fetal Hemoglobin similarity (1) #119 - Nov 2009 Designed DNA Crystal similarity (1) #240 - Dec 2019 Hypoxia-Inducible Factors similarity (1) #23 - Nov 2001 DNA similarity (1) #190 - Oct 2015 Two-component Systems similarity (1) #92 - Aug 2007 Anabolic Steroids similarity (1) #241 - Jan 2020 Twenty Years of Molecules similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#67 - Jul 2005
TATA-Binding Protein
similarity (1)
#91 - Jul 2007
Thymine Dimers
similarity (1)
#255 - Mar 2021
Cisplatin and DNA
similarity (1)
#168 - Dec 2013
DNA Helicase
similarity (1)
#253 - Jan 2021
Expressome
similarity (1)
#172 - Apr 2014
RecA and Rad51
similarity (1)
#122 - Feb 2010
Enhanceosome
similarity (1)
#181 - Jan 2015
Cascade and CRISPR
similarity (1)
#84 - Dec 2006
Transposase
similarity (1)
#48 - Dec 2003
Catabolite Activator Protein
similarity (1)
#227 - Nov 2018
Telomerase
similarity (1)
#112 - Apr 2009
Oct and Sox Transcription Factors
similarity (1)
#150 - Jun 2012
Sliding Clamps
similarity (1)
#180 - Dec 2014
TAL Effectors
similarity (1)
#135 - Mar 2011
Integrase
similarity (1)
#40 - Apr 2003
RNA Polymerase
similarity (1)
#155 - Nov 2012
Vitamin D Receptor
similarity (1)
#87 - Mar 2007
Zinc Fingers
similarity (1)
#73 - Jan 2006
Topoisomerase
similarity (1)
#3 - Mar 2000
DNA Polymerase
similarity (1)
#139 - Jul 2011
DNA Methyltransferase
similarity (1)
#125 - May 2010
Parvoviruses
similarity (1)
#131 - Nov 2010
Inteins
similarity (1)
#8 - Aug 2000
Restriction Enzymes
similarity (1)
#7 - Jul 2000
Nucleosome
similarity (1)
#55 - Jul 2004
DNA Ligase
similarity (1)
#45 - Sep 2003
Estrogen Receptor
similarity (1)
#33 - Sep 2002
HIV Reverse Transcriptase
similarity (1)
#39 - Mar 2003
lac Repressor
similarity (1)
#160 - Apr 2013
Actinomycin
similarity (1)
#31 - Jul 2002
p53 Tumor Suppressor
similarity (1)
#258 - Jun 2021
Glucocorticoid Receptor and Dexamethasone
similarity (1)
#257 - May 2021
Fetal Hemoglobin
similarity (1)
#119 - Nov 2009
Designed DNA Crystal
similarity (1)
#240 - Dec 2019
Hypoxia-Inducible Factors
similarity (1)
#23 - Nov 2001
DNA
similarity (1)
#190 - Oct 2015
Two-component Systems
similarity (1)
#92 - Aug 2007
Anabolic Steroids
similarity (1)
#241 - Jan 2020
Twenty Years of Molecules
similarity (1)

Deposited unit

I: DNA (5'-D(*TP*AP*AP*CP*TP*CP*AP*AP*TP*CP*GP*CP*GP*CP*GP*CP*GP*AP*TP*TP*GP*AP*GP*T)-3')

J: DNA (5'-D(*TP*AP*AP*CP*TP*CP*AP*AP*TP*CP*GP*CP*GP*CP*GP*CP*GP*AP*TP*TP*GP*AP*GP*T)-3')

K: DNA (5'-D(*TP*AP*AP*CP*TP*CP*AP*AP*TP*CP*GP*CP*GP*CP*GP*CP*GP*AP*TP*TP*GP*AP*GP*T)-3')

L: DNA (5'-D(*TP*AP*AP*CP*TP*CP*AP*AP*TP*CP*GP*CP*GP*CP*GP*CP*GP*AP*TP*TP*GP*AP*GP*T)-3')

