PDB-2x3d: Crystal Structure of SSo6206 from Sulfolobus solfataricus P2

ID or keywords:

Entry

Database: PDB / ID: 2x3d

Title

Crystal Structure of SSo6206 from Sulfolobus solfataricus P2

Components

SSO6206

Keywords

UNKNOWN FUNCTION

Function / homology

MTH889-like domain / Protein of unknown function DUF211 / MTH889-like domain superfamily / Uncharacterized ArCR, COG1888 / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta / Uncharacterized protein

Function and homology information

Biological species

SULFOLOBUS SOLFATARICUS (archaea)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.7 Å

Authors

Oke, M. / Carter, L.G. / Johnson, K.A. / Liu, H. / McMahon, S.A. / McEwan, A.R. / White, M.F. / Naismith, J.H.

Citation

Journal: J. Struct. Funct. Genomics / Year: 2010
Title: The Scottish Structural Proteomics Facility: targets, methods and outputs.
Authors: Oke, M. / Carter, L.G. / Johnson, K.A. / Liu, H. / McMahon, S.A. / Yan, X. / Kerou, M. / Weikart, N.D. / Kadi, N. / Sheikh, M.A. / Schmelz, S. / Dorward, M. / Zawadzki, M. / Cozens, C. / ...

History

Deposition	Jan 24, 2010	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jul 28, 2010	Provider: repository / Type: Initial release
Revision 1.1	May 7, 2011	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Version format compliance
Revision 1.3	Mar 28, 2018	Group: Database references / Structure summary / Category: audit_author / citation / citation_author Item: _audit_author.name / _citation.country ..._audit_author.name / _citation.country / _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name
Revision 1.4	Jan 23, 2019	Group: Advisory / Data collection / Derived calculations Category: pdbx_validate_symm_contact / struct_conn / struct_conn_type
Revision 1.5	Dec 20, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_sheet Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_sheet.number_strands

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	2x3d.cif.gz	283 KB	Display	PDBx/mmCIF format
PDB format	pdb2x3d.ent.gz	235.6 KB	Display	PDB format
PDBx/mmJSON format	2x3d.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/x3/2x3d ftp://data.pdbj.org/pub/pdb/validation_reports/x3/2x3d	HTTPS FTP

-
Related structure data

Related structure data	2ivyC 2jg5C 2jg6C 2vw8C 2vxzC 2wj9C 2x0oC 2x3eC 2x3fC 2x3gC 2x3lC 2x3mC 2x3nC 2x3oC 2x48C 2x4gC 2x4hC 2x4iC 2x4jC 2x4kC 2x4lC 2x5cC 2x5dC 2x5fC 2x5gC 2x5hC 2x5pC 2x5qC 2x5rC 2x5tC 2x7bC 2x7iC 2xu2C 2raqS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	3aou-d 5y3k-d 2502 1680 3v4h-2 5ah2-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: SSO6206

B: SSO6206

C: SSO6206

D: SSO6206

E: SSO6206

F: SSO6206

G: SSO6206

H: SSO6206

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

1

A: SSO6206

B: SSO6206

C: SSO6206

D: SSO6206

E: SSO6206

F: SSO6206

G: SSO6206

H: SSO6206

A: SSO6206

B: SSO6206

C: SSO6206

D: SSO6206

E: SSO6206

F: SSO6206

G: SSO6206

H: SSO6206

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

Unit cell

Length a, b, c (Å)	151.090, 82.980, 69.860
Angle α, β, γ (deg.)	90.00, 109.70, 90.00
Int Tables number	5
Space group name H-M	C121

