PDB-6bom: Crystal structure of mutant 2-methylcitrate synthase mcsAG306A fr...

ID or keywords:

Entry

Database: PDB / ID: 6bom

Title

Crystal structure of mutant 2-methylcitrate synthase mcsAG306A from Aspergillus fumigatus.

Components

2-methylcitrate synthase, mitochondrial

Keywords

TRANSFERASE / mcsA / 2-methylcitrate synthase / citrate synthase

Function / homology

Function and homology information

2-methylcitrate synthase / 2-methylcitrate synthase activity / propionate catabolic process, 2-methylcitrate cycle / citrate synthase activity / citrate synthase (unknown stereospecificity) / : / tricarboxylic acid cycle / carbohydrate metabolic process / mitochondrial matrix / identical protein binding
Similarity search - Function

Biological species

Neosartorya fumigata (mold)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.05 Å

Authors

Schlachter, C. / Chruszcz, M.

Citation

Journal: Biol.Chem. / Year: 2019
Title: Comparative studies of Aspergillus fumigatus 2-methylcitrate synthase and human citrate synthase.
Authors: Schlachter, C.R. / Klapper, V. / Radford, T. / Chruszcz, M.

History

Deposition	Nov 20, 2017	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 28, 2018	Provider: repository / Type: Initial release
Revision 1.1	Jun 17, 2020	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2	Oct 4, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	6bom.cif.gz	1011.2 KB	Display	PDBx/mmCIF format
PDB format	pdb6bom.ent.gz	844.5 KB	Display	PDB format
PDBx/mmJSON format	6bom.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	6bom_validation.pdf.gz	490 KB	Display	wwPDB validaton report
Full document	6bom_full_validation.pdf.gz	509.7 KB	Display
Data in XML	6bom_validation.xml.gz	97.2 KB	Display
Data in CIF	6bom_validation.cif.gz	139.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/bo/6bom ftp://data.pdbj.org/pub/pdb/validation_reports/bo/6bom	HTTPS FTP

-
Related structure data

Related structure data	5uqoSC 5uqqC 5uqrC 5uqsC 5uquC 5uzpC 5uzqC 5uzrC 6bolC 6bonC 6booC 6bopC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6bop-2 5uqq-1 5uzq-1 5uqo-d 5yg3-2 5xmq-1 2jgt-d 2rkw-d 5xmr-2 2r2n-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) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

5uqoSC

S: Starting model for refinement

C: citing same article (ref.)

Similar structure data

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#93 - Sep 2007 Citrate Synthase similarity (10) #154 - Oct 2012 Citric Acid Cycle similarity (7)

Deposited unit

A: 2-methylcitrate synthase, mitochondrial

B: 2-methylcitrate synthase, mitochondrial

C: 2-methylcitrate synthase, mitochondrial

D: 2-methylcitrate synthase, mitochondrial

E: 2-methylcitrate synthase, mitochondrial

F: 2-methylcitrate synthase, mitochondrial

hetero molecules

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

1

A: 2-methylcitrate synthase, mitochondrial

B: 2-methylcitrate synthase, mitochondrial

hetero molecules

defined by author&software
Evidence: gel filtration
97.3 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: 2-methylcitrate synthase, mitochondrial

D: 2-methylcitrate synthase, mitochondrial

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

3

E: 2-methylcitrate synthase, mitochondrial

F: 2-methylcitrate synthase, mitochondrial

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

Unit cell

Length a, b, c (Å)	82.021, 128.860, 258.462
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: _ / Refine code: _

