PDB-4a8p: Crystal structure of putrescine transcarbamylase from Enterococcu...

ID or keywords:

Entry

Database: PDB / ID: 4a8p

Title

Crystal structure of putrescine transcarbamylase from Enterococcus faecalis with N5-(phosphonoacetyl)-L-ornithine

Components

PUTRESCINE CARBAMOYLTRANSFERASE

Keywords

TRANSFERASE / ORNITHINE AGMATINE DEIMINASE ROUTE

Function / homology

Function and homology information

putrescine carbamoyltransferase / putrescine biosynthetic process from arginine via N-carbamoylputrescine / putrescine carbamoyltransferase activity / ornithine carbamoyltransferase activity / amino acid binding / cytoplasm
Similarity search - Function

Biological species

ENTEROCOCCUS FAECALIS (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2 Å

Authors

Polo, L.M. / Gil-Ortiz, F. / Rubio, V.

Citation

Journal: Plos One / Year: 2012
Title: New Insight Into the Transcarbamylase Family: The Structure of Putrescine Transcarbamylase, a Key Catalyst for Fermentative Utilization of Agmatine
Authors: Polo, L.M. / Gil-Ortiz, F. / Cantin, A. / Rubio, V.

History

Deposition	Nov 21, 2011	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Feb 15, 2012	Provider: repository / Type: Initial release
Revision 1.1	Mar 14, 2012	Group: Other
Revision 1.2	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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Remark 650

HELIX DETERMINATION METHOD: AUTHOR PROVIDED.

Remark 700

SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	4a8p.cif.gz	777.1 KB	Display	PDBx/mmCIF format
PDB format	pdb4a8p.ent.gz	648.7 KB	Display	PDB format
PDBx/mmJSON format	4a8p.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	4a8p_validation.pdf.gz	1.9 MB	Display	wwPDB validaton report
Full document	4a8p_full_validation.pdf.gz	2 MB	Display
Data in XML	4a8p_validation.xml.gz	72.2 KB	Display
Data in CIF	4a8p_validation.cif.gz	99.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/a8/4a8p ftp://data.pdbj.org/pub/pdb/validation_reports/a8/4a8p	HTTPS FTP

-
Related structure data

Related structure data	4a8hSC 4a8tC C: citing same article (ref.) S: Starting model for refinement
Similar structure data	4a8h-1 4a8h-2 4jqo-d 2otc-2 6yw9-d 2ovy-2 4am8-1 4p1r-1 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

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#215 - Nov 2017 Aspartate Transcarbamoylase similarity (6)

Deposited unit

A: PUTRESCINE CARBAMOYLTRANSFERASE

B: PUTRESCINE CARBAMOYLTRANSFERASE

C: PUTRESCINE CARBAMOYLTRANSFERASE

D: PUTRESCINE CARBAMOYLTRANSFERASE

E: PUTRESCINE CARBAMOYLTRANSFERASE

F: PUTRESCINE CARBAMOYLTRANSFERASE

hetero molecules

243 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: PUTRESCINE CARBAMOYLTRANSFERASE

B: PUTRESCINE CARBAMOYLTRANSFERASE

C: PUTRESCINE CARBAMOYLTRANSFERASE

hetero molecules

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

2

D: PUTRESCINE CARBAMOYLTRANSFERASE

E: PUTRESCINE CARBAMOYLTRANSFERASE

F: PUTRESCINE CARBAMOYLTRANSFERASE

hetero molecules

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

Unit cell

Length a, b, c (Å)	81.520, 81.710, 82.280
Angle α, β, γ (deg.)	105.43, 102.80, 100.75
Int Tables number	1
Space group name H-M	P1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
1	2	A
2	2	C
1	3	D
2	3	E
1	4	D
2	4	F

