PDB-3ppc: Crystal structure of the Candida albicans methionine synthase by ...

ID or keywords:

Entry

Database: PDB / ID: 3ppc

Title

Crystal structure of the Candida albicans methionine synthase by surface entropy reduction, tyrosine variant with zinc

Components

5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase

Keywords

TRANSFERASE / cobalamin-independent / Surface entropy reduction

Function / homology

Function and homology information

L-methionine biosynthetic process from L-homoserine via O-acetyl-L-homoserine / symbiont-mediated perturbation of host immune response / 5-methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase / 5-methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase activity / methionine metabolic process / fungal biofilm matrix / 'de novo' L-methionine biosynthetic process / hyphal cell wall / fungal-type cell wall / methionine biosynthetic process ...
Similarity search - Function

Biological species

Candida albicans (yeast)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.2 Å

Authors

Ubhi, D. / Kavanagh, K. / Monzingo, A.F. / Robertus, J.D.

Citation

Journal: Arch.Biochem.Biophys. / Year: 2011
Title: Structure of Candida albicans methionine synthase determined by employing surface residue mutagenesis.
Authors: Ubhi, D. / Kavanagh, K.L. / Monzingo, A.F. / Robertus, J.D.

History

Deposition	Nov 24, 2010	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 12, 2011	Provider: repository / Type: Initial release
Revision 1.1	Sep 6, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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	3ppc.cif.gz	572.5 KB	Display	PDBx/mmCIF format
PDB format	pdb3ppc.ent.gz	466.3 KB	Display	PDB format
PDBx/mmJSON format	3ppc.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	3ppc_validation.pdf.gz	429.4 KB	Display	wwPDB validaton report
Full document	3ppc_full_validation.pdf.gz	434.1 KB	Display
Data in XML	3ppc_validation.xml.gz	52.4 KB	Display
Data in CIF	3ppc_validation.cif.gz	75.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/pp/3ppc ftp://data.pdbj.org/pub/pdb/validation_reports/pp/3ppc	HTTPS FTP

-
Related structure data

Related structure data	3ppfC 3ppgC 3pphC 1u1hS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	3oha-d 5ek3-d 3mfh-d 4pk6-d 3pph-1 6mq6-d 1vhd-d 3hgv-d 4zty-d 3pph-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

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: 5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase

B: 5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase

hetero molecules

177 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: 5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase

hetero molecules

defined by author&software
88.7 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: 5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase

hetero molecules

defined by author&software
88.6 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	77.676, 92.685, 190.970
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 / Refine code: 2

