PDB-3tcx: Structure of Engineered Single Domain ICAM-1 D1 with High-Affinit...

ID or keywords:

Entry

Database: PDB / ID: 3tcx

Title

Structure of Engineered Single Domain ICAM-1 D1 with High-Affinity aL Integrin I Domain of Native C-Terminal Helix Conformation

Components

Integrin alpha-L
Intercellular adhesion molecule 1

Keywords

CELL ADHESION / Rossmann Fold / Immunoglobulin-Like Fold / Membrane

Function / homology

Function and homology information

regulation of leukocyte mediated cytotoxicity / T cell extravasation / positive regulation of cellular extravasation / regulation of ruffle assembly / memory T cell extravasation / T cell antigen processing and presentation / integrin alphaL-beta2 complex / ICAM-3 receptor activity / membrane to membrane docking / T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.6 Å

Authors

Kang, S. / Kim, C.U. / Gu, X. / Owens, R.M. / van Rijn, S.J. / Boonyaleepun, V. / Mao, Y. / Springer, T.A. / Jin, M.M.

Citation

Journal: To be Published
Title: Structure of Engineered Single Domain ICAM-1 D1 with High-Affinity L Integrin I Domain of Native C-Terminal Helix Conformation
Authors: Kang, S. / Kim, C.U. / Gu, X. / Owens, R.M. / van Rijn, S.J. / Boonyaleepun, V. / Mao, Y. / Springer, T.A. / Jin, M.M.

History

Deposition	Aug 9, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 31, 2011	Provider: repository / Type: Initial release
Revision 1.1	Sep 7, 2011	Group: Other
Revision 1.2	Nov 12, 2014	Group: Structure summary
Revision 1.3	Nov 6, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_label_asym_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 / _struct_ref_seq_dif.details / _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	3tcx.cif.gz	1.5 MB	Display	PDBx/mmCIF format
PDB format	pdb3tcx.ent.gz	1.3 MB	Display	PDB format
PDBx/mmJSON format	3tcx.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	3tcx_validation.pdf.gz	523.6 KB	Display	wwPDB validaton report
Full document	3tcx_full_validation.pdf.gz	551.8 KB	Display
Data in XML	3tcx_validation.xml.gz	128.7 KB	Display
Data in CIF	3tcx_validation.cif.gz	169 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/tc/3tcx ftp://data.pdbj.org/pub/pdb/validation_reports/tc/3tcx	HTTPS FTP

-
Related structure data

Similar structure data	3hgy-d 6w9w-d 3qqa-d 3zco-1 5xd2-d 4yhr-d 1rgs-d 5v7l-d 4j37-d 3tt0-2 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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

Similar structure data

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#134 - Feb 2011 Integrin similarity (19) #186 - Jun 2015 Receptor for Advanced Glycation End Products similarity (1) #55 - Jul 2004 DNA Ligase similarity (3) #166 - Oct 2013 Proteasome similarity (3) #202 - Oct 2016 Dipeptidyl Peptidase 4 similarity (1) #214 - Oct 2017 Chimeric Antigen Receptors similarity (1) #83 - Nov 2006 Fibrin 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 (19)
#186 - Jun 2015
Receptor for Advanced Glycation End Products
similarity (1)
#55 - Jul 2004
DNA Ligase
similarity (3)
#166 - Oct 2013
Proteasome
similarity (3)
#202 - Oct 2016
Dipeptidyl Peptidase 4
similarity (1)
#214 - Oct 2017
Chimeric Antigen Receptors
similarity (1)
#83 - Nov 2006
Fibrin
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: Intercellular adhesion molecule 1

B: Integrin alpha-L

C: Intercellular adhesion molecule 1

D: Integrin alpha-L

E: Intercellular adhesion molecule 1

F: Integrin alpha-L

G: Intercellular adhesion molecule 1

H: Integrin alpha-L

I: Intercellular adhesion molecule 1

J: Integrin alpha-L

K: Intercellular adhesion molecule 1

L: Integrin alpha-L

M: Intercellular adhesion molecule 1

N: Integrin alpha-L

O: Intercellular adhesion molecule 1

P: Integrin alpha-L

Q: Intercellular adhesion molecule 1

R: Integrin alpha-L

S: Intercellular adhesion molecule 1

T: Integrin alpha-L

U: Intercellular adhesion molecule 1

V: Integrin alpha-L

W: Intercellular adhesion molecule 1

X: Integrin alpha-L

Y: Intercellular adhesion molecule 1

Z: Integrin alpha-L

a: Intercellular adhesion molecule 1

b: Integrin alpha-L

hetero molecules

418 kDa, 28 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Intercellular adhesion molecule 1