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Refine code	Auth asym-ID	Auth seq-ID
1	1	1	5	A	2 - 72
2	1	1	5	B	2 - 72
1	2	1	6	A	73 - 86
2	2	1	6	B	73 - 86
1	3	1	5	A	87 - 225
2	3	1	5	B	87 - 225
1	4	1	6	A	226 - 240
2	4	1	6	B	226 - 240
1	5	1	3	A	241 - 318
2	5	1	3	B	241 - 318
1	6	1	5	A	319 - 400
2	6	1	5	B	319 - 400
1	1	2	5	A	2 - 72
2	1	2	5	C	2 - 72
1	2	2	6	A	73 - 86
2	2	2	6	C	73 - 86
1	3	2	5	A	87 - 225
2	3	2	5	C	87 - 225
1	4	2	6	A	226 - 240
2	4	2	6	C	226 - 240
1	5	2	3	A	241 - 318
2	5	2	3	C	241 - 318
1	6	2	5	A	319 - 400
2	6	2	5	C	319 - 400
1	1	3	3	D	2 - 72
2	1	3	3	E	2 - 72
1	2	3	6	D	73 - 86
2	2	3	6	E	73 - 86
1	3	3	3	D	87 - 180
2	3	3	3	E	87 - 180
1	4	3	6	D	181 - 190
2	4	3	6	E	181 - 190
1	5	3	5	D	191 - 225
2	5	3	5	E	191 - 225
1	6	3	6	D	226 - 240
2	6	3	6	E	226 - 240
1	7	3	3	D	241 - 318
2	7	3	3	E	241 - 318
1	8	3	5	D	319 - 400
2	8	3	5	E	319 - 400
1	1	4	3	D	2 - 72
2	1	4	3	F	2 - 72
1	2	4	6	D	73 - 86
2	2	4	6	F	73 - 86
1	3	4	3	D	87 - 180
2	3	4	3	F	87 - 180
1	4	4	6	D	181 - 190
2	4	4	6	F	181 - 190
1	5	4	5	D	191 - 225
2	5	4	5	F	191 - 225
1	6	4	6	D	226 - 240
2	6	4	6	F	226 - 240
1	7	4	3	D	241 - 318
2	7	4	3	F	241 - 318
1	8	4	5	D	319 - 400
2	8	4	5	F	319 - 400

NCS ensembles :

ID
1
2
3
4

NCS oper:

ID	Code	Matrix	Vector
1	given	(-0.177, -0.237, 0.955), (0.984, -0.048, 0.17), (0.006, 0.97, 0.242)	31.249, -1.463, -19.603
2	given	(-0.178, 0.984, 0.018), (-0.224, -0.059, 0.973), (0.958, 0.169, 0.231)	6.998, 26.125, -25.237
3	given	(-0.746, -0.597, 0.294), (-0.597, 0.406, -0.692), (0.294, -0.692, -0.66)	12.553, -24.725, -54.605
4	given	(-0.425, 0.517, -0.743), (0.514, -0.538, -0.668), (-0.745, -0.666, -0.037)	-19.239, -27.475, -32.86
5	given	(0.591, -0.633, -0.5), (-0.64, -0.745, 0.188), (-0.492, 0.209, -0.845)	-15.018, 1.154, -57.589

#1: Protein	PUTRESCINE CARBAMOYLTRANSFERASE / PTC / PTCASE / AGMATINE CATABOLISM PROTEIN B / PUTRESCINE TRANSCARBAMOYLASE / PUTRESCINE TRANSCARBAMYLASE Mass: 40141.398 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ENTEROCOCCUS FAECALIS (bacteria) / Strain: SD10 / Plasmid: PET22 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q837U7, putrescine carbamoyltransferase
#2: Chemical	ChemComp-PAO / N-(PHOSPHONOACETYL)-L-ORNITHINE Mass: 254.178 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₇H₁₅N₂O₆P
#3: Chemical	ChemComp-NI / NICKEL (II) ION Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#4: Chemical	ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₄H₁₂NO₃ / Comment: pH buffer*YM
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 535 / 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: 2.02 Å³/Da / Density % sol: 39.2 % / Description: NONE
Crystal grow	pH: 5.5 Details: 0.2 M AMMONIUM ACETATE, 25% POLYETHYLENE GLYCOL 3350, 0.1 M BIS-TRIS PH 5.5, 1 MM N5- (PHOSPHONOACETYL)-L-ORNITHINE