M: DNA (5'-D(*TP*AP*AP*CP*TP*CP*AP*AP*TP*CP*GP*CP*GP*CP*GP*CP*GP*AP*TP*TP*GP*AP*GP*T)-3')

N: DNA (5'-D(*TP*AP*AP*CP*TP*CP*AP*AP*TP*CP*GP*CP*GP*CP*GP*CP*GP*AP*TP*TP*GP*AP*GP*T)-3')

O: DNA (5'-D(*TP*AP*AP*CP*TP*CP*AP*AP*TP*CP*GP*CP*GP*CP*GP*CP*GP*AP*TP*TP*GP*AP*GP*T)-3')

P: DNA (5'-D(*TP*AP*AP*CP*TP*CP*AP*AP*TP*CP*GP*CP*GP*CP*GP*CP*GP*AP*TP*TP*GP*AP*GP*T)-3')

A: MarR family transcriptional regulator

B: MarR family transcriptional regulator

C: MarR family transcriptional regulator

D: MarR family transcriptional regulator

E: MarR family transcriptional regulator

F: MarR family transcriptional regulator

G: MarR family transcriptional regulator

H: MarR family transcriptional regulator

199 kDa, 16 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

I: DNA (5'-D(*TP*AP*AP*CP*TP*CP*AP*AP*TP*CP*GP*CP*GP*CP*GP*CP*GP*AP*TP*TP*GP*AP*GP*T)-3')

J: DNA (5'-D(*TP*AP*AP*CP*TP*CP*AP*AP*TP*CP*GP*CP*GP*CP*GP*CP*GP*AP*TP*TP*GP*AP*GP*T)-3')

A: MarR family transcriptional regulator

B: MarR family transcriptional regulator

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

2

K: DNA (5'-D(*TP*AP*AP*CP*TP*CP*AP*AP*TP*CP*GP*CP*GP*CP*GP*CP*GP*AP*TP*TP*GP*AP*GP*T)-3')

L: DNA (5'-D(*TP*AP*AP*CP*TP*CP*AP*AP*TP*CP*GP*CP*GP*CP*GP*CP*GP*AP*TP*TP*GP*AP*GP*T)-3')

C: MarR family transcriptional regulator

D: MarR family transcriptional regulator

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

3

M: DNA (5'-D(*TP*AP*AP*CP*TP*CP*AP*AP*TP*CP*GP*CP*GP*CP*GP*CP*GP*AP*TP*TP*GP*AP*GP*T)-3')

N: DNA (5'-D(*TP*AP*AP*CP*TP*CP*AP*AP*TP*CP*GP*CP*GP*CP*GP*CP*GP*AP*TP*TP*GP*AP*GP*T)-3')

E: MarR family transcriptional regulator

F: MarR family transcriptional regulator

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

4

O: DNA (5'-D(*TP*AP*AP*CP*TP*CP*AP*AP*TP*CP*GP*CP*GP*CP*GP*CP*GP*AP*TP*TP*GP*AP*GP*T)-3')

P: DNA (5'-D(*TP*AP*AP*CP*TP*CP*AP*AP*TP*CP*GP*CP*GP*CP*GP*CP*GP*AP*TP*TP*GP*AP*GP*T)-3')

G: MarR family transcriptional regulator

H: MarR family transcriptional regulator

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

Unit cell

Length a, b, c (Å)	150.325, 290.504, 52.584
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P2₁2₁2

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Component-ID: _ / Refine code: _