Dom-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	MET	MET	GLY	GLY	A	A	1 - 28	23 - 50
2	1	MET	MET	GLY	GLY	B	B	1 - 28	23 - 50
1	2	LEU	LEU	GLU	GLU	A	A	35 - 44	57 - 66
2	2	LEU	LEU	GLU	GLU	B	B	35 - 44	57 - 66
1	3	HIS	HIS	SER	SER	A	A	45 - 73	67 - 95
2	3	HIS	HIS	SER	SER	B	B	45 - 73	67 - 95
1	4	LEU	LEU	ASP	ASP	A	A	75 - 87	97 - 109
2	4	LEU	LEU	ASP	ASP	B	B	75 - 87	97 - 109
1	5	LEU	LEU	TYR	TYR	A	A	88 - 104	110 - 126
2	5	LEU	LEU	TYR	TYR	B	B	88 - 104	110 - 126
1	6	THR	THR	TRP	TRP	A	A	115 - 122	137 - 144
2	6	THR	THR	TRP	TRP	B	B	115 - 122	137 - 144
1	7	PHE	PHE	PHE	PHE	A	A	123 - 134	145 - 156
2	7	PHE	PHE	PHE	PHE	B	B	123 - 134	145 - 156
1	8	SER	SER	THR	THR	A	A	135 - 138	157 - 160
2	8	SER	SER	THR	THR	B	B	135 - 138	157 - 160
1	9	ILE	ILE	ALA	ALA	A	A	148 - 157	170 - 179
2	9	ILE	ILE	ALA	ALA	B	B	148 - 157	170 - 179
1	10	LYS	LYS	VAL	VAL	A	A	158 - 167	180 - 189
2	10	LYS	LYS	VAL	VAL	B	B	158 - 167	180 - 189
1	11	ILE	ILE	ASP	ASP	A	A	168 - 181	190 - 203
2	11	ILE	ILE	ASP	ASP	B	B	168 - 181	190 - 203
1	12	LYS	LYS	LEU	LEU	A	A	182 - 193	204 - 215
2	12	LYS	LYS	LEU	LEU	B	B	182 - 193	204 - 215
1	13	PRO	PRO	GLN	GLN	A	A	194 - 205	216 - 227
2	13	PRO	PRO	GLN	GLN	B	B	194 - 205	216 - 227
1	14	LYS	LYS	VAL	VAL	A	A	206 - 215	228 - 237
2	14	LYS	LYS	VAL	VAL	B	B	206 - 215	228 - 237
1	15	GLN	GLN	LYS	LYS	A	A	216 - 235	238 - 257
2	15	GLN	GLN	LYS	LYS	B	B	216 - 235	238 - 257
1	16	ALA	ALA	LEU	LEU	A	A	237 - 346	259 - 368
2	16	ALA	ALA	LEU	LEU	B	B	237 - 346	259 - 368
1	17	GLU	GLU	LYS	LYS	A	A	347 - 375	369 - 397
2	17	GLU	GLU	LYS	LYS	B	B	347 - 375	369 - 397
1	18	ASP	ASP	SER	SER	A	A	381 - 397	403 - 419
2	18	ASP	ASP	SER	SER	B	B	381 - 397	403 - 419
1	19	ALA	ALA	PRO	PRO	A	A	419 - 442	441 - 464
2	19	ALA	ALA	PRO	PRO	B	B	419 - 442	441 - 464
1	20	THR	THR	GLN	GLN	A	A	443 - 451	465 - 473
2	20	THR	THR	GLN	GLN	B	B	443 - 451	465 - 473
1	21	TYR	TYR	PRO	PRO	A	A	472 - 500	494 - 522
2	21	TYR	TYR	PRO	PRO	B	B	472 - 500	494 - 522
1	22	GLU	GLU	PHE	PHE	A	A	501 - 518	523 - 540
2	22	GLU	GLU	PHE	PHE	B	B	501 - 518	523 - 540
1	23	THR	THR	PRO	PRO	A	A	519 - 534	541 - 556
2	23	THR	THR	PRO	PRO	B	B	519 - 534	541 - 556
1	24	PRO	PRO	ALA	ALA	A	A	535 - 546	557 - 568
2	24	PRO	PRO	ALA	ALA	B	B	535 - 546	557 - 568
1	25	MET	MET	PRO	PRO	A	A	547 - 570	569 - 592
2	25	MET	MET	PRO	PRO	B	B	547 - 570	569 - 592
1	26	VAL	VAL	LEU	LEU	A	A	571 - 596	593 - 618
2	26	VAL	VAL	LEU	LEU	B	B	571 - 596	593 - 618
1	27	ASP	ASP	VAL	VAL	A	A	598 - 613	620 - 635
2	27	ASP	ASP	VAL	VAL	B	B	598 - 613	620 - 635
1	28	ASP	ASP	ARG	ARG	A	A	614 - 619	636 - 641
2	28	ASP	ASP	ARG	ARG	B	B	614 - 619	636 - 641
1	29	GLY	GLY	PHE	PHE	A	A	621 - 641	643 - 663
2	29	GLY	GLY	PHE	PHE	B	B	621 - 641	643 - 663
1	30	ARG	ARG	PHE	PHE	A	A	642 - 658	664 - 680
2	30	ARG	ARG	PHE	PHE	B	B	642 - 658	664 - 680
1	31	LEU	LEU	GLU	GLU	A	A	663 - 679	685 - 701
2	31	LEU	LEU	GLU	GLU	B	B	663 - 679	685 - 701
1	32	GLN	GLN	ASP	ASP	A	A	690 - 705	712 - 727
2	32	GLN	GLN	ASP	ASP	B	B	690 - 705	712 - 727
1	33	ILE	ILE	SER	SER	A	A	711 - 719	733 - 741
2	33	ILE	ILE	SER	SER	B	B	711 - 719	733 - 741
1	34	ILE	ILE	TRP	TRP	A	A	721 - 734	743 - 756
2	34	ILE	ILE	TRP	TRP	B	B	721 - 734	743 - 756
1	35	VAL	VAL	VAL	VAL	A	A	735 - 757	757 - 779
2	35	VAL	VAL	VAL	VAL	B	B	735 - 757	757 - 779
1	36	GLU	GLU	ALA	ALA	A	A	758 - 765	780 - 787
2	36	GLU	GLU	ALA	ALA	B	B	758 - 765	780 - 787
1	37	PHE	PHE	ALA	ALA	A	A	140 - 146	162 - 168
2	37	PHE	PHE	ALA	ALA	B	B	140 - 146	162 - 168
1	38	CYS	CYS	ASP	ASP	A	A	659 - 662	681 - 684
2	38	CYS	CYS	ASP	ASP	B	B	659 - 662	681 - 684