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873
Detector	Type: MARRESEARCH / Detector: CCD / Date: Dec 13, 2009
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.873 Å / Relative weight: 1
Reflection	Resolution: 2→30 Å / Num. obs: 114553 / % possible obs: 87.5 % / Observed criterion σ(I): 2 / Redundancy: 1.6 % / B_iso Wilson estimate: 27.1 Å² / R_merge(I) obs: 0.12 / Net I/σ(I): 10.9
Reflection shell	Resolution: 2→30 Å / Redundancy: 1.6 % / R_merge(I) obs: 0.42 / Mean I/σ(I) obs: 1.8 / % possible all: 87.5

-
Processing

Software

Name	Version	Classification
REFMAC	5.5.0102	refinement
MOSFLM		data reduction
SCALA		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4A8H

4a8h

Resolution: 2→25 Å / Cor.coef. F_o:F_c: 0.953 / Cor.coef. F_o:F_c free: 0.932 / SU B: 11.176 / SU ML: 0.14 / Cross valid method: THROUGHOUT / ESU R: 0.253 / ESU R Free: 0.195 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DISORDERED RESIDUES ARE, 78-82 FROM CHAIN D, 78-83 CHAIN E, 74-84 CHAIN F, 232-235 CHAIN D AND 230-238 CHAIN F

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.23732	5763	5.1 %	RANDOM
R_work	0.19593	-	-	-
obs	0.198	108160	87.57 %	-

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: 33.299 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.59 Å²	-1.12 Å²	-0.94 Å²
2-	-	-0.41 Å²	-1.11 Å²
3-	-	-	-0.42 Å²

Refinement step

Cycle: LAST / Resolution: 2→25 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	15479	0	114	535	16128

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.022	15860
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.009	1.964	21456
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.762	5	1994
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.733	24.848	724
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.363	15	2680
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.611	15	72
X-RAY DIFFRACTION	r_chiral_restr	0.07	0.2	2430
X-RAY DIFFRACTION	r_gen_planes_refined	0.003	0.021	11944
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	0.223	1.5	9973
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	0.423	2	15953
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	0.833	3	5887
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	1.321	4.5	5503
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	312	tight positional	0.07	0.05
1	2	B	312	tight positional	0.07	0.05
2	1	A	312	tight positional	0.08	0.05
2	2	C	312	tight positional	0.08	0.05
3	1	D	972	tight positional	0.1	0.05
3	2	E	972	tight positional	0.1	0.05
4	1	D	972	tight positional	0.08	0.05
4	2	F	972	tight positional	0.08	0.05
1	1	A	916	medium positional	0.14	0.5
1	2	B	916	medium positional	0.14	0.5
2	1	A	924	medium positional	0.12	0.5
2	2	C	924	medium positional	0.12	0.5
3	1	D	216	medium positional	0.16	0.5
3	2	E	216	medium positional	0.16	0.5
4	1	D	220	medium positional	0.2	0.5
4	2	F	220	medium positional	0.2	0.5
1	1	A	1364	loose positional	0.23	5
1	2	B	1364	loose positional	0.23	5
2	1	A	1380	loose positional	0.21	5
2	2	C	1380	loose positional	0.21	5
3	1	D	1301	loose positional	0.21	5
3	2	E	1301	loose positional	0.21	5
4	1	D	1266	loose positional	0.16	5
4	2	F	1266	loose positional	0.16	5
1	1	A	312	tight thermal	0.41	0.5
1	2	B	312	tight thermal	0.41	0.5
2	1	A	312	tight thermal	0.18	0.5
2	2	C	312	tight thermal	0.18	0.5
3	1	D	972	tight thermal	0.24	0.5
3	2	E	972	tight thermal	0.24	0.5
4	1	D	972	tight thermal	0.29	0.5
4	2	F	972	tight thermal	0.29	0.5
1	1	A	916	medium thermal	0.35	2
1	2	B	916	medium thermal	0.35	2
2	1	A	924	medium thermal	0.23	2
2	2	C	924	medium thermal	0.23	2
3	1	D	216	medium thermal	0.16	2
3	2	E	216	medium thermal	0.16	2
4	1	D	220	medium thermal	0.21	2
4	2	F	220	medium thermal	0.21	2
1	1	A	1364	loose thermal	0.42	10
1	2	B	1364	loose thermal	0.42	10
2	1	A	1380	loose thermal	0.32	10
2	2	C	1380	loose thermal	0.32	10
3	1	D	1301	loose thermal	0.33	10
3	2	E	1301	loose thermal	0.33	10
4	1	D	1266	loose thermal	0.31	10
4	2	F	1266	loose thermal	0.31	10