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	DT	DT	DT	DT	I	A	1 - 24	1 - 24
2	1	DT	DT	DT	DT	J	B	1 - 24	1 - 24
1	2	DT	DT	DT	DT	I	A	1 - 24	1 - 24
2	2	DT	DT	DT	DT	K	C	1 - 24	1 - 24
1	3	DT	DT	DT	DT	I	A	1 - 24	1 - 24
2	3	DT	DT	DT	DT	L	D	1 - 24	1 - 24
1	4	DT	DT	DT	DT	I	A	1 - 24	1 - 24
2	4	DT	DT	DT	DT	M	E	1 - 24	1 - 24
1	5	DT	DT	DT	DT	I	A	1 - 24	1 - 24
2	5	DT	DT	DT	DT	N	F	1 - 24	1 - 24
1	6	DT	DT	DT	DT	I	A	1 - 24	1 - 24
2	6	DT	DT	DT	DT	O	G	1 - 24	1 - 24
1	7	DT	DT	DT	DT	I	A	1 - 24	1 - 24
2	7	DT	DT	DT	DT	P	H	1 - 24	1 - 24
1	8	DT	DT	DT	DT	J	B	1 - 24	1 - 24
2	8	DT	DT	DT	DT	K	C	1 - 24	1 - 24
1	9	DT	DT	DT	DT	J	B	1 - 24	1 - 24
2	9	DT	DT	DT	DT	L	D	1 - 24	1 - 24
1	10	DT	DT	DT	DT	J	B	1 - 24	1 - 24
2	10	DT	DT	DT	DT	M	E	1 - 24	1 - 24
1	11	DT	DT	DT	DT	J	B	1 - 24	1 - 24
2	11	DT	DT	DT	DT	N	F	1 - 24	1 - 24
1	12	DT	DT	DT	DT	J	B	1 - 24	1 - 24
2	12	DT	DT	DT	DT	O	G	1 - 24	1 - 24
1	13	DT	DT	DT	DT	J	B	1 - 24	1 - 24
2	13	DT	DT	DT	DT	P	H	1 - 24	1 - 24
1	14	DT	DT	DT	DT	K	C	1 - 24	1 - 24
2	14	DT	DT	DT	DT	L	D	1 - 24	1 - 24
1	15	DT	DT	DT	DT	K	C	1 - 24	1 - 24
2	15	DT	DT	DT	DT	M	E	1 - 24	1 - 24
1	16	DT	DT	DT	DT	K	C	1 - 24	1 - 24
2	16	DT	DT	DT	DT	N	F	1 - 24	1 - 24
1	17	DT	DT	DT	DT	K	C	1 - 24	1 - 24
2	17	DT	DT	DT	DT	O	G	1 - 24	1 - 24
1	18	DT	DT	DT	DT	K	C	1 - 24	1 - 24
2	18	DT	DT	DT	DT	P	H	1 - 24	1 - 24
1	19	DT	DT	DT	DT	L	D	1 - 24	1 - 24
2	19	DT	DT	DT	DT	M	E	1 - 24	1 - 24
1	20	DT	DT	DT	DT	L	D	1 - 24	1 - 24
2	20	DT	DT	DT	DT	N	F	1 - 24	1 - 24
1	21	DT	DT	DT	DT	L	D	1 - 24	1 - 24
2	21	DT	DT	DT	DT	O	G	1 - 24	1 - 24
1	22	DT	DT	DT	DT	L	D	1 - 24	1 - 24
2	22	DT	DT	DT	DT	P	H	1 - 24	1 - 24
1	23	DT	DT	DT	DT	M	E	1 - 24	1 - 24
2	23	DT	DT	DT	DT	N	F	1 - 24	1 - 24
1	24	DT	DT	DT	DT	M	E	1 - 24	1 - 24
2	24	DT	DT	DT	DT	O	G	1 - 24	1 - 24
1	25	DT	DT	DT	DT	M	E	1 - 24	1 - 24
2	25	DT	DT	DT	DT	P	H	1 - 24	1 - 24
1	26	DT	DT	DT	DT	N	F	1 - 24	1 - 24
2	26	DT	DT	DT	DT	O	G	1 - 24	1 - 24
1	27	DT	DT	DT	DT	N	F	1 - 24	1 - 24
2	27	DT	DT	DT	DT	P	H	1 - 24	1 - 24
1	28	DT	DT	DT	DT	O	G	1 - 24	1 - 24
2	28	DT	DT	DT	DT	P	H	1 - 24	1 - 24
1	29	GLN	GLN	GLU	GLU	A	I	3 - 145	5 - 147
2	29	GLN	GLN	GLU	GLU	B	J	3 - 145	5 - 147
1	30	GLU	GLU	GLU	GLU	A	I	4 - 145	6 - 147
2	30	GLU	GLU	GLU	GLU	C	K	4 - 145	6 - 147