B: Integrin alpha-L

hetero molecules

defined by author&software
29.9 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Intercellular adhesion molecule 1

D: Integrin alpha-L

hetero molecules

defined by author&software
29.9 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

E: Intercellular adhesion molecule 1

F: Integrin alpha-L

hetero molecules

defined by author&software
29.9 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

G: Intercellular adhesion molecule 1

H: Integrin alpha-L

hetero molecules

defined by author&software
29.9 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

5

I: Intercellular adhesion molecule 1

J: Integrin alpha-L

hetero molecules

defined by author&software
29.9 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

6

K: Intercellular adhesion molecule 1

L: Integrin alpha-L

hetero molecules

defined by author&software
29.9 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

7

M: Intercellular adhesion molecule 1

N: Integrin alpha-L

hetero molecules

defined by author&software
29.9 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

8

O: Intercellular adhesion molecule 1

P: Integrin alpha-L

hetero molecules

defined by author&software
29.9 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

9

Q: Intercellular adhesion molecule 1

R: Integrin alpha-L

hetero molecules

defined by author&software
29.9 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

10

S: Intercellular adhesion molecule 1

T: Integrin alpha-L

hetero molecules

defined by author&software
29.9 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

11

U: Intercellular adhesion molecule 1

V: Integrin alpha-L

hetero molecules

defined by author&software
29.9 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

12

W: Intercellular adhesion molecule 1

X: Integrin alpha-L

hetero molecules

defined by author&software
29.9 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

13

Y: Intercellular adhesion molecule 1

Z: Integrin alpha-L

hetero molecules

defined by author&software
29.9 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

14

a: Intercellular adhesion molecule 1

b: Integrin alpha-L

hetero molecules

defined by author&software
29.9 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	104.041, 166.334, 299.372
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Component-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / Refine code: 1

Dom-ID	Ens-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	THR	THR	A	A	1 - 85	1 - 85
2	1	THR	THR	C	C	1 - 85	1 - 85
3	1	THR	THR	E	E	1 - 85	1 - 85
4	1	THR	THR	G	G	1 - 85	1 - 85
5	1	THR	THR	I	I	1 - 85	1 - 85
6	1	THR	THR	K	K	1 - 85	1 - 85
7	1	THR	THR	M	M	1 - 85	1 - 85
8	1	THR	THR	O	O	1 - 85	1 - 85
9	1	THR	THR	Q	Q	1 - 85	1 - 85
10	1	THR	THR	S	S	1 - 85	1 - 85
11	1	THR	THR	U	U	1 - 85	1 - 85
12	1	THR	THR	W	W	1 - 85	1 - 85
13	1	THR	THR	Y	Y	1 - 85	1 - 85
14	1	THR	THR	a	AA	1 - 85	1 - 85
1	2	MG	MG	B	B - CA	128 - 901	1
2	2	MG	MG	D	D - DA	128 - 901	1
3	2	MG	MG	F	F - EA	128 - 901	1
4	2	MG	MG	H	H - FA	128 - 901	1
5	2	MG	MG	J	J - GA	128 - 901	1
6	2	MG	MG	L	L - HA	128 - 901	1
7	2	MG	MG	N	N - IA	128 - 901	1
8	2	MG	MG	P	P - JA	128 - 901	1
9	2	MG	MG	R	R - KA	128 - 901	1
10	2	MG	MG	T	T - LA	128 - 901	1
11	2	MG	MG	V	V - MA	128 - 901	1
12	2	MG	MG	X	X - NA	128 - 901	1
13	2	MG	MG	Z	Z - OA	128 - 901	1
14	2	MG	MG	b	BA - PA	128 - 901	1

NCS ensembles :