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Refine code	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	1	ARG	ARG	GLU	GLU	2	A	A	4 - 24	5 - 25
2	1	1	ARG	ARG	GLU	GLU	2	B	B	4 - 24	5 - 25
3	1	1	ARG	ARG	GLU	GLU	2	C	C	4 - 24	5 - 25
4	1	1	ARG	ARG	GLU	GLU	2	D	D	4 - 24	5 - 25
5	1	1	ARG	ARG	GLU	GLU	2	E	E	4 - 24	5 - 25
6	1	1	ARG	ARG	GLU	GLU	2	F	F	4 - 24	5 - 25
7	1	1	ARG	ARG	GLU	GLU	2	G	G	4 - 24	5 - 25
8	1	1	ARG	ARG	GLU	GLU	2	H	H	4 - 24	5 - 25
1	2	1	ILE	ILE	ILE	ILE	2	A	A	26 - 63	27 - 64
2	2	1	ILE	ILE	ILE	ILE	2	B	B	26 - 63	27 - 64
3	2	1	ILE	ILE	ILE	ILE	2	C	C	26 - 63	27 - 64
4	2	1	ILE	ILE	ILE	ILE	2	D	D	26 - 63	27 - 64
5	2	1	ILE	ILE	ILE	ILE	2	E	E	26 - 63	27 - 64
6	2	1	ILE	ILE	ILE	ILE	2	F	F	26 - 63	27 - 64
7	2	1	ILE	ILE	ILE	ILE	2	G	G	26 - 63	27 - 64
8	2	1	ILE	ILE	ILE	ILE	2	H	H	26 - 63	27 - 64
1	1	2	ARG	ARG	ASN	ASN	2	A	A	64 - 84	65 - 85
2	1	2	ARG	ARG	ASN	ASN	2	B	B	64 - 84	65 - 85
3	1	2	ARG	ARG	ASN	ASN	2	C	C	64 - 84	65 - 85
4	1	2	ARG	ARG	ASN	ASN	2	D	D	64 - 84	65 - 85
5	1	2	ARG	ARG	ASN	ASN	2	E	E	64 - 84	65 - 85
6	1	2	ARG	ARG	ASN	ASN	2	F	F	64 - 84	65 - 85
7	1	2	ARG	ARG	ASN	ASN	2	G	G	64 - 84	65 - 85
8	1	2	ARG	ARG	ASN	ASN	2	H	H	64 - 84	65 - 85
1	1	3	GLY	GLY	ILE	ILE	4	A	A	0 - 3	1 - 4
2	1	3	GLY	GLY	ILE	ILE	4	B	B	0 - 3	1 - 4
3	1	3	GLY	GLY	ILE	ILE	4	C	C	0 - 3	1 - 4
4	1	3	GLY	GLY	ILE	ILE	4	D	D	0 - 3	1 - 4
5	1	3	GLY	GLY	ILE	ILE	4	E	E	0 - 3	1 - 4
6	1	3	GLY	GLY	ILE	ILE	4	G	G	0 - 3	1 - 4
7	1	3	GLY	GLY	ILE	ILE	4	H	H	0 - 3	1 - 4
1	1	4	ARG	ARG	GLY	GLY	6	A	A	85 - 89	86 - 90
2	1	4	ARG	ARG	GLY	GLY	6	B	B	85 - 89	86 - 90
3	1	4	ARG	ARG	GLY	GLY	6	C	C	85 - 89	86 - 90
4	1	4	ARG	ARG	GLY	GLY	6	D	D	85 - 89	86 - 90
5	1	4	ARG	ARG	GLY	GLY	6	E	E	85 - 89	86 - 90
6	1	4	ARG	ARG	GLY	GLY	6	F	F	85 - 89	86 - 90
7	1	4	ARG	ARG	GLY	GLY	6	G	G	85 - 89	86 - 90
8	1	4	ARG	ARG	GLY	GLY	6	H	H	85 - 89	86 - 90

NCS ensembles :

ID
1
2
3
4

#1: Protein	SSO6206 Mass: 10552.231 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SULFOLOBUS SOLFATARICUS (archaea) / Strain: P2 / Plasmid: PEHISTEV / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q97ZR0
#2: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 11 / 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: 2.7 Å³/Da / Density % sol: 55 % / Description: NONE
Crystal grow	pH: 7.75 Details: CRYSTALLIZATION CONDITIONS ARE REPORTED IN MCEWAN ET AL.(2006)OVEREXPRESSION, PURIFICATION, CRYSTALLIZATION AND DATA COLLECTION OF SULFOLOBUS SOLFATARICUS SSO6206, A NOVEL HIGHLY CONSERVED ...Details: CRYSTALLIZATION CONDITIONS ARE REPORTED IN MCEWAN ET AL.(2006)OVEREXPRESSION, PURIFICATION, CRYSTALLIZATION AND DATA COLLECTION OF SULFOLOBUS SOLFATARICUS SSO6206, A NOVEL HIGHLY CONSERVED PROTEIN. ACTA CRYSTALLOGRAPHICA SECTION F. F62, 228-230, PH 7.75

Crystal

Density Matthews: 2.7 Å³/Da / Density % sol: 55 % / Description: NONE

Crystal grow

pH: 7.75
Details: CRYSTALLIZATION CONDITIONS ARE REPORTED IN MCEWAN ET AL.(2006)OVEREXPRESSION, PURIFICATION, CRYSTALLIZATION AND DATA COLLECTION OF SULFOLOBUS SOLFATARICUS SSO6206, A NOVEL HIGHLY CONSERVED ...