LS refinement shell

Resolution: 2→2.052 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.35	424	-
R_work	0.314	7930	-
obs	-	-	87.6 %

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	1.3769	0.7865	-0.4909	4.3391	-0.4573	1.1112	-0.0225	-0.1486	-0.0399	0.2211	0.0595	-0.0347	0.0906	-0.0378	-0.037	0.0307	0.0145	-0.0129	0.0854	0.0073	0.0164	6.057	5.028	9.175
2	1.9208	0.5229	-0.4009	1.281	0.3549	0.2889	-0.1062	0.2286	-0.133	-0.2463	0.103	-0.0431	-0.0284	-0.0263	0.0032	0.1605	0.0057	-0.0134	0.0838	0.014	0.0819	9.213	6.159	-5.962
3	2.1838	-2.1878	-1.5351	2.3336	1.2442	1.7145	0.0844	0.4658	-0.7102	-0.3358	-0.3777	0.8059	0.4609	-0.5509	0.2933	0.5228	-0.1512	-0.099	0.299	-0.1053	0.4216	13.642	-4.859	-14.769
4	2.5865	-0.1157	-0.4096	1.11	-0.1402	0.7654	-0.109	0.0712	-0.3042	-0.0821	0.0921	-0.038	0.2257	-0.0228	0.0169	0.1211	-0.0174	-0.0009	0.0532	0.0157	0.0595	5.552	-3.974	-1.208
5	2.4865	-0.165	0.5308	1.6815	-0.5845	1.5771	-0.0546	-0.0838	-0.1658	0.129	0.069	-0.0265	-0.017	-0.2253	-0.0145	0.0793	-0.0345	-0.0037	0.0643	0.0349	0.0798	-12.981	-4.009	5.83
6	1.5814	0.5728	0.2496	1.8139	-0.1587	1.7181	-0.0868	0.2013	-0.0765	-0.1748	0.0953	0.1869	0.1368	-0.2612	-0.0084	0.0994	-0.0513	-0.0238	0.1489	0.0243	0.0953	-16.948	-0.919	-2.278
7	9.8199	-6.1498	5.5629	4.4445	-3.1976	4.7934	0.0627	-0.1065	0.0051	-0.1143	0.039	-0.1524	0.3202	0.255	-0.1016	0.1031	0.047	0.0052	0.1007	0.0068	0.0401	10.442	3.801	5.666
8	8.7182	4.5938	-6.0246	3.6658	-3.9119	8.0084	-0.0179	-0.1387	-0.2006	0.1364	0.0403	-0.3429	-0.1902	0.5626	-0.0224	0.1395	0.0317	-0.0431	0.1415	-0.0846	0.1621	38.455	8.272	1.949
9	2.0427	-0.0172	0.6422	0.4941	-0.3558	1.3816	0.0139	-0.03	0.0474	-0.0144	0.0608	0.0367	-0.052	-0.0075	-0.0748	0.0931	0.0014	0.0283	0.0351	0.0165	0.03	11.464	26.913	-16.04
10	2.8311	0.1988	-0.3113	0.0711	-0.0565	0.0916	-0.2575	0.861	-0.2987	-0.1311	0.1689	0.0122	0.1602	-0.1339	0.0886	0.5686	-0.2689	-0.0703	0.4456	0.0225	0.2687	-2.399	8.729	-16.299
11	1.8138	0.3667	0.0547	1.4649	-1.5287	8.4551	0.0112	0.0101	-0.1533	-0.1956	0.0128	0.1627	0.2389	-0.4298	-0.0241	0.0773	0.0086	-0.0155	0.0791	0.0352	0.0866	-1.52	17.192	-14.841