NCS ensembles :

#1: Protein	5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase / Cobalamin-independent methionine synthase / Methionine synthase / vitamin-B12 independent isozyme Mass: 88465.250 Da / Num. of mol.: 2 / Mutation: K103Y, K104Y, E107Y Source method: isolated from a genetically manipulated source Source: (gene. exp.) Candida albicans (yeast) / Strain: BWP17 / Gene: CaO19.10083, CaO19.2551, MET6 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P82610, 5-methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase
#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 433 / 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 Å³/Da / Density % sol: 38.36 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 250 mM NaI, 20% (w/v) PEG 3350, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

ALS

/ Beamline: 8.3.1 / Wavelength: 1.11587 Å

Detector

Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 13, 2009 / Details: Double Flat Crystal, Si (111)

Radiation

Monochromator: Double Flat Crystal, Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1.11587 Å / Relative weight: 1

Reflection

Resolution: 2.2→50 Å / Num. all: 68226 / Num. obs: 68226 / % possible obs: 96.5 % / Redundancy: 6.4 % / R_merge(I) obs: 0.097 / Net I/σ(I): 13.2

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	R_sym value	Diffraction-ID	% possible all
2.2-2.32	4.8	0.453	1.7	0.453	1	82.7
2.32-2.46	6.1	0.373	2	0.373	1	95.2
2.46-2.63	6.3	0.269	2.8	0.269	1	98.3
2.63-2.84	6.4	0.191	3.9	0.191	1	99.5
2.84-3.11	6.7	0.13	5.6	0.13	1	100
3.11-3.48	7	0.088	7.9	0.088	1	100
3.48-4.02	7	0.063	10.6	0.063	1	99.9
4.02-4.92	6.9	0.058	10.6	0.058	1	99.8
4.92-6.96	6.4	0.057	11.1	0.057	1	99.8
6.96-50	6.8	0.043	11.6	0.043	1	99.7

-
Processing

Software

Name	Version	Classification
SCALA	3.3.9	data scaling
REFMAC	5.5.0066	refinement
PDB_EXTRACT	3.1	data extraction
ADSC	Quantum	data collection
MOSFLM		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 1U1H

1u1h

Resolution: 2.2→50 Å / Cor.coef. F_o:F_c: 0.943 / Cor.coef. F_o:F_c free: 0.916 / Occupancy max: 1 / Occupancy min: 1 / SU B: 11.93 / SU ML: 0.14 / Cross valid method: THROUGHOUT / ESU R: 0.335 / ESU R Free: 0.223 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.23104	3436	5 %	RANDOM
R_work	0.18164	-	-	-
obs	0.18418	64713	96.31 %	-
all	-	68226	-	-

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: 25.326 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.25 Å²	0 Å²	0 Å²
2-	-	-0.37 Å²	0 Å²
3-	-	-	0.63 Å²

Refinement step

Cycle: LAST / Resolution: 2.2→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11295	0	10	433	11738

