PDB-1gtn: Structure of the trp RNA-binding attenuation protein (TRAP) bound...

ID or keywords:

Entry

Database: PDB / ID: 1gtn

Title

Structure of the trp RNA-binding attenuation protein (TRAP) bound to an RNA molecule containing 11 GAGCC repeats

Components

(GAGCC)11G 56-NUCLEOTIDE RNA
TRP RNA-BINDING ATTENUATION PROTEIN

Keywords

RNA BINDING PROTEIN/RNA / RNA BINDING PROTEIN-RNA COMPLEX / TRANSCRIPTION ATTENUATION /

RNA-BINDING PROTEIN / TRP RNA

Function / homology

Function and homology information

DNA-templated transcription termination / regulation of DNA-templated transcription /

RNA binding / identical protein binding
Similarity search - Function

Biological species

BACILLUS STEAROTHERMOPHILUS (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.5 Å

Authors

Hopcroft, N.H. / Wendt, A.L. / Gollnick, P. / Antson, A.A.

Citation

Journal: Acta Crystallogr.,Sect.D / Year: 2002
Title: Specificity of Trap-RNA Interactions: Crystal Structures of Two Complexes with Different RNA Sequences
Authors: Hopcroft, N.H. / Wendt, A.L. / Gollnick, P. / Antson, A.A.

History

Deposition	Jan 16, 2002	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Apr 5, 2002	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	1gtn.cif.gz	327.2 KB	Display	PDBx/mmCIF format
PDB format	pdb1gtn.ent.gz	263.8 KB	Display	PDB format
PDBx/mmJSON format	1gtn.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/gt/1gtn ftp://data.pdbj.org/pub/pdb/validation_reports/gt/1gtn	HTTPS FTP

-
Related structure data

Related structure data	1gtfSC 1c9s 1qaw S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5ef0-1 5eew-1 1gtf-1 5ef1-1 5ef2-1 5ef3-1 1c9s-1 5eeu-1 1qaw-d 5eey-1 5eez-1 5eex-1 5eev-1 1utd-1 3aqd-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) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

1gtfSC

1c9s

1qaw

S: Starting model for refinement

C: citing same article (ref.)