12	1.3689	-0.486	-0.3157	0.5331	-0.6851	3.2489	0.081	-0.0008	0.1844	-0.091	0.0596	0.0739	-0.119	-0.1264	-0.1406	0.1266	0.0231	-0.0174	0.0265	0.0387	0.1238	4.959	30.186	-28.012
13	2.0626	-0.5147	0.1681	2.0923	1.2623	2.0758	0.0833	0.2221	0.108	-0.117	-0.0435	0.1294	-0.1788	-0.2711	-0.0398	0.1849	0.0237	0.0189	0.1334	0.0769	0.0591	2.353	33.105	-39.12
14	4.0031	0.8009	0.8216	0.4538	1.6067	7.285	0.1658	0.3557	-0.7187	0.1883	-0.0696	-0.1359	0.8516	-0.5803	-0.0962	0.3141	-0.0206	-0.045	0.2234	-0.0108	0.1625	6.318	19.635	-48.839
15	0.8273	-0.3466	-0.5149	0.6885	0.5981	3.1064	0.0399	0.1884	0.1095	-0.2042	0.0246	-0.0233	-0.0981	0.0254	-0.0644	0.1163	-0.0234	0.0218	0.0861	0.0283	0.0714	15.747	27.952	-33.051
16	2.8519	-4.2643	3.0687	11.5709	-6.8472	9.0713	0.1368	-0.0954	0.0301	0.3928	-0.0355	0.0108	0.1121	0.124	-0.1012	0.0881	-0.0347	0.0057	0.1585	-0.0615	0.0546	7.704	20.188	11.883
17	1.2118	-0.311	-1.0661	0.6034	0.125	2.4575	-0.0111	-0.0405	0.0337	0.0624	0.051	-0.1647	0.0346	0.1804	-0.04	0.0764	-0.0103	0.0067	0.0547	-0.0366	0.0827	37.303	6.574	-12.247
18	0.314	-0.37	-0.5753	2.0595	-0.1919	1.5256	-0.0001	0.1508	-0.1108	-0.1139	-0.141	0.2642	0.0803	-0.2946	0.1411	0.0748	0.0048	0.0243	0.1121	-0.0293	0.1001	22.239	5.926	-15.308
19	10.392	-3.2922	3.2373	2.5413	-2.7769	3.1107	0.2973	0.9673	-1.1212	-0.8167	0.6365	0.82	0.9403	-0.8609	-0.9338	0.6689	-0.3066	-0.2774	0.841	0.1729	0.3189	15.873	10.119	-27.659
20	1.3114	-0.728	-0.0041	3.006	-0.6284	1.1374	0.0205	0.2655	-0.0794	-0.2297	-0.0637	-0.0284	0.0516	0.068	0.0431	0.0861	-0.0077	0.0282	0.0821	-0.0464	0.0632	30.092	4.419	-23.781
21	2.2552	0.7132	-0.6652	3.1917	0.0423	2.0994	-0.0813	0.1164	-0.3926	-0.0871	-0.0509	-0.2078	0.109	0.1886	0.1321	0.1282	0.0074	0.0767	0.0937	-0.0765	0.166	40.19	-12.81	-22.708
22	2.4018	0.7912	-0.3874	1.1233	-0.0852	1.5181	-0.1194	0.214	-0.4499	-0.13	0.0426	-0.0361	0.3235	-0.0614	0.0769	0.2225	0.0054	0.0648	0.0817	-0.0983	0.2434	32.283	-18.098	-21.398
23	2.9611	5.7633	-2.4172	12.92	-4.9339	3.2395	-0.0563	0.1586	0.1376	-0.0056	0.1556	0.0265	-0.078	0.1002	-0.0993	0.068	-0.0013	-0.0131	0.0893	0.0059	0.0732	34.021	9.99	-14.502
24	14.3655	-4.7954	-3.6553	5.0411	2.0963	3.0317	0.2923	-0.2396	0.7332	-0.0696	-0.1467	-0.0419	-0.2833	-0.0466	-0.1456	0.1629	-0.0541	-0.0011	0.0865	0.0074	0.0902	24.392	36.463	-10.583