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.018	0.022	11537
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	7582
X-RAY DIFFRACTION	r_angle_refined_deg	1.506	1.964	15713
X-RAY DIFFRACTION	r_angle_other_deg	1.023	3	18607
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.167	5	1479
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.875	24.788	472
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.386	15	1833
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	14.884	15	48
X-RAY DIFFRACTION	r_chiral_restr	0.093	0.2	1820
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.021	12909
X-RAY DIFFRACTION	r_gen_planes_other	0.003	0.02	2242
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	1.873	3	7426
X-RAY DIFFRACTION	r_mcbond_other	0.415	3	2980
X-RAY DIFFRACTION	r_mcangle_it	3.219	5	11923
X-RAY DIFFRACTION	r_scbond_it	5.095	7	4111
X-RAY DIFFRACTION	r_scangle_it	7.505	11	3790
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-ID	Number	Type	Rms dev position (Å)	Weight position
1	163	TIGHT POSITIONAL	0.06	0.05
1	209	MEDIUM POSITIONAL	0.06	0.5
1	163	TIGHT THERMAL	0.22	0.5
1	209	MEDIUM THERMAL	0.19	2
2	59	TIGHT POSITIONAL	0.04	0.05
2	86	MEDIUM POSITIONAL	0.05	0.5
2	59	TIGHT THERMAL	0.25	0.5
2	86	MEDIUM THERMAL	0.18	2
3	172	TIGHT POSITIONAL	0.04	0.05
3	208	MEDIUM POSITIONAL	0.04	0.5
3	172	TIGHT THERMAL	0.28	0.5
3	208	MEDIUM THERMAL	0.24	2
4	77	TIGHT POSITIONAL	0.05	0.05
4	97	MEDIUM POSITIONAL	0.05	0.5
4	77	TIGHT THERMAL	0.2	0.5
4	97	MEDIUM THERMAL	0.17	2
5	99	TIGHT POSITIONAL	0.05	0.05
5	130	MEDIUM POSITIONAL	0.06	0.5
5	99	TIGHT THERMAL	0.27	0.5
5	130	MEDIUM THERMAL	0.18	2
6	48	TIGHT POSITIONAL	0.04	0.05
6	52	MEDIUM POSITIONAL	0.05	0.5
6	48	TIGHT THERMAL	0.21	0.5
6	52	MEDIUM THERMAL	0.19	2
7	71	TIGHT POSITIONAL	0.04	0.05
7	117	MEDIUM POSITIONAL	0.04	0.5
7	71	TIGHT THERMAL	0.3	0.5
7	117	MEDIUM THERMAL	0.23	2
8	24	TIGHT POSITIONAL	0.02	0.05
8	22	MEDIUM POSITIONAL	0.03	0.5
8	24	TIGHT THERMAL	0.19	0.5
8	22	MEDIUM THERMAL	0.23	2
9	59	TIGHT POSITIONAL	0.04	0.05
9	78	MEDIUM POSITIONAL	0.04	0.5
9	59	TIGHT THERMAL	0.26	0.5
9	78	MEDIUM THERMAL	0.25	2
10	58	TIGHT POSITIONAL	0.05	0.05
10	68	MEDIUM POSITIONAL	0.04	0.5
10	58	TIGHT THERMAL	0.23	0.5
10	68	MEDIUM THERMAL	0.19	2
11	81	TIGHT POSITIONAL	0.04	0.05
11	91	MEDIUM POSITIONAL	0.05	0.5
11	81	TIGHT THERMAL	0.24	0.5
11	91	MEDIUM THERMAL	0.23	2
12	71	TIGHT POSITIONAL	0.05	0.05
12	75	MEDIUM POSITIONAL	0.05	0.5
12	71	TIGHT THERMAL	0.2	0.5
12	75	MEDIUM THERMAL	0.17	2
13	70	TIGHT POSITIONAL	0.05	0.05
13	103	MEDIUM POSITIONAL	0.05	0.5
13	70	TIGHT THERMAL	0.33	0.5
13	103	MEDIUM THERMAL	0.26	2
14	59	TIGHT POSITIONAL	0.03	0.05
14	55	MEDIUM POSITIONAL	0.04	0.5
14	59	TIGHT THERMAL	0.27	0.5
14	55	MEDIUM THERMAL	0.14	2
15	118	TIGHT POSITIONAL	0.04	0.05
15	145	MEDIUM POSITIONAL	0.13	0.5
15	118	TIGHT THERMAL	0.24	0.5
15	145	MEDIUM THERMAL	0.22	2