ID
1
2

#1: Protein	Intercellular adhesion molecule 1 / ICAM-1 / CD54 / HUMAN RHINOVIRUS RECEPTOR Mass: 9214.620 Da / Num. of mol.: 14 / Fragment: DOMAIN 1, unp residues 29-112 / Mutation: T2V, I10T, T23A, P38V, P63V, S67A, T78A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ICAM1 / Production host: Escherichia coli (E. coli) / References: UniProt: P05362
#2: Protein	Integrin alpha-L / CD11A / LYMPHOCYTE FUNCTION-ASSOCIATED ANTIGEN 1 ALPHA CHAIN / LFA-1 ALPHA CHAIN / LEUKOCYTE ...CD11A / LYMPHOCYTE FUNCTION-ASSOCIATED ANTIGEN 1 ALPHA CHAIN / LFA-1 ALPHA CHAIN / LEUKOCYTE FUNCTION-ASSOCIATED MOLECULE 1 ALPHA CHAIN / ITGAL Mass: 20622.619 Da / Num. of mol.: 14 / Fragment: I DOMAIN, unp residues 154-332 / Mutation: F265S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ITGAL, CD11A / Production host: Escherichia coli (E. coli) / References: UniProt: P20701
#3: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Mg
Has protein modification	Y
Sequence details	THIS IS A NATURAL VARIANT

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 3.1 Å³/Da / Density % sol: 60.33 %
Crystal grow	Temperature: 277 K / Method: evaporation / pH: 6 / Details: pH 6.0, EVAPORATION, temperature 277K

-
Data collection

Diffraction source	Source: SYNCHROTRON / Site: CHESS / Beamline: F1
Detector	Date: Oct 14, 2009
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Relative weight: 1
Reflection	Resolution: 3.6→50 Å / Num. obs: 58846

-
Processing

Software

Name	Version	Classification
HKL-2000		data collection
PHASER		phasing
REFMAC	5.5.0102	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 3.6→49.54 Å / Cor.coef. F_o:F_c: 0.928 / Cor.coef. F_o:F_c free: 0.916 / SU B: 70.436 / SU ML: 0.484 / Cross valid method: THROUGHOUT / ESU R Free: 0.628 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.23356	2984	5.1 %	RANDOM
R_work	0.21762	-	-	-
obs	0.21845	55823	96.07 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 165.66 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.41 Å²	0 Å²	0 Å²
2-	-	-0.01 Å²	0 Å²
3-	-	-	-0.41 Å²

Refinement step

Cycle: LAST / Resolution: 3.6→49.54 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	29316	0	14	0	29330