25	1.7643	0.0609	0.4163	0.6999	-0.1873	1.0839	-0.0202	0.0791	-0.0802	-0.0384	0.0201	-0.1013	0.1533	0.0956	0.0001	0.0515	0.0262	0.0171	0.0647	-0.0043	0.1061	3.851	-27.781	-63.449
26	2.5247	0.3731	1.6384	0.2537	-0.2579	2.5933	-0.0823	-0.3085	0.503	0.1058	-0.1134	0.0969	-0.193	0.0294	0.1957	0.1758	0.0346	-0.0254	0.1607	-0.0157	0.1852	-0.181	-16.831	-53.899
27	1.209	-0.4699	2.7962	0.1952	-1.0755	6.5291	-0.4954	-0.0362	0.2031	0.2547	0.0087	-0.1083	-1.0775	0.0212	0.4867	0.5311	-0.0416	-0.1622	0.4963	-0.0847	0.3227	-1.657	-20.606	-40.087
28	2.2629	0.7503	-0.446	1.2644	-0.4825	0.9598	-0.0008	-0.0994	0.025	0.139	-0.0716	-0.191	0.0822	0.1944	0.0723	0.0501	0.0505	-0.0241	0.1267	0.0047	0.1424	13.738	-22.471	-55.357
29	2.1304	-1.1112	0.3782	3.9781	-0.8066	0.9008	-0.161	-0.0819	0.3935	0.3389	-0.0387	-0.5452	-0.2397	0.3579	0.1996	0.0869	-0.0387	-0.077	0.2853	0.0111	0.3286	26.291	-10.465	-58.983
30	1.2368	0.9461	0.0091	6.1409	-1.5106	0.6785	-0.2155	0.3193	0.9408	0.0091	0.0742	0.2865	-0.2533	0.174	0.1413	0.2315	-0.1173	-0.2058	0.2235	0.232	0.7637	14.621	-4.006	-64.921
31	2.6562	2.0731	0.8414	17.4288	-2.4319	0.956	0.0429	0.0014	-0.1682	0.0313	-0.0302	-0.0263	0.1336	-0.0002	-0.0127	0.1756	0.0189	0.0777	0.0932	-0.0158	0.0697	1.987	-29.297	-59.646
32	12.7569	-2.5385	-4.5265	3.7542	1.9437	4.5404	0.0094	-0.0595	-0.5338	0.1201	-0.2827	0.452	0.408	-0.4504	0.2732	0.2451	-0.1008	-0.0427	0.1925	-0.0186	0.1411	-22.013	-41.345	-53.145
33	1.7784	-0.8576	-0.493	1.3876	0.3855	1.8611	0.0494	-0.1643	-0.1463	0.2737	-0.1266	0.2443	0.2234	-0.2847	0.0772	0.1404	-0.0867	0.0421	0.199	-0.036	0.0851	-24.759	-31.135	-43.46
34	1.5292	-0.0252	-0.3268	0.7936	0.3296	0.2116	-0.0139	-0.0831	0.2004	0.2479	0.0864	-0.0564	0.0737	0.0844	-0.0725	0.2106	-0.0433	0.0062	0.1749	-0.0163	0.087	-13.175	-21.201	-42.804
35	1.8773	-3.0312	-3.4783	5.0213	5.765	6.7403	0.21	-0.2251	0.4493	-0.1751	0.2904	-0.6353	-0.3417	0.326	-0.5005	0.3969	-0.1541	-0.0992	0.4807	-0.1631	0.5879	-17.708	-7.719	-41.222
36	1.2379	-0.4196	0.6362	1.9402	-0.4799	2.0641	0.0769	-0.2584	-0.0097	0.4367	-0.1453	0.1282	0.1557	-0.2546	0.0684	0.229	-0.09	0.0908	0.2233	-0.0429	0.0585	-20.961	-25.527	-31.91