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9537
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 20, 2008 / Details: MIRRORS
Radiation	Monochromator: SI(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9537 Å / Relative weight: 1
Reflection	Resolution: 2.7→29.6 Å / Num. obs: 21244 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 5 % / B_iso Wilson estimate: 0 Å² / R_merge(I) obs: 0.08 / Net I/σ(I): 12.8
Reflection shell	Resolution: 2.7→2.77 Å / Redundancy: 5 % / R_merge(I) obs: 0.51 / Mean I/σ(I) obs: 3.7 / % possible all: 100

-
Processing

Software

Name	Version	Classification
REFMAC	5.5.0090	refinement
HKL-2000		data reduction
SCALEPACK		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2RAQ

2raq

Resolution: 2.7→29.63 Å / Cor.coef. F_o:F_c: 0.925 / Cor.coef. F_o:F_c free: 0.918 / SU B: 28.899 / SU ML: 0.271 / Cross valid method: THROUGHOUT / ESU R: 0 / ESU R Free: 0.346 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE STRUCTURE IS ONLY ORDERED FROM RESIDUES 0 TO 89. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF ...

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.24731	1155	5.2 %	RANDOM
R_work	0.2262	-	-	-
obs	0.22734	21244	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

Displacement parameters

B_iso mean: 21.734 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.06 Å²	-0 Å²	0.25 Å²
2-	-	-0.48 Å²	0 Å²
3-	-	-	0.71 Å²

Refinement step

Cycle: LAST / Resolution: 2.7→29.63 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5462	0	0	11	5473

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.022	5527
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	3735
X-RAY DIFFRACTION	r_angle_refined_deg	1.124	1.998	7436
X-RAY DIFFRACTION	r_angle_other_deg	0.805	3	9216
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.914	5	726
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	31.202	25	224
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.08	15	1130
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.764	15	48
X-RAY DIFFRACTION	r_chiral_restr	0.065	0.2	935
X-RAY DIFFRACTION	r_gen_planes_refined	0.003	0.02	6025
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	959
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	0.228	1.5	3557
X-RAY DIFFRACTION	r_mcbond_other	0.068	1.5	1495
X-RAY DIFFRACTION	r_mcangle_it	0.454	2	5787
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	0.981	3	1970
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	1.675	4.5	1642
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	346	tight positional	0.02	0.05
1	2	B	346	tight positional	0.02	0.05
1	3	C	346	tight positional	0.02	0.05
1	4	D	346	tight positional	0.02	0.05
1	5	E	346	tight positional	0.02	0.05
1	6	F	346	tight positional	0.03	0.05
1	7	G	346	tight positional	0.02	0.05
1	8	H	346	tight positional	0.02	0.05
2	1	A	124	tight positional	0.02	0.05