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.022	29904
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.418	1.973	40418
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.957	5	3682
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	41.143	25.506	1246
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	20.497	15	5544
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	10.878	15	70
X-RAY DIFFRACTION	r_chiral_restr	0.093	0.2	4662
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.021	21812
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.316	1.5	18508
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	0.643	2	30058
X-RAY DIFFRACTION	r_scbond_it	0.922	3	11396
X-RAY DIFFRACTION	r_scangle_it	1.659	4.5	10360
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	641	TIGHT POSITIONAL	0.06	0.05
1	2	C	641	TIGHT POSITIONAL	0.06	0.05
1	3	E	641	TIGHT POSITIONAL	0.05	0.05
1	4	G	641	TIGHT POSITIONAL	0.06	0.05
1	5	I	641	TIGHT POSITIONAL	0.05	0.05
1	6	K	641	TIGHT POSITIONAL	0.06	0.05
1	7	M	641	TIGHT POSITIONAL	0.05	0.05
1	8	O	641	TIGHT POSITIONAL	0.05	0.05
1	9	Q	641	TIGHT POSITIONAL	0.05	0.05
1	10	S	641	TIGHT POSITIONAL	0.05	0.05
1	11	A	641	TIGHT POSITIONAL	0.05	0.05
1	12	C	641	TIGHT POSITIONAL	0.05	0.05
1	13	E	641	TIGHT POSITIONAL	0.04	0.05
1	14	G	641	TIGHT POSITIONAL	0.04	0.05
1	1	A	641	TIGHT THERMAL	0.09	0.5
1	2	C	641	TIGHT THERMAL	0.09	0.5
1	3	E	641	TIGHT THERMAL	0.07	0.5
1	4	G	641	TIGHT THERMAL	0.08	0.5
1	5	I	641	TIGHT THERMAL	0.07	0.5
1	6	K	641	TIGHT THERMAL	0.08	0.5
1	7	M	641	TIGHT THERMAL	0.06	0.5
1	8	O	641	TIGHT THERMAL	0.07	0.5
1	9	Q	641	TIGHT THERMAL	0.07	0.5
1	10	S	641	TIGHT THERMAL	0.07	0.5
1	11	A	641	TIGHT THERMAL	0.08	0.5
1	12	C	641	TIGHT THERMAL	0.07	0.5
1	13	E	641	TIGHT THERMAL	0.06	0.5
1	14	G	641	TIGHT THERMAL	0.06	0.5
2	1	B	1454	TIGHT POSITIONAL	0.05	0.05
2	2	D	1454	TIGHT POSITIONAL	0.04	0.05
2	3	F	1454	TIGHT POSITIONAL	0.03	0.05
2	4	H	1454	TIGHT POSITIONAL	0.03	0.05
2	5	J	1454	TIGHT POSITIONAL	0.03	0.05
2	6	L	1454	TIGHT POSITIONAL	0.05	0.05
2	7	N	1454	TIGHT POSITIONAL	0.03	0.05
2	8	P	1454	TIGHT POSITIONAL	0.03	0.05
2	9	R	1454	TIGHT POSITIONAL	0.03	0.05
2	10	T	1454	TIGHT POSITIONAL	0.03	0.05
2	11	B	1454	TIGHT POSITIONAL	0.04	0.05
2	12	D	1454	TIGHT POSITIONAL	0.04	0.05
2	13	F	1454	TIGHT POSITIONAL	0.03	0.05
2	14	H	1454	TIGHT POSITIONAL	0.02	0.05
2	1	B	1454	TIGHT THERMAL	0.07	0.5
2	2	D	1454	TIGHT THERMAL	0.06	0.5
2	3	F	1454	TIGHT THERMAL	0.04	0.5
2	4	H	1454	TIGHT THERMAL	0.04	0.5
2	5	J	1454	TIGHT THERMAL	0.04	0.5
2	6	L	1454	TIGHT THERMAL	0.07	0.5
2	7	N	1454	TIGHT THERMAL	0.04	0.5
2	8	P	1454	TIGHT THERMAL	0.04	0.5
2	9	R	1454	TIGHT THERMAL	0.04	0.5
2	10	T	1454	TIGHT THERMAL	0.05	0.5
2	11	B	1454	TIGHT THERMAL	0.05	0.5
2	12	D	1454	TIGHT THERMAL	0.06	0.5
2	13	F	1454	TIGHT THERMAL	0.04	0.5
2	14	H	1454	TIGHT THERMAL	0.03	0.5

LS refinement shell

Resolution: 3.6→3.689 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.229	177	-
R_work	0.225	3465	-
obs	-	-	81.7 %