1	31	GLN	GLN	LEU	LEU	A	I	3 - 143	5 - 145
2	31	GLN	GLN	LEU	LEU	D	L	3 - 143	5 - 145
1	32	GLN	GLN	ILE	ILE	A	I	3 - 144	5 - 146
2	32	GLN	GLN	ILE	ILE	E	M	3 - 144	5 - 146
1	33	GLN	GLN	ILE	ILE	A	I	3 - 144	5 - 146
2	33	GLN	GLN	ILE	ILE	F	N	3 - 144	5 - 146
1	34	GLN	GLN	GLU	GLU	A	I	3 - 145	5 - 147
2	34	GLN	GLN	GLU	GLU	G	O	3 - 145	5 - 147
1	35	GLN	GLN	GLU	GLU	A	I	3 - 145	5 - 147
2	35	GLN	GLN	GLU	GLU	H	P	3 - 145	5 - 147
1	36	GLU	GLU	GLU	GLU	B	J	4 - 145	6 - 147
2	36	GLU	GLU	GLU	GLU	C	K	4 - 145	6 - 147
1	37	MET	MET	ILE	ILE	B	J	1 - 144	3 - 146
2	37	MET	MET	ILE	ILE	D	L	1 - 144	3 - 146
1	38	MET	MET	GLU	GLU	B	J	1 - 145	3 - 147
2	38	MET	MET	GLU	GLU	E	M	1 - 145	3 - 147
1	39	MET	MET	GLU	GLU	B	J	1 - 145	3 - 147
2	39	MET	MET	GLU	GLU	F	N	1 - 145	3 - 147
1	40	GLN	GLN	GLU	GLU	B	J	3 - 145	5 - 147
2	40	GLN	GLN	GLU	GLU	G	O	3 - 145	5 - 147
1	41	MET	MET	GLU	GLU	B	J	1 - 145	3 - 147
2	41	MET	MET	GLU	GLU	H	P	1 - 145	3 - 147
1	42	GLU	GLU	LEU	LEU	C	K	4 - 143	6 - 145
2	42	GLU	GLU	LEU	LEU	D	L	4 - 143	6 - 145
1	43	GLU	GLU	ILE	ILE	C	K	4 - 144	6 - 146
2	43	GLU	GLU	ILE	ILE	E	M	4 - 144	6 - 146
1	44	GLU	GLU	ILE	ILE	C	K	4 - 144	6 - 146
2	44	GLU	GLU	ILE	ILE	F	N	4 - 144	6 - 146
1	45	GLU	GLU	GLU	GLU	C	K	4 - 145	6 - 147
2	45	GLU	GLU	GLU	GLU	G	O	4 - 145	6 - 147
1	46	GLU	GLU	ILE	ILE	C	K	4 - 144	6 - 146
2	46	GLU	GLU	ILE	ILE	H	P	4 - 144	6 - 146
1	47	ASN	ASN	ILE	ILE	D	L	0 - 144	2 - 146
2	47	ASN	ASN	ILE	ILE	E	M	0 - 144	2 - 146
1	48	ASN	ASN	LEU	LEU	D	L	0 - 143	2 - 145
2	48	ASN	ASN	LEU	LEU	F	N	0 - 143	2 - 145
1	49	GLN	GLN	LEU	LEU	D	L	3 - 143	5 - 145
2	49	GLN	GLN	LEU	LEU	G	O	3 - 143	5 - 145
1	50	MET	MET	LEU	LEU	D	L	1 - 143	3 - 145
2	50	MET	MET	LEU	LEU	H	P	1 - 143	3 - 145
1	51	ASN	ASN	GLU	GLU	E	M	0 - 145	2 - 147
2	51	ASN	ASN	GLU	GLU	F	N	0 - 145	2 - 147
1	52	GLN	GLN	ILE	ILE	E	M	3 - 144	5 - 146
2	52	GLN	GLN	ILE	ILE	G	O	3 - 144	5 - 146
1	53	MET	MET	GLU	GLU	E	M	1 - 145	3 - 147
2	53	MET	MET	GLU	GLU	H	P	1 - 145	3 - 147
1	54	GLN	GLN	ILE	ILE	F	N	3 - 144	5 - 146
2	54	GLN	GLN	ILE	ILE	G	O	3 - 144	5 - 146
1	55	MET	MET	GLU	GLU	F	N	1 - 145	3 - 147
2	55	MET	MET	GLU	GLU	H	P	1 - 145	3 - 147
1	56	GLN	GLN	ILE	ILE	G	O	3 - 144	5 - 146
2	56	GLN	GLN	ILE	ILE	H	P	3 - 144	5 - 146