37	2.8763	0.2994	0.0545	2.6077	-0.8905	1.8413	-0.0356	-0.422	0.0559	0.7406	-0.0615	-0.0843	-0.2526	-0.083	0.0971	0.6052	-0.123	0.0054	0.3248	0.0154	0.0831	-15.549	-31.016	-17.739
38	0.935	-0.356	0.546	1.0987	-1.6829	5.1418	-0.0161	-0.2227	-0.2245	0.4074	-0.157	-0.2561	0.3407	0.3451	0.1731	0.6218	-0.1178	-0.1608	0.2529	0.0785	0.2346	-5.448	-37.729	-26.185
39	16.344	-7.345	5.9394	4.1819	-3.2618	2.6157	0.1555	-0.1093	-0.1212	-0.0278	-0.0283	0.265	0.0514	-0.1233	-0.1272	0.0857	-0.0477	0.0589	0.3355	-0.145	0.1203	-28.153	-25.559	-45.609
40	7.1964	3.5899	-3.5026	8.5557	-6.388	9.7562	-0.1312	0.5458	0.1708	-0.3827	0.3939	0.4505	-0.0131	-0.3709	-0.2627	0.0683	-0.0175	-0.0438	0.1438	-0.0785	0.1741	-32.511	-13.464	-68.869
41	1.5809	0.0467	0.345	2.8723	-0.3762	1.1495	-0.0912	0.1614	0.3164	-0.1064	-0.0405	-0.0014	-0.0983	-0.0777	0.1316	0.0547	0.0399	-0.0259	0.0953	-0.0174	0.1449	-21.385	-3.751	-65.681
42	2.0816	1.665	-0.0718	3.7427	0.6944	1.0762	0.189	-0.3457	0.2299	0.8001	-0.1282	-0.4526	0.1322	0.0323	-0.0607	0.2168	0.0386	-0.1355	0.1451	-0.0438	0.2524	-14.595	-6.819	-52.484
43	12.5973	5.8171	-4.5599	4.3588	-3.3523	2.6056	0.1229	-1.6941	0.2902	0.6182	-0.6607	-0.6862	-0.4546	0.5531	0.5378	0.3111	-0.0013	-0.2222	0.3247	-0.0951	0.4564	-1.574	-5.701	-54.344
44	1.6901	-1.1819	-0.4568	2.2743	0.5718	1.0681	-0.0638	-0.0181	0.525	0.0656	-0.0113	-0.1754	-0.2343	-0.0254	0.0752	0.1329	0.0335	-0.0888	0.1069	-0.0239	0.3026	-17.496	6.882	-58.21
45	2.1874	0.3505	-0.8738	1.9572	-0.5368	2.3578	-0.0259	-0.3779	0.5213	0.4101	-0.0948	-0.0785	-0.4998	-0.0797	0.1207	0.342	0.1063	-0.1473	0.247	-0.1811	0.5168	-26.404	19.481	-47.726
46	2.8927	-0.9291	-1.6983	4.1409	1.8668	2.2103	-0.0928	-0.5047	0.4764	0.4999	-0.0048	0.3236	0.1501	-0.2577	0.0976	0.2169	0.0848	-0.0103	0.4469	-0.213	0.3355	-31.845	5.827	-44.418
47	7.2892	-0.6587	-7.4505	0.7842	-0.5977	14.0756	-0.1663	0.1942	0.1362	-0.0434	-0.143	-0.081	-0.29	0.039	0.3093	0.0857	0.0128	-0.0487	0.0639	-0.0184	0.1622	-17.1	-4.994	-65.983
48	4.0967	-6.8997	0.9605	16.8	-3.622	4.6907	0.0564	0.2298	0.0364	-0.3457	-0.1974	-0.27	0.3697	-0.0272	0.1411	0.0566	-0.0536	0.0155	0.1389	-0.0267	0.0748	-3.125	-26.519	-76.261