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	8.6105	-2.9224	3.4574	13.3018	-6.6085	12.215	0.0161	0.0886	-0.1802	-0.3557	0.0788	0.2917	0.4164	-0.0694	-0.0949	0.0142	0.0524	0.0139	0.1463	-0.0731	0.3506	-12.255	-9.255	29.071
2	8.9384	2.3245	-0.0787	8.7046	-1.8675	9.3094	-0.6325	0.7197	-0.0613	-1.1937	0.3375	-1.363	-0.316	2.1119	0.295	0.2148	-0.2118	0.1544	0.9226	-0.0572	0.5298	6.618	6.735	15.279
3	16.6928	-7.3845	5.9496	9.2946	-3.1996	9.5448	-0.6042	-0.7968	0.0425	0.6189	0.5666	0.063	-0.4164	-0.367	0.0375	0.084	0.1708	-0.0021	0.3894	-0.1318	0.2805	-19.911	8.814	43.332
4	11.9577	3.4365	-0.2497	7.4155	-0.8541	8.3186	-0.1345	-1.3107	1.3035	0.4188	0.1202	-1.3731	-1.7248	1.3724	0.0143	0.5025	-0.1672	-0.2611	0.7271	-0.3686	1.1231	5.726	20.651	45.571
5	15.0321	-8.365	-3.5267	15.0488	3.2775	12.0041	0.0907	0.3717	0.6871	0.0988	0.7354	0.5796	-1.4919	-0.0647	-0.826	0.4794	0.0813	0.1928	1.0077	0.145	0.8475	58.549	25.053	27.939
6	8.1861	2.0993	-1.5507	8.6266	0.0293	17.2565	-0.1256	1.7909	-0.1653	-1.9262	2.0781	2.2909	1.8293	-3.7458	-1.9525	0.5437	-0.5091	-0.8729	2.6938	0.6189	2.1221	41.768	7.124	13.474
7	18.3598	-8.7539	-7.2519	13.6975	3.7099	6.4595	-0.4704	-1.23	-0.2838	0.7136	0.7804	0.8611	-0.285	-0.1107	-0.31	0.1157	0.2252	-0.0076	0.6146	0.0886	0.5144	66.222	7.835	43.185
8	12.3523	2.2383	0.7429	8.363	0.0837	9.275	-0.0711	-1.1094	-1.9836	0.8684	0.4322	2.1115	1.088	-2.0508	-0.3611	0.3438	0.0765	0.4119	1.3685	0.5918	2.1739	40.857	-4.607	45.277
9	17.4443	-4.1304	-5.5153	15.6832	-4.868	21.0621	-0.7265	-1.0126	-0.5512	-0.2225	-0.6673	-0.6843	1.7682	1.8112	1.3938	0.515	0.3773	0.1899	0.5471	0.3896	0.8463	31.216	53.694	38.112
10	9.6288	1.3726	-1.339	3.4648	-1.9632	17.7142	-0.6587	0.9605	-1.5521	-0.9308	0.6073	1.0981	3.2456	-3.8345	0.0514	1.1704	-0.6853	-0.0227	1.2887	0.0022	1.4938	9.256	48.44	20.753
11	11.4351	-9.4624	-2.7023	14.0214	4.2302	9.621	-0.2426	-0.5114	-0.2085	0.5645	0.4304	-0.4176	-0.2052	0.3999	-0.1878	0.4973	0.1153	0.132	0.2062	0.1338	0.223	33.882	76.933	29.547
12	9.461	0.7101	-1.6187	5.0697	1.4995	9.8074	-0.0006	1.7026	-0.0273	-1.0754	0.0607	0.3775	-0.3393	-1.0079	-0.0601	0.5525	0.2353	-0.0008	0.5688	0.1088	0.3287	29.427	69.115	2.653
13	6.2533	5.6822	-2.2394	15.8989	-3.227	8.4455	0.3575	0.0924	0.0106	-0.0299	-0.1061	-0.0996	0.1494	-0.1641	-0.2514	0.4975	-0.2726	0.0078	0.5143	-0.1492	0.575	2.184	48.125	100.147
14	7.4255	-1.616	-2.3833	7.906	-0.8136	8.5102	0.0287	2.0536	-0.5518	-1.6371	-0.2019	-0.8241	1.1381	0.1226	0.1731	1.3832	-0.1322	0.4111	1.1892	-0.4286	0.9857	19.126	45.015	77.439
15	6.984	2.2876	0.0638	25.0528	-5.3228	7.6463	-0.1661	-0.0346	-1.0342	1.0208	0.3277	-0.937	0.4726	-0.0802	-0.1616	0.1458	-0.0004	-0.1184	0.2585	-0.1998	0.7959	19.693	58.869	113.941
16	4.7673	-1.0007	-1.8787	8.5447	0.6358	10.6282	0.0789	0.1686	-0.8293	-0.2034	0.3032	-2.3483	1.7739	2.6197	-0.3821	0.7491	0.5822	-0.0137	1.2005	-0.5268	2.4377	40.05	41.522	104.15
17	15.4316	-10.4183	2.7617	15.1525	-1.2601	8.3473	-0.3062	-0.4132	0.1611	0.1747	0.1777	0.7056	-0.1373	-0.4359	0.1285	0.7655	0.2259	-0.2879	0.214	0.0056	0.4002	7.906	-61.714	30.421
18	8.5487	1.5748	-2.2028	10.0725	-1.4817	9.4183	0.3046	2.1668	-0.284	-3.8334	-0.0308	0.6335	0.3274	-0.8036	-0.2739	2.4921	0.5614	-0.5418	0.9776	-0.033	0.5159	8.782	-54.337	3.044
19	16.052	-8.8265	1.4446	11.6314	-1.03	6.1218	-0.1761	-0.5397	0.2237	0.0325	0.24	-0.0506	-0.1623	0.1648	-0.0639	0.5843	0.0572	0.0897	0.1635	0.0364	0.6043	11.216	-38.237	38.181
20	7.7431	-1.1249	-2.1325	7.1899	0.4563	10.1964	0.9038	0.4577	1.7085	-2.1152	-0.1976	-1.5248	-1.9392	1.378	-0.7062	1.6712	-0.1438	0.7076	0.5348	0.217	1.2827	31.022	-33.035	18.66
21	4.5516	1.9638	-0.8182	21.5841	-2.6969	6.7637	0.0557	-0.0619	-0.1405	0.3648	-0.1796	0.3902	-0.4858	-0.2531	0.124	0.3642	-0.2283	-0.0347	0.5245	0.0321	0.3368	-33.485	3.968	105.005
22	6.4518	-1.0693	-2.3162	6.6528	-1.3072	13.5917	0.397	1.7256	-0.2467	-0.971	-0.3217	0.728	-0.6242	-2.686	-0.0752	0.6403	0.165	-0.2152	1.4129	-0.1356	0.5725	-38.674	13.239	78.629
23	3.7807	1.7558	-0.3287	19.9277	1.9939	6.3514	0.1635	-0.1113	-0.0086	0.8925	-0.1071	-0.6282	0.0223	0.3617	-0.0564	0.3617	-0.2802	0.003	0.5396	-0.1327	0.3394	-9.642	11.722	104.093
24	4.996	-0.4728	1.18	7.7892	0.9511	13.5774	0.3488	0.9655	-0.1081	-0.8835	-0.017	-0.8427	0.5398	1.4428	-0.3319	0.4783	0.0042	0.2188	0.6979	-0.1276	0.5206	-6.041	2.343	77.475
25	9.9819	-7.0554	4.4749	16.7798	-5.9597	12.2386	-0.0271	-0.4119	-1.0883	0.5005	0.4682	0.3732	0.4025	-0.1944	-0.4411	0.5495	0.3371	0.1199	0.6152	-0.0099	0.5852	-58.196	51.128	48.583
26	11.3917	-1.3838	2.6154	9.2118	-0.0921	8.799	-0.8798	-3.1652	1.0262	2.8251	1.4393	-1.4702	-0.2638	0.6806	-0.5595	1.7643	1.0408	-0.4606	2.0259	-0.6517	1.1381	-40.78	55.431	70.603
27	8.4078	-3.8266	-2.1997	21.7488	0.2556	7.252	0.7139	0.6268	1.1298	-1.6415	-0.2831	-0.7154	-0.9187	-0.4858	-0.4307	0.5853	0.4419	0.226	0.8025	-0.0825	0.8736	-39.394	40.47	34.51
28	8.0145	-0.6344	0.2165	11.9352	2.0322	7.5758	0.7753	-0.8072	3.4336	-1.1692	0.6674	-4.633	-1.6795	2.0862	-1.4427	1.0566	-0.1656	0.8852	1.5254	-0.7947	4.1443	-20.206	59.218	43.897