2	2	B	124	tight positional	0.02	0.05
2	3	C	124	tight positional	0.02	0.05
2	4	D	124	tight positional	0.03	0.05
2	5	E	124	tight positional	0.02	0.05
2	6	F	124	tight positional	0.03	0.05
2	7	G	124	tight positional	0.03	0.05
2	8	H	124	tight positional	0.03	0.05
1	1	A	385	medium positional	0.02	0.5
1	2	B	385	medium positional	0.02	0.5
1	3	C	385	medium positional	0.02	0.5
1	4	D	385	medium positional	0.02	0.5
1	5	E	385	medium positional	0.03	0.5
1	6	F	385	medium positional	0.03	0.5
1	7	G	385	medium positional	0.02	0.5
1	8	H	385	medium positional	0.02	0.5
2	1	A	143	medium positional	0.02	0.5
2	2	B	143	medium positional	0.02	0.5
2	3	C	143	medium positional	0.02	0.5
2	4	D	143	medium positional	0.03	0.5
2	5	E	143	medium positional	0.04	0.5
2	6	F	143	medium positional	0.04	0.5
2	7	G	143	medium positional	0.03	0.5
2	8	H	143	medium positional	0.03	0.5
3	1	A	40	medium positional	0.38	0.5
3	2	B	40	medium positional	0.35	0.5
3	3	C	40	medium positional	0.39	0.5
3	4	D	40	medium positional	0.72	0.5
3	5	E	40	medium positional	0.64	0.5
3	3	F	40	medium positional	0.44	0.5
3	6	G	40	medium positional	0.4	0.5
4	1	A	72	loose positional	0.28	5
4	2	B	72	loose positional	0.35	5
4	3	C	72	loose positional	0.48	5
4	4	D	72	loose positional	0.5	5
4	5	E	72	loose positional	0.24	5
4	6	F	72	loose positional	0.65	5
4	7	G	72	loose positional	0.43	5
4	8	H	72	loose positional	0.28	5
1	1	A	346	tight thermal	0.04	0.5
1	2	B	346	tight thermal	0.04	0.5
1	3	C	346	tight thermal	0.05	0.5
1	4	D	346	tight thermal	0.04	0.5
1	5	E	346	tight thermal	0.04	0.5
1	6	F	346	tight thermal	0.04	0.5
1	7	G	346	tight thermal	0.04	0.5
1	8	H	346	tight thermal	0.04	0.5
2	1	A	124	tight thermal	0.04	0.5
2	2	B	124	tight thermal	0.03	0.5
2	3	C	124	tight thermal	0.04	0.5
2	4	D	124	tight thermal	0.04	0.5
2	5	E	124	tight thermal	0.04	0.5
2	6	F	124	tight thermal	0.03	0.5
2	7	G	124	tight thermal	0.04	0.5
2	8	H	124	tight thermal	0.04	0.5
1	1	A	385	medium thermal	0.04	2
1	2	B	385	medium thermal	0.04	2
1	3	C	385	medium thermal	0.04	2
1	4	D	385	medium thermal	0.04	2
1	5	E	385	medium thermal	0.04	2
1	6	F	385	medium thermal	0.04	2
1	7	G	385	medium thermal	0.04	2
1	8	H	385	medium thermal	0.04	2
2	1	A	143	medium thermal	0.04	2
2	2	B	143	medium thermal	0.04	2
2	3	C	143	medium thermal	0.05	2
2	4	D	143	medium thermal	0.05	2
2	5	E	143	medium thermal	0.05	2
2	6	F	143	medium thermal	0.05	2
2	7	G	143	medium thermal	0.05	2
2	8	H	143	medium thermal	0.05	2
3	1	A	40	medium thermal	0.35	2
3	2	B	40	medium thermal	0.21	2
3	3	C	40	medium thermal	0.2	2
3	4	D	40	medium thermal	0.29	2
3	5	E	40	medium thermal	0.44	2
3	3	F	40	medium thermal	0.35	2
3	6	G	40	medium thermal	0.35	2
4	1	A	72	loose thermal	1.87	10
4	2	B	72	loose thermal	0.55	10
4	3	C	72	loose thermal	1.32	10
4	4	D	72	loose thermal	5.66	10
4	5	E	72	loose thermal	1.27	10
4	6	F	72	loose thermal	1.34	10
4	7	G	72	loose thermal	2.82	10
4	8	H	72	loose thermal	0.55	10