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 38
2	X-RAY DIFFRACTION	2	A	39 - 68
3	X-RAY DIFFRACTION	3	A	69 - 87
4	X-RAY DIFFRACTION	4	A	88 - 148
5	X-RAY DIFFRACTION	5	A	149 - 187
6	X-RAY DIFFRACTION	6	A	188 - 295
7	X-RAY DIFFRACTION	7	A	296 - 315
8	X-RAY DIFFRACTION	8	A	316 - 339
9	X-RAY DIFFRACTION	9	B	1 - 69
10	X-RAY DIFFRACTION	10	B	70 - 88
11	X-RAY DIFFRACTION	11	B	89 - 107
12	X-RAY DIFFRACTION	12	B	108 - 171
13	X-RAY DIFFRACTION	13	B	172 - 235
14	X-RAY DIFFRACTION	14	B	236 - 252
15	X-RAY DIFFRACTION	15	B	253 - 312
16	X-RAY DIFFRACTION	16	B	313 - 339
17	X-RAY DIFFRACTION	17	C	1 - 40
18	X-RAY DIFFRACTION	18	C	41 - 68
19	X-RAY DIFFRACTION	19	C	69 - 87
20	X-RAY DIFFRACTION	20	C	88 - 148
21	X-RAY DIFFRACTION	21	C	149 - 187
22	X-RAY DIFFRACTION	22	C	188 - 295
23	X-RAY DIFFRACTION	23	C	296 - 315
24	X-RAY DIFFRACTION	24	C	316 - 339
25	X-RAY DIFFRACTION	25	D	1 - 44
26	X-RAY DIFFRACTION	26	D	45 - 68
27	X-RAY DIFFRACTION	27	D	69 - 87
28	X-RAY DIFFRACTION	28	D	88 - 182
29	X-RAY DIFFRACTION	29	D	183 - 272
30	X-RAY DIFFRACTION	30	D	273 - 296
31	X-RAY DIFFRACTION	31	D	297 - 315
32	X-RAY DIFFRACTION	32	D	316 - 339
33	X-RAY DIFFRACTION	33	E	1 - 43
34	X-RAY DIFFRACTION	34	E	44 - 68
35	X-RAY DIFFRACTION	35	E	69 - 90
36	X-RAY DIFFRACTION	36	E	91 - 171
37	X-RAY DIFFRACTION	37	E	172 - 249
38	X-RAY DIFFRACTION	38	E	250 - 298
39	X-RAY DIFFRACTION	39	E	299 - 317
40	X-RAY DIFFRACTION	40	E	318 - 337
41	X-RAY DIFFRACTION	41	F	1 - 44
42	X-RAY DIFFRACTION	42	F	45 - 68
43	X-RAY DIFFRACTION	43	F	69 - 87
44	X-RAY DIFFRACTION	44	F	88 - 182
45	X-RAY DIFFRACTION	45	F	183 - 259
46	X-RAY DIFFRACTION	46	F	260 - 296
47	X-RAY DIFFRACTION	47	F	297 - 315
48	X-RAY DIFFRACTION	48	F	316 - 339

-
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