Similar structure data

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#121 - Jan 2010 70S Ribosomes similarity (1) #130 - Oct 2010 Riboswitches similarity (1) #16 - Apr 2001 Aminoacyl-tRNA Synthetases similarity (1) #157 - Jan 2013 Transfer-Messenger RNA similarity (1) #229 - Jan 2019 Fluorescent RNA Aptamers similarity (1) #181 - Jan 2015 Cascade and CRISPR similarity (1) #253 - Jan 2021 Expressome similarity (1) #260 - Aug 2021 Ribonuclease P similarity (1) #249 - Sep 2020 SARS-CoV-2 RNA-dependent RNA Polymerase similarity (1) #15 - Mar 2001 Transfer RNA similarity (1) #146 - Feb 2012 Aminoglycoside Antibiotics similarity (1) #210 - Jun 2017 Adenine Riboswitch in Action similarity (1) #10 - Oct 2000 Ribosome similarity (1) #87 - Mar 2007 Zinc Fingers similarity (1) #245 - May 2020 Spliceosomes similarity (1) #262 - Oct 2021 Fifty Years of Open Access to PDB Structures similarity (1) #65 - May 2005 Self-splicing RNA similarity (1) #98 - Feb 2008 Small Interfering RNA similarity (1) #226 - Oct 2018 Aminoglycoside Antibiotics and Resistance similarity (1) #105 - Sep 2008 Ribonuclease A similarity (1) #230 - Feb 2019 Initiation Factor eIF4E similarity (1) #227 - Nov 2018 Telomerase similarity (1) #161 - May 2013 Ricin similarity (1) #143 - Nov 2011 Toll-like Receptors similarity (1) #106 - Oct 2008 Poly(A) Polymerase similarity (1) #266 - Feb 2022 Oligosaccharyltransferase similarity (1) #81 - Sep 2006 Elongation Factors similarity (1) #104 - Aug 2008 Selenocysteine Synthase similarity (1) #89 - May 2007 Aconitase and Iron Regulatory Protein 1 similarity (1) #241 - Jan 2020 Twenty Years of Molecules similarity (1) #228 - Dec 2018 Directed Evolution of Enzymes similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#121 - Jan 2010
70S Ribosomes
similarity (1)
#130 - Oct 2010
Riboswitches
similarity (1)
#16 - Apr 2001
Aminoacyl-tRNA Synthetases
similarity (1)
#157 - Jan 2013
Transfer-Messenger RNA
similarity (1)
#229 - Jan 2019
Fluorescent RNA Aptamers
similarity (1)
#181 - Jan 2015
Cascade and CRISPR
similarity (1)
#253 - Jan 2021
Expressome
similarity (1)
#260 - Aug 2021
Ribonuclease P
similarity (1)
#249 - Sep 2020
SARS-CoV-2 RNA-dependent RNA Polymerase
similarity (1)
#15 - Mar 2001
Transfer RNA
similarity (1)
#146 - Feb 2012
Aminoglycoside Antibiotics
similarity (1)
#210 - Jun 2017
Adenine Riboswitch in Action
similarity (1)
#10 - Oct 2000
Ribosome
similarity (1)
#87 - Mar 2007
Zinc Fingers
similarity (1)
#245 - May 2020
Spliceosomes
similarity (1)
#262 - Oct 2021
Fifty Years of Open Access to PDB Structures
similarity (1)
#65 - May 2005
Self-splicing RNA
similarity (1)
#98 - Feb 2008
Small Interfering RNA
similarity (1)
#226 - Oct 2018
Aminoglycoside Antibiotics and Resistance
similarity (1)
#105 - Sep 2008
Ribonuclease A
similarity (1)
#230 - Feb 2019
Initiation Factor eIF4E
similarity (1)
#227 - Nov 2018
Telomerase
similarity (1)
#161 - May 2013
Ricin
similarity (1)
#143 - Nov 2011
Toll-like Receptors
similarity (1)
#106 - Oct 2008
Poly(A) Polymerase
similarity (1)
#266 - Feb 2022
Oligosaccharyltransferase
similarity (1)
#81 - Sep 2006
Elongation Factors
similarity (1)
#104 - Aug 2008
Selenocysteine Synthase
similarity (1)
#89 - May 2007
Aconitase and Iron Regulatory Protein 1
similarity (1)
#241 - Jan 2020
Twenty Years of Molecules
similarity (1)
#228 - Dec 2018
Directed Evolution of Enzymes
similarity (1)

Deposited unit

A: TRP RNA-BINDING ATTENUATION PROTEIN

B: TRP RNA-BINDING ATTENUATION PROTEIN

C: TRP RNA-BINDING ATTENUATION PROTEIN

D: TRP RNA-BINDING ATTENUATION PROTEIN

E: TRP RNA-BINDING ATTENUATION PROTEIN

F: TRP RNA-BINDING ATTENUATION PROTEIN

G: TRP RNA-BINDING ATTENUATION PROTEIN

H: TRP RNA-BINDING ATTENUATION PROTEIN

I: TRP RNA-BINDING ATTENUATION PROTEIN

J: TRP RNA-BINDING ATTENUATION PROTEIN

K: TRP RNA-BINDING ATTENUATION PROTEIN

L: TRP RNA-BINDING ATTENUATION PROTEIN

M: TRP RNA-BINDING ATTENUATION PROTEIN

N: TRP RNA-BINDING ATTENUATION PROTEIN

O: TRP RNA-BINDING ATTENUATION PROTEIN

P: TRP RNA-BINDING ATTENUATION PROTEIN

Q: TRP RNA-BINDING ATTENUATION PROTEIN

R: TRP RNA-BINDING ATTENUATION PROTEIN

S: TRP RNA-BINDING ATTENUATION PROTEIN

T: TRP RNA-BINDING ATTENUATION PROTEIN

U: TRP RNA-BINDING ATTENUATION PROTEIN

V: TRP RNA-BINDING ATTENUATION PROTEIN

W: (GAGCC)11G 56-NUCLEOTIDE RNA

hetero molecules

205 kDa, 23 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: TRP RNA-BINDING ATTENUATION PROTEIN