NCS ensembles :

#1: DNA chain	DNA (5'-D(TPAPAPCPTPCPAPAPTPCPGPCPGPCPGPCPGPAPTPTPGPAPGPT)-3') Mass: 7369.767 Da / Num. of mol.: 8 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Protein	MarR family transcriptional regulator Mass: 17555.832 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus epidermidis (bacteria) / Gene: ADT70_02765, SETS_06435 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0N1EJ89, UniProt: Q5HKZ1*PLUS

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.95 Å³/Da / Density % sol: 58.25 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, hanging drop Details: 100mM sodium cacodylate, 100mM NaCl, 50mM MgCl2, 12% PEG 5000

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9735 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 19, 2011
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9735 Å / Relative weight: 1
Reflection	Resolution: 3→50 Å / Num. obs: 47129 / % possible obs: 99.3 % / Redundancy: 14.1 % / Net I/σ(I): 24
Reflection shell	Resolution: 3→3.11 Å

-
Processing

Software

Name	Version	Classification
REFMAC	5.7.0029	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4HBL

4hbl

Resolution: 3→30 Å / Cor.coef. F_o:F_c: 0.93 / Cor.coef. F_o:F_c free: 0.913 / SU B: 17.415 / SU ML: 0.318 / Cross valid method: THROUGHOUT / ESU R Free: 0.425 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.25675	2380	5.1 %	RANDOM
R_work	0.22596	-	-	-
obs	0.22756	44652	99.02 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 92.104 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	3.48 Å²	0 Å²	-0 Å²
2-	-	-5.08 Å²	-0 Å²
3-	-	-	1.6 Å²

Refinement step

Cycle: 1 / Resolution: 3→30 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9112	3912	0	0	13024

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.017	13641
X-RAY DIFFRACTION	r_bond_other_d	0.006	0.02	11059
X-RAY DIFFRACTION	r_angle_refined_deg	1.256	1.683	19213
X-RAY DIFFRACTION	r_angle_other_deg	1.794	3	25552
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.836	5	1083
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.945	25.172	493
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	18.646	15	1794
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.761	15	56
X-RAY DIFFRACTION	r_chiral_restr	0.091	0.2	1963
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	12739
X-RAY DIFFRACTION	r_gen_planes_other	0.005	0.02	3185
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
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it
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 / Type: interatomic distance / Weight position: 0.05