16	648	TIGHT POSITIONAL	0.05	0.05
16	699	MEDIUM POSITIONAL	0.05	0.5
16	648	TIGHT THERMAL	0.24	0.5
16	699	MEDIUM THERMAL	0.21	2
17	174	TIGHT POSITIONAL	0.05	0.05
17	209	MEDIUM POSITIONAL	0.06	0.5
17	174	TIGHT THERMAL	0.24	0.5
17	209	MEDIUM THERMAL	0.22	2
18	102	TIGHT POSITIONAL	0.05	0.05
18	79	MEDIUM POSITIONAL	0.07	0.5
18	102	TIGHT THERMAL	0.2	0.5
18	79	MEDIUM THERMAL	0.22	2
19	141	TIGHT POSITIONAL	0.04	0.05
19	198	MEDIUM POSITIONAL	0.04	0.5
19	141	TIGHT THERMAL	0.24	0.5
19	198	MEDIUM THERMAL	0.18	2
20	52	TIGHT POSITIONAL	0.04	0.05
20	49	MEDIUM POSITIONAL	0.04	0.5
20	52	TIGHT THERMAL	0.24	0.5
20	49	MEDIUM THERMAL	0.16	2
21	171	TIGHT POSITIONAL	0.04	0.05
21	148	MEDIUM POSITIONAL	0.05	0.5
21	171	TIGHT THERMAL	0.26	0.5
21	148	MEDIUM THERMAL	0.2	2
22	106	TIGHT POSITIONAL	0.06	0.05
22	144	MEDIUM POSITIONAL	0.06	0.5
22	106	TIGHT THERMAL	0.22	0.5
22	144	MEDIUM THERMAL	0.18	2
23	93	TIGHT POSITIONAL	0.04	0.05
23	117	MEDIUM POSITIONAL	0.04	0.5
23	93	TIGHT THERMAL	0.24	0.5
23	117	MEDIUM THERMAL	0.19	2
24	69	TIGHT POSITIONAL	0.07	0.05
24	81	MEDIUM POSITIONAL	0.06	0.5
24	69	TIGHT THERMAL	0.26	0.5
24	81	MEDIUM THERMAL	0.28	2
25	140	TIGHT POSITIONAL	0.05	0.05
25	164	MEDIUM POSITIONAL	0.05	0.5
25	140	TIGHT THERMAL	0.21	0.5
25	164	MEDIUM THERMAL	0.24	2
26	153	TIGHT POSITIONAL	0.05	0.05
26	195	MEDIUM POSITIONAL	0.05	0.5
26	153	TIGHT THERMAL	0.29	0.5
26	195	MEDIUM THERMAL	0.22	2
27	94	TIGHT POSITIONAL	0.05	0.05
27	87	MEDIUM POSITIONAL	0.06	0.5
27	94	TIGHT THERMAL	0.21	0.5
27	87	MEDIUM THERMAL	0.23	2
28	35	TIGHT POSITIONAL	0.04	0.05
28	33	MEDIUM POSITIONAL	0.05	0.5
28	35	TIGHT THERMAL	0.2	0.5
28	33	MEDIUM THERMAL	0.18	2
29	123	TIGHT POSITIONAL	0.04	0.05
29	162	MEDIUM POSITIONAL	0.04	0.5
29	123	TIGHT THERMAL	0.23	0.5
29	162	MEDIUM THERMAL	0.19	2
30	101	TIGHT POSITIONAL	0.04	0.05
30	114	MEDIUM POSITIONAL	0.04	0.5
30	101	TIGHT THERMAL	0.3	0.5
30	114	MEDIUM THERMAL	0.26	2
31	101	TIGHT POSITIONAL	0.03	0.05
31	82	MEDIUM POSITIONAL	0.04	0.5
31	101	TIGHT THERMAL	0.23	0.5
31	82	MEDIUM THERMAL	0.18	2
32	93	TIGHT POSITIONAL	0.04	0.05
32	105	MEDIUM POSITIONAL	0.03	0.5
32	93	TIGHT THERMAL	0.15	0.5
32	105	MEDIUM THERMAL	0.15	2
33	53	TIGHT POSITIONAL	0.04	0.05
33	48	MEDIUM POSITIONAL	0.03	0.5
33	53	TIGHT THERMAL	0.18	0.5
33	48	MEDIUM THERMAL	0.12	2
34	83	TIGHT POSITIONAL	0.04	0.05
34	129	MEDIUM POSITIONAL	0.04	0.5
34	83	TIGHT THERMAL	0.23	0.5
34	129	MEDIUM THERMAL	0.17	2
35	134	TIGHT POSITIONAL	0.03	0.05
35	125	MEDIUM POSITIONAL	0.04	0.5
35	134	TIGHT THERMAL	0.24	0.5
35	125	MEDIUM THERMAL	0.16	2
36	48	TIGHT POSITIONAL	0.03	0.05
36	55	MEDIUM POSITIONAL	0.04	0.5
36	48	TIGHT THERMAL	0.24	0.5
36	55	MEDIUM THERMAL	0.16	2
37	42	TIGHT POSITIONAL	0.05	0.05
37	40	MEDIUM POSITIONAL	0.12	0.5
37	42	TIGHT THERMAL	0.17	0.5
37	40	MEDIUM THERMAL	0.18	2
38	24	TIGHT POSITIONAL	0.03	0.05
38	7	MEDIUM POSITIONAL	0.03	0.5
38	24	TIGHT THERMAL	0.08	0.5
38	7	MEDIUM THERMAL	0.28	2