B: TRP RNA-BINDING ATTENUATION PROTEIN

C: TRP RNA-BINDING ATTENUATION PROTEIN

D: TRP RNA-BINDING ATTENUATION PROTEIN

E: TRP RNA-BINDING ATTENUATION PROTEIN

F: TRP RNA-BINDING ATTENUATION PROTEIN

G: TRP RNA-BINDING ATTENUATION PROTEIN

H: TRP RNA-BINDING ATTENUATION PROTEIN

I: TRP RNA-BINDING ATTENUATION PROTEIN

J: TRP RNA-BINDING ATTENUATION PROTEIN

K: TRP RNA-BINDING ATTENUATION PROTEIN

hetero molecules

defined by author&software
93.3 kDa, 11 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

L: TRP RNA-BINDING ATTENUATION PROTEIN

M: TRP RNA-BINDING ATTENUATION PROTEIN

N: TRP RNA-BINDING ATTENUATION PROTEIN

O: TRP RNA-BINDING ATTENUATION PROTEIN

P: TRP RNA-BINDING ATTENUATION PROTEIN

Q: TRP RNA-BINDING ATTENUATION PROTEIN

R: TRP RNA-BINDING ATTENUATION PROTEIN

S: TRP RNA-BINDING ATTENUATION PROTEIN

T: TRP RNA-BINDING ATTENUATION PROTEIN

U: TRP RNA-BINDING ATTENUATION PROTEIN

V: TRP RNA-BINDING ATTENUATION PROTEIN

W: (GAGCC)11G 56-NUCLEOTIDE RNA

hetero molecules

defined by author&software
111 kDa, 12 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	145.839, 111.722, 138.715
Angle α, β, γ (deg.)	90.00, 117.78, 90.00
Int Tables number	5
Space group name H-M	C121

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:
NCS ensembles :

ID
1
2

Details

BIOMOLECULE 1 IS AN 11 MER WHILST BIOMOLECULE 2 IS A12 MER CONSISTING OF AN 11 MER WITH BOUND RNA CHAIN

#1: Protein	... TRP RNA-BINDING ATTENUATION PROTEIN Mass: 8257.377 Da / Num. of mol.: 22 Source method: isolated from a genetically manipulated source Details: THE STRUCTURE CONTAINS 2 11-MER MOLECULES (CHAINS A TO K AND L TO V), (RESIDUES 1-75) (SOME N- AND C-TERMINAL RESIDUES MISSING DUE TO DISORDER) Source: (gene. exp.) BACILLUS STEAROTHERMOPHILUS (bacteria) / Plasmid: PTZSTMTRB / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): SG62052/PGP1-2 / References: UniProt: Q9X6J6
#2: RNA chain	(GAGCC)11G 56-NUCLEOTIDE RNA Mass: 18230.039 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Chemical	... ChemComp-TRP / TRYPTOPHAN / Tryptophan Type: L-peptide linking / Mass: 204.225 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: C₁₁H₁₂N₂O₂
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 73 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

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

-
Sample preparation

Crystal

Density Matthews: 2.5 Å³/Da / Density % sol: 50.4 %

Crystal grow

pH: 8
Details: 0.2M K-GLUTAMATE, 50MM TRIETHANOLAMINE PH8.0,10MM MGCL2, 8-11% MONOMETHYL PEG 2000,+0.4M KCL AT END, pH 8.00

Crystal grow

*PLUS

pH: 7.8 / Method: vapor diffusion, hanging drop

Components of the solutions

*PLUS

ID	Conc.	Common name	Crystal-ID	Sol-ID	Details	Chemical formula
1	15 mg/ml	protein-RNA	1	drop
2	70 mM	potassium phosphate	1	drop	pH7.8
3	10 mM	L-tryptophan	1	drop
4	0.2 M	potassium glutamate	1	reservoir
5	50 mM	tri-ethanolamine	1	reservoir	pH8.0
6	10 mM		1	reservoir		MgCl2
7	8-11 %	PEG2000 MME	1	reservoir