LS refinement shell

Resolution: 2.7→2.77 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.372	93	-
R_work	0.305	1545	-
obs	-	-	100 %

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	6.4283	4.0342	-2.8064	9.0631	-2.922	10.5019	-0.0862	0.1714	0.2026	0.2601	0.2769	0.6136	-0.0094	-0.6094	-0.1907	0.0728	0.0467	0.0149	0.0953	0.0164	0.1127	-28.573	-16.291	12.927
2	10.6952	5.7716	-3.0961	3.8823	-3.9405	8.1896	-0.0941	0.3923	0.2861	0.1731	0.2636	0.27	-0.3098	-0.3115	-0.1695	0.2954	0.0334	0.0925	0.0694	-0.0711	0.2677	-23.521	-10.194	13.355
3	4.9233	-0.7148	-0.0448	11.1674	-3.6851	8.5262	0.0165	-0.0994	-0.1541	-0.1146	0.2688	0.7967	0.3339	-0.3613	-0.2853	0.0591	0.0222	0.0233	0.1159	-0.0321	0.2091	-31.691	-39.326	11.847
4	3.2676	4.8344	0.5544	13.786	-3.3084	8.4773	0.0074	-0.1092	-0.1228	0.0738	-0.0195	0.6318	-0.1809	-0.3384	0.0121	0.1158	0.1053	0.0445	0.1659	-0.0377	0.2831	-32.393	-31.549	11.668
5	8.4785	-2.9654	1.4645	8.5063	-1.9075	8.2268	0.224	-0.3367	-0.2305	-0.0502	-0.043	0.1907	0.1856	-0.1107	-0.181	0.0156	-0.0104	-0.007	0.1617	-0.0259	0.018	-17.092	-57.394	13.55
6	2.1874	-3.4956	2.1446	13.2844	-2.4994	6.8033	0.3216	-0.0247	-0.1064	0.1198	-0.2243	0.7325	-0.0049	-0.261	-0.0972	0.1327	0.0077	0.0423	0.2609	-0.0044	0.178	-23.184	-52.758	12.34
7	10.5813	0.5283	4.2319	4.3537	1.0553	9.6547	0.2853	-0.0982	-0.379	0.2527	-0.0101	-0.1575	0.1599	0.5651	-0.2752	0.1119	-0.0171	0.0201	0.1095	-0.0011	0.0489	5.642	-58.861	17.546
8	10.9873	-3.6986	6.3408	3.2862	0.0771	7.3591	0.1808	0.0945	-0.0857	0.2135	-0.2015	-0.0693	0.2432	0.1006	0.0207	0.1569	-0.1036	0.0619	0.1703	-0.0083	0.1269	-1.929	-60.02	16.188
9	5.8379	2.4229	1.2891	9.3077	4.1799	11.1745	0.072	-0.2606	0.0276	0.2425	-0.0249	-0.5135	-0.0518	0.0557	-0.0471	0.1105	0.0119	0.0008	0.1209	0.0815	0.1131	23.684	-44.55	20.1
10	12.4365	2.4291	7.1083	3.9533	3.8268	10.8112	-0.0832	-0.2681	-0.282	0.1132	-0.0156	-0.3046	0.1984	-0.1635	0.0988	0.2528	-0.0678	0.0475	0.1382	0.0998	0.1799	18.626	-50.547	19.258
11	4.1172	-0.7552	-1.1118	11.0429	2.8585	9.8372	-0.0895	-0.381	0.3562	0.2874	0.3277	-0.4607	-0.221	0.4756	-0.2382	0.081	0.0045	-0.0839	0.1565	-0.0187	0.1324	27.133	-21.296	20.142
12	6.4349	3.3643	1.4987	12.2211	5.6621	6.418	-0.3368	-0.4224	0.0308	-0.1271	0.3384	-0.2886	0.0978	0.1445	-0.0016	0.2592	0.0933	-0.0381	0.1722	0.0807	0.153	27.907	-29.48	19.633
13	9.7726	-4.0842	-1.3183	10.0082	0.9388	7.3151	0.0283	-0.5345	0.3321	0.3564	0.1555	-0.0916	-0.1209	-0.1582	-0.1838	0.048	-0.0078	-0.0158	0.1625	-0.0067	0.0303	12.423	-3.578	17.669
14	5.5841	-6.5777	-3.6985	11.1193	2.4265	7.4588	-0.0701	-0.396	0.3121	0.3795	0.0982	-0.3643	0.0558	0.1527	-0.0281	0.0948	0.0004	-0.0782	0.3449	-0.0401	0.1527	18.561	-8.24	18.16
15	10.4361	1.4427	-1.8075	4.4098	-0.9593	8.0642	0.1313	-0.2561	0.5391	0.3504	0.0183	0.2644	-0.103	-0.3372	-0.1495	0.0649	-0.0026	-0.0029	0.0519	-0.0101	0.106	-10.593	-1.88	15.145
16	11.082	-3.0342	-4.0344	5.1161	0.4093	7.4792	-0.0689	-0.2939	0.1799	0.4838	0.0895	0.0403	-0.0649	0.3404	-0.0206	0.1711	-0.062	-0.0711	0.165	-0.0327	0.1049	-2.335	-1.65	16.177

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	0 - 63
2	X-RAY DIFFRACTION	2	A	64 - 89
3	X-RAY DIFFRACTION	3	B	0 - 63
4	X-RAY DIFFRACTION	4	B	64 - 89
5	X-RAY DIFFRACTION	5	C	0 - 63
6	X-RAY DIFFRACTION	6	C	64 - 89
7	X-RAY DIFFRACTION	7	D	0 - 63
8	X-RAY DIFFRACTION	8	D	64 - 89
9	X-RAY DIFFRACTION	9	E	0 - 63
10	X-RAY DIFFRACTION	10	E	64 - 89
11	X-RAY DIFFRACTION	11	F	2 - 63
12	X-RAY DIFFRACTION	12	F	64 - 89
13	X-RAY DIFFRACTION	13	G	0 - 63
14	X-RAY DIFFRACTION	14	G	64 - 89
15	X-RAY DIFFRACTION	15	H	0 - 63
16	X-RAY DIFFRACTION	16	H	64 - 90

-
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