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	I	1570	0.04
1	2	J	1570	0.04
2	1	I	1576	0.03
2	2	K	1576	0.03
3	1	I	1560	0.06
3	2	L	1560	0.06
4	1	I	1582	0.03
4	2	M	1582	0.03
5	1	I	1577	0.03
5	2	N	1577	0.03
6	1	I	1565	0.07
6	2	O	1565	0.07
7	1	I	1572	0.05
7	2	P	1572	0.05
8	1	J	1579	0.03
8	2	K	1579	0.03
9	1	J	1586	0.04
9	2	L	1586	0.04
10	1	J	1580	0.03
10	2	M	1580	0.03
11	1	J	1579	0.03
11	2	N	1579	0.03
12	1	J	1567	0.07
12	2	O	1567	0.07
13	1	J	1574	0.05
13	2	P	1574	0.05
14	1	K	1569	0.05
14	2	L	1569	0.05
15	1	K	1588	0.01
15	2	M	1588	0.01
16	1	K	1582	0.02
16	2	N	1582	0.02
17	1	K	1575	0.06
17	2	O	1575	0.06
18	1	K	1580	0.04
18	2	P	1580	0.04
19	1	L	1572	0.05
19	2	M	1572	0.05
20	1	L	1572	0.05
20	2	N	1572	0.05
21	1	L	1560	0.08
21	2	O	1560	0.08
22	1	L	1566	0.04
22	2	P	1566	0.04
23	1	M	1589	0.01
23	2	N	1589	0.01
24	1	M	1578	0.06
24	2	O	1578	0.06
25	1	M	1584	0.04
25	2	P	1584	0.04
26	1	N	1577	0.06
26	2	O	1577	0.06
27	1	N	1583	0.04
27	2	P	1583	0.04
28	1	O	1569	0.07
28	2	P	1569	0.07
29	1	A	7324	0.11
29	2	B	7324	0.11
30	1	A	7347	0.1
30	2	C	7347	0.1
31	1	A	7263	0.1
31	2	D	7263	0.1
32	1	A	7339	0.1
32	2	E	7339	0.1
33	1	A	7317	0.11
33	2	F	7317	0.11
34	1	A	7426	0.09
34	2	G	7426	0.09
35	1	A	7339	0.09
35	2	H	7339	0.09
36	1	B	7376	0.1
36	2	C	7376	0.1
37	1	B	7506	0.09
37	2	D	7506	0.09
38	1	B	7530	0.11
38	2	E	7530	0.11
39	1	B	7530	0.1
39	2	F	7530	0.1
40	1	B	7460	0.09
40	2	G	7460	0.09
41	1	B	7714	0.1
41	2	H	7714	0.1
42	1	C	7198	0.11
42	2	D	7198	0.11
43	1	C	7343	0.09
43	2	E	7343	0.09
44	1	C	7278	0.11
44	2	F	7278	0.11
45	1	C	7390	0.1
45	2	G	7390	0.1
46	1	C	7354	0.1
46	2	H	7354	0.1
47	1	D	7541	0.1
47	2	E	7541	0.1
48	1	D	7485	0.09
48	2	F	7485	0.09
49	1	D	7335	0.1
49	2	G	7335	0.1
50	1	D	7455	0.09
50	2	H	7455	0.09
51	1	E	7517	0.11
51	2	F	7517	0.11
52	1	E	7385	0.1
52	2	G	7385	0.1
53	1	E	7537	0.1
53	2	H	7537	0.1
54	1	F	7400	0.1
54	2	G	7400	0.1
55	1	F	7545	0.1
55	2	H	7545	0.1
56	1	G	7420	0.09
56	2	H	7420	0.09

LS refinement shell

Resolution: 3→3.077 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.327	166	-
R_work	0.311	3207	-
obs	-	-	98.11 %

-
News

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

New format data for meta-information of EMDB entries

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

Related info.:EMDB header

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

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

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

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

+
Mar 5, 2020. Novel coronavirus structure data

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

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

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

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

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

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

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

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

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

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

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

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

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

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

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

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

+
Jul 12, 2017. Major update of PDB

-
Yorodumi