-
Data collection

Diffraction	Mean temperature: 120 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.946
Detector	Date: Feb 15, 1999
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.946 Å / Relative weight: 1
Reflection	Resolution: 2.5→20 Å / Num. obs: 65753 / % possible obs: 94.6 % / Redundancy: 1.8 % / R_merge(I) obs: 0.05 / Net I/σ(I): 13.5
Reflection shell	Resolution: 2.5→2.59 Å / Redundancy: 1.6 % / R_merge(I) obs: 0.265 / Mean I/σ(I) obs: 2.4 / % possible all: 77
Reflection	PLUS Lowest resolution: 20 Å / R_merge(I) obs*: 0.05
Reflection shell	PLUS Highest resolution: 2.5 Å / % possible obs: 77 % / Num. unique obs*: 5337

-
Processing

Software

Name	Version	Classification
REFMAC	5.1.07	refinement
DENZO		data reduction
SCALEPACK		data scaling
AMoRE		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1GTF

1gtf

Resolution: 2.5→19.84 Å / Cor.coef. F_o:F_c: 0.933 / Cor.coef. F_o:F_c free: 0.914 / SU B: 14.27 / SU ML: 0.294 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.654 / ESU R Free: 0.313 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: THE ASYMMETRIC UNIT CONTAINS TWO PROTEIN MOLECULES, EACH MADE UP OF 11 IDENTICAL POLYPEPTIDE CHAINS. ONE OF THESE 11-MERS HAS THE SINGLE RNA MOLECULE BOUND TO IT. THE PROTEIN CHAINS ARE ...

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.273	1312	2 %	RANDOM
R_work	0.235	-	-	-
obs	0.236	63405	100 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.5→19.84 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11855	968	345	73	13241