LS refinement shell

Resolution: 2.2→2.257 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.296	207	-
R_work	0.244	3769	-
obs	-	-	77.54 %

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	0.4394	0.1177	0.0411	0.7247	0.2542	0.479	0.0047	-0.0581	0.0797	0.0294	-0.0084	0.0395	-0.0651	-0.0679	0.0037	0.0316	-0.0113	0.003	0.0632	-0.015	0.0658	-1.9938	8.6849	36.4685
2	0.3879	0.0915	-0.0613	0.8435	-0.129	0.4186	0.0385	-0.0446	-0.0001	0.0045	-0.0027	-0.0817	-0.0002	0.014	-0.0357	0.0207	-0.0164	-0.0219	0.0434	0.001	0.0475	11.6103	-3.1152	32.217
3	7.4416	16.0673	6.6025	47.8482	34.4389	36.8378	0.4824	-0.439	-0.7484	0.9441	-0.5881	-1.0956	0.1698	0.3584	0.1056	0.0554	-0.0148	-0.0981	1.1268	0.0601	0.1903	2.5518	-27.7047	12.7265
4	0.4196	0.0514	-0.2826	0.6394	0.1007	1.3885	-0.0038	0.0385	-0.0132	0.0131	0.053	0.017	0.0222	0.0006	-0.0492	0.0037	0.0111	0.0047	0.0471	0.0143	0.0127	-27.2616	-3.5499	8.7605
5	0.823	0.2531	0.3506	0.3675	0.1839	0.3617	0.0441	0.0256	-0.0549	0.013	-0.0182	-0.0666	0.0119	0.0346	-0.026	0.0219	-0.0047	-0.002	0.0391	0.0011	0.0488	-12.885	-10.4949	15.0453
6	0.6177	0.0642	-0.2872	0.5204	-0.3451	0.7804	0.0572	0.0152	0.0478	-0.0336	0.0213	-0.1017	-0.1173	0.0265	-0.0785	0.0574	-0.0046	0.0336	0.0375	-0.0172	0.0632	-18.5913	7.6502	1.515
7	0.625	-0.1091	0.0578	0.4218	0.0901	0.4307	0.022	-0.0251	-0.037	0.0579	0.0061	-0.0397	0.059	0.0476	-0.0281	0.0453	-0.0126	-0.0044	0.0193	-0.0046	0.0188	-33.2225	31.2074	35.5063
8	0.4341	0.0464	-0.1389	0.6191	0.1592	0.6243	0.0292	0.0033	0.0306	0.0062	-0.0272	0.0773	-0.0116	-0.0441	-0.002	0.0117	-0.0112	0.0069	0.0256	-0.0151	0.0203	-47.7459	42.7989	33.8972
9	0.9895	-0.4022	-0.423	1.2565	0.8707	1.4066	0.039	-0.0709	-0.0858	0.1261	0.0803	-0.001	-0.0071	0.214	-0.1194	0.0337	-0.0222	0.0167	0.0817	-0.0202	0.0732	-14.3538	53.1519	10.5921
10	0.5371	0.208	-0.5973	0.39	-0.196	0.6993	0.0527	0.0002	0.0605	0.0146	0.0604	-0.0151	-0.0671	0.0387	-0.1131	0.0314	-0.014	0.024	0.0642	-0.0317	0.09	-23.9997	54.3636	17.9166
11	1.1818	-0.1572	0.0497	1.1885	0.8594	1.5864	0.0895	-0.0795	-0.169	0.098	0.0338	0.1169	0.2433	0.0148	-0.1233	0.0721	0.0039	-0.0177	0.0266	0.0167	0.0818	-17.4969	39.1059	1.7986

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	-1 - 140
2	X-RAY DIFFRACTION	2	A	141 - 402
3	X-RAY DIFFRACTION	3	A	403 - 412
4	X-RAY DIFFRACTION	4	A	414 - 505
5	X-RAY DIFFRACTION	5	A	506 - 641
6	X-RAY DIFFRACTION	6	A	642 - 767
7	X-RAY DIFFRACTION	7	B	0 - 140
8	X-RAY DIFFRACTION	8	B	141 - 397
9	X-RAY DIFFRACTION	9	B	398 - 511
10	X-RAY DIFFRACTION	10	B	512 - 641
11	X-RAY DIFFRACTION	11	B	642 - 767

-
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