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 85
2	X-RAY DIFFRACTION	2	B	128 - 307
3	X-RAY DIFFRACTION	3	C	1 - 85
4	X-RAY DIFFRACTION	4	D	128 - 307
5	X-RAY DIFFRACTION	5	E	1 - 85
6	X-RAY DIFFRACTION	6	F	128 - 307
7	X-RAY DIFFRACTION	7	G	1 - 85
8	X-RAY DIFFRACTION	8	H	128 - 307
9	X-RAY DIFFRACTION	9	I	1 - 85
10	X-RAY DIFFRACTION	10	J	128 - 307
11	X-RAY DIFFRACTION	11	K	1 - 85
12	X-RAY DIFFRACTION	12	L	128 - 307
13	X-RAY DIFFRACTION	13	M	1 - 85
14	X-RAY DIFFRACTION	14	N	128 - 307
15	X-RAY DIFFRACTION	15	O	1 - 85
16	X-RAY DIFFRACTION	16	P	128 - 307
17	X-RAY DIFFRACTION	17	Q	1 - 85
18	X-RAY DIFFRACTION	18	R	128 - 307
19	X-RAY DIFFRACTION	19	S	1 - 85
20	X-RAY DIFFRACTION	20	T	128 - 307
21	X-RAY DIFFRACTION	21	U	1 - 85
22	X-RAY DIFFRACTION	22	V	128 - 307
23	X-RAY DIFFRACTION	23	W	1 - 85
24	X-RAY DIFFRACTION	24	X	128 - 307
25	X-RAY DIFFRACTION	25	Y	1 - 85
26	X-RAY DIFFRACTION	26	Z	128 - 307
27	X-RAY DIFFRACTION	27	a	1 - 85
28	X-RAY DIFFRACTION	28	b	128 - 307

-
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