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.018	0.021	13345
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg
X-RAY DIFFRACTION	r_angle_other_deg	1.842	2.008	18072
X-RAY DIFFRACTION	r_dihedral_angle_1_deg
X-RAY DIFFRACTION	r_dihedral_angle_2_deg
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	18.287	15	2214
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.994	15	88
X-RAY DIFFRACTION	r_chiral_restr	0.107	0.2	2058
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	9541
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.246	0.2	4616
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	0.151	0.2	459
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	0.386	0.2	55
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.339	0.2	16
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	0.458	1.5	7584
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	0.786	2	12139
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	1.201	3	5761
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	1.706	4	5933
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	10	tight positional	0.16	0.3
1	2	B	10	tight positional	0.14	0.3
1	3	C	10	tight positional	0.22	0.3
1	4	D	10	tight positional	0.22	0.3
1	5	E	10	tight positional	0.16	0.3
1	6	F	10	tight positional	0.21	0.3
1	7	G	10	tight positional	0.18	0.3
1	8	H	10	tight positional	0.21	0.3
1	9	I	10	tight positional	0.17	0.3
1	10	J	10	tight positional	0.18	0.3
1	11	K	10	tight positional	0.9	0.3
2	1	L	636	tight positional	0.18	0.3
2	2	M	636	tight positional	0.2	0.3
2	3	N	636	tight positional	0.16	0.3
2	4	O	636	tight positional	0.21	0.3
2	5	P	636	tight positional	0.22	0.3
2	6	Q	636	tight positional	0.17	0.3
2	7	R	636	tight positional	0.19	0.3
2	8	S	636	tight positional	0.22	0.3
2	9	T	636	tight positional	0.19	0.3
2	10	U	636	tight positional	0.17	0.3
2	11	V	636	tight positional	0.21	0.3
1	1	A	269	medium positional	0.1	0.1
1	2	B	269	medium positional	0.1	0.1
1	3	C	269	medium positional	0.1	0.1
1	4	D	269	medium positional	0.1	0.1
1	5	E	269	medium positional	0.1	0.1
1	6	F	269	medium positional	0.11	0.1
1	7	G	269	medium positional	0.1	0.1
1	8	H	269	medium positional	0.1	0.1
1	9	I	269	medium positional	0.1	0.1
1	10	J	269	medium positional	0.11	0.1
1	11	K	269	medium positional	0.1	0.1
2	1	L	269	medium positional	0.02	0.1
2	2	M	269	medium positional	0.02	0.1
2	3	N	269	medium positional	0.02	0.1
2	4	O	269	medium positional	0.02	0.1
2	5	P	269	medium positional	0.02	0.1
2	6	Q	269	medium positional	0.02	0.1
2	7	R	269	medium positional	0.02	0.1
2	8	S	269	medium positional	0.02	0.1
2	9	T	269	medium positional	0.02	0.1
2	10	U	269	medium positional	0.02	0.1
2	11	V	269	medium positional	0.02	0.1
1	1	A	253	loose positional	0.63	2
1	2	B	253	loose positional	0.56	2
1	3	C	253	loose positional	0.81	2
1	4	D	253	loose positional	0.68	2
1	5	E	253	loose positional	0.72	2
1	6	F	253	loose positional	0.97	2
1	7	G	253	loose positional	0.48	2
1	8	H	253	loose positional	0.51	2
1	9	I	253	loose positional	0.59	2
1	10	J	253	loose positional	0.47	2
1	11	K	253	loose positional	0.44	2
2	1	L	253	loose positional	0.05	2
2	2	M	253	loose positional	0.05	2
2	3	N	253	loose positional	0.06	2
2	4	O	253	loose positional	0.05	2
2	5	P	253	loose positional	0.05	2
2	6	Q	253	loose positional	0.06	2
2	7	R	253	loose positional	0.04	2
2	8	S	253	loose positional	0.04	2
2	9	T	253	loose positional	0.05	2
2	10	U	253	loose positional	0.04	2
2	11	V	253	loose positional	0.04	2
1	1	A	10	tight thermal	0.48	1
1	2	B	10	tight thermal	0.4	1
1	3	C	10	tight thermal	0.67	1
1	4	D	10	tight thermal	0.23	1
1	5	E	10	tight thermal	0.38	1
1	6	F	10	tight thermal	0.55	1
1	7	G	10	tight thermal	0.61	1
1	8	H	10	tight thermal	0.18	1
1	9	I	10	tight thermal	0.43	1
1	10	J	10	tight thermal	0.36	1
1	11	K	10	tight thermal	0.34	1
2	1	L	636	tight thermal	2.2	1
2	2	M	636	tight thermal	2.02	1
2	3	N	636	tight thermal	2.58	1
2	4	O	636	tight thermal	1.55	1
2	5	P	636	tight thermal	1.97	1
2	6	Q	636	tight thermal	2.37	1
2	7	R	636	tight thermal	2.47	1
2	8	S	636	tight thermal	1.35	1
2	9	T	636	tight thermal	2.09	1
2	10	U	636	tight thermal	1.91	1
2	11	V	636	tight thermal	1.86	1
1	1	A	269	medium thermal	0.27	1
1	2	B	269	medium thermal	0.26	1
1	3	C	269	medium thermal	0.27	1
1	4	D	269	medium thermal	0.25	1
1	5	E	269	medium thermal	0.3	1
1	6	F	269	medium thermal	0.28	1
1	7	G	269	medium thermal	0.32	1
1	8	H	269	medium thermal	0.28	1
1	9	I	269	medium thermal	0.27	1
1	10	J	269	medium thermal	0.28	1
1	11	K	269	medium thermal	0.26	1
2	1	L	269	medium thermal	2.51	1
2	2	M	269	medium thermal	2.44	1
2	3	N	269	medium thermal	2.5	1
2	4	O	269	medium thermal	2.39	1
2	5	P	269	medium thermal	2.62	1
2	6	Q	269	medium thermal	2.54	1
2	7	R	269	medium thermal	2.71	1
2	8	S	269	medium thermal	2.54	1
2	9	T	269	medium thermal	2.51	1
2	10	U	269	medium thermal	2.53	1
2	11	V	269	medium thermal	2.47	1
1	1	A	253	loose thermal	0.39	1
1	2	B	253	loose thermal	0.35	1
1	3	C	253	loose thermal	0.38	1
1	4	D	253	loose thermal	0.37	1
1	5	E	253	loose thermal	0.38	1
1	6	F	253	loose thermal	0.42	1
1	7	G	253	loose thermal	0.49	1
1	8	H	253	loose thermal	0.42	1
1	9	I	253	loose thermal	0.35	1
1	10	J	253	loose thermal	0.41	1
1	11	K	253	loose thermal	0.36	1
2	1	L	253	loose thermal	3.08	1
2	2	M	253	loose thermal	2.93	1
2	3	N	253	loose thermal	3.08	1
2	4	O	253	loose thermal	3.04	1
2	5	P	253	loose thermal	3.06	1
2	6	Q	253	loose thermal	3.23	1
2	7	R	253	loose thermal	3.48	1
2	8	S	253	loose thermal	3.23	1
2	9	T	253	loose thermal	2.95	1
2	10	U	253	loose thermal	3.19	1
2	11	V	253	loose thermal	3	1

LS refinement shell

Resolution: 2.5→2.56 Å / Total num. of bins used: 20 /

	R_factor	Num. reflection
R_free	0.376	72
R_work	0.334	3795

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	0.5535	-0.0765	-0.62	0.7053	0.0774	2.4044	-0.0144	0.0867	-0.0091	-0.4004	-0.0719	-0.1503	0.1883	0.1571	0.0864	0.2606	0.0523	0.0041	0.1789	-0.0037	0.2962	57.1446	0.0758	14.1041
2	0.6707	-0.0236	-0.6611	0.7785	0.0049	2.542	-0.0262	0.088	-0.0277	-0.2031	-0.0319	-0.064	0.1249	0.0623	0.0581	0.0178	-0.0011	-0.0728	0.206	-0.0067	0.2975	46.3265	-0.025	44.9895

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	7 - 74
2	X-RAY DIFFRACTION	1	A	81 - 181
3	X-RAY DIFFRACTION	1	B	6 - 74
4	X-RAY DIFFRACTION	1	B	81
5	X-RAY DIFFRACTION	1	C	6 - 74
6	X-RAY DIFFRACTION	1	C	81
7	X-RAY DIFFRACTION	1	D	7 - 75
8	X-RAY DIFFRACTION	1	D	81
9	X-RAY DIFFRACTION	1	E	7 - 74
10	X-RAY DIFFRACTION	1	E	81
11	X-RAY DIFFRACTION	1	F	7 - 75
12	X-RAY DIFFRACTION	1	F	81
13	X-RAY DIFFRACTION	1	G	6 - 75
14	X-RAY DIFFRACTION	1	G	81
15	X-RAY DIFFRACTION	1	H	7 - 75
16	X-RAY DIFFRACTION	1	H	81
17	X-RAY DIFFRACTION	1	I	7 - 75
18	X-RAY DIFFRACTION	1	I	81
19	X-RAY DIFFRACTION	1	J	7 - 74
20	X-RAY DIFFRACTION	1	J	81
21	X-RAY DIFFRACTION	1	K	7 - 75
22	X-RAY DIFFRACTION	1	K	81
23	X-RAY DIFFRACTION	2	L	5 - 74
24	X-RAY DIFFRACTION	2	L	81
25	X-RAY DIFFRACTION	2	M	5 - 75
26	X-RAY DIFFRACTION	2	M	81
27	X-RAY DIFFRACTION	2	N	5 - 74
28	X-RAY DIFFRACTION	2	N	81
29	X-RAY DIFFRACTION	2	O	5 - 75
30	X-RAY DIFFRACTION	2	O	81
31	X-RAY DIFFRACTION	2	P	5 - 74
32	X-RAY DIFFRACTION	2	P	81
33	X-RAY DIFFRACTION	2	Q	5 - 74
34	X-RAY DIFFRACTION	2	Q	81
35	X-RAY DIFFRACTION	2	R	5 - 74
36	X-RAY DIFFRACTION	2	R	81
37	X-RAY DIFFRACTION	2	S	5 - 74
38	X-RAY DIFFRACTION	2	S	81
39	X-RAY DIFFRACTION	2	T	5 - 74
40	X-RAY DIFFRACTION	2	T	81
41	X-RAY DIFFRACTION	2	U	5 - 74
42	X-RAY DIFFRACTION	2	U	81
43	X-RAY DIFFRACTION	2	V	5 - 74
44	X-RAY DIFFRACTION	2	V	81

Refinement

*PLUS

Lowest resolution: 20 Å / R_factor obs: 0.235 / R_factor R_free: 0.273 / R_factor R_work: 0.235

Solvent computation

*PLUS

Displacement parameters

*PLUS

Refine LS restraints

*PLUS

Refine-ID	Type	Dev ideal	Dev ideal target
X-RAY DIFFRACTION	r_bond_d	0.019	0.02
X-RAY DIFFRACTION	r_angle_d
X-RAY DIFFRACTION	r_angle_deg	2	2

-
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://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