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	THR	THR	LEU	LEU	A	A	30 - 463	6 - 439
2	1	THR	THR	LEU	LEU	B	B	30 - 463	6 - 439
1	2	THR	THR	LEU	LEU	A	A	30 - 463	6 - 439
2	2	THR	THR	LEU	LEU	C	C	30 - 463	6 - 439
1	3	THR	THR	LYS	LYS	A	A	30 - 464	6 - 440
2	3	THR	THR	LYS	LYS	D	D	30 - 464	6 - 440
1	4	ALA	ALA	LEU	LEU	A	A	31 - 463	7 - 439
2	4	ALA	ALA	LEU	LEU	E	E	31 - 463	7 - 439
1	5	ALA	ALA	LEU	LEU	A	A	31 - 463	7 - 439
2	5	ALA	ALA	LEU	LEU	F	F	31 - 463	7 - 439
1	6	THR	THR	LYS	LYS	B	B	30 - 464	6 - 440
2	6	THR	THR	LYS	LYS	C	C	30 - 464	6 - 440
1	7	THR	THR	LEU	LEU	B	B	30 - 463	6 - 439
2	7	THR	THR	LEU	LEU	D	D	30 - 463	6 - 439
1	8	ALA	ALA	LEU	LEU	B	B	31 - 463	7 - 439
2	8	ALA	ALA	LEU	LEU	E	E	31 - 463	7 - 439
1	9	ALA	ALA	LEU	LEU	B	B	31 - 463	7 - 439
2	9	ALA	ALA	LEU	LEU	F	F	31 - 463	7 - 439
1	10	THR	THR	LEU	LEU	C	C	30 - 463	6 - 439
2	10	THR	THR	LEU	LEU	D	D	30 - 463	6 - 439
1	11	ALA	ALA	LEU	LEU	C	C	31 - 463	7 - 439
2	11	ALA	ALA	LEU	LEU	E	E	31 - 463	7 - 439
1	12	ALA	ALA	LEU	LEU	C	C	31 - 463	7 - 439
2	12	ALA	ALA	LEU	LEU	F	F	31 - 463	7 - 439
1	13	ALA	ALA	LEU	LEU	D	D	31 - 463	7 - 439
2	13	ALA	ALA	LEU	LEU	E	E	31 - 463	7 - 439
1	14	ALA	ALA	LEU	LEU	D	D	31 - 463	7 - 439
2	14	ALA	ALA	LEU	LEU	F	F	31 - 463	7 - 439
1	15	ALA	ALA	LYS	LYS	E	E	31 - 464	7 - 440
2	15	ALA	ALA	LYS	LYS	F	F	31 - 464	7 - 440

NCS ensembles :

ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

#1: Protein	2-methylcitrate synthase, mitochondrial / Methylcitrate synthase / (2S / 3S)-2-methylcitrate synthase / Citrate synthase 2 Mass: 48571.453 Da / Num. of mol.: 6 / Mutation: G306A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Neosartorya fumigata (strain CEA10 / CBS 144.89 / FGSC A1163) (mold) Strain: CEA10 / CBS 144.89 / FGSC A1163 / Gene: mcsA, AFUB_094700 / Production host: Escherichia coli (E. coli) References: UniProt: B0YD89, 2-methylcitrate synthase, citrate synthase (unknown stereospecificity)
#2: Chemical	ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₁₂NO₃ / Comment: pH buffer*YM
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1059 / 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: 2.34 Å³/Da / Density % sol: 47.51 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1 M Tris pH 7.5 25% PEG3350

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
Detector	Type: RAYONIX MX300-HS / Detector: CCD / Date: Apr 7, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.05→40 Å / Num. obs: 171718 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 5.6 % / R_merge(I) obs: 0.065 / R_pim(I) all: 0.039 / R_rim(I) all: 0.091 / R_sym value: 0.065 / Net I/σ(I): 29.2
Reflection shell	Resolution: 2.05→2.09 Å / Redundancy: 5.8 % / R_merge(I) obs: 0.691 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 8490 / R_pim(I) all: 0.323 / R_rim(I) all: 0.783 / R_sym value: 0.691 / % possible all: 100

-
Processing

Software

Name	Version	Classification
REFMAC	5.8.0158	refinement
HKL-2000		data reduction
HKL-2000		data scaling
MOLREP		phasing
HKL-3000		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5UQO

5uqo

Resolution: 2.05→40 Å / Cor.coef. F_o:F_c: 0.967 / Cor.coef. F_o:F_c free: 0.955 / Cross valid method: THROUGHOUT / ESU R: 0.199 / ESU R Free: 0.16 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.21159	8687	5.1 %	RANDOM
R_work	0.18124	-	-	-
obs	0.18277	162833	99.68 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å

Displacement parameters

B_iso mean: 48.877 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.25 Å²	-0 Å²	-0 Å²
2-	-	-0.82 Å²	0 Å²
3-	-	-	0.57 Å²

Refinement step

Cycle: 1 / Resolution: 2.05→40 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	20263	0	8	1059	21330

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.016	0.019	20793
X-RAY DIFFRACTION	r_bond_other_d	0	0.02	19543
X-RAY DIFFRACTION	r_angle_refined_deg	1.642	1.97	28239
X-RAY DIFFRACTION	r_angle_other_deg	3.632	3	45365
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.333	5	2614
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.753	24.178	888
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.688	15	3477
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.126	15	109
X-RAY DIFFRACTION	r_chiral_restr	0.116	0.2	3143
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.021	23123
X-RAY DIFFRACTION	r_gen_planes_other	0.014	0.02	4122
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	1.958	3.115	10466
X-RAY DIFFRACTION	r_mcbond_other	1.958	3.114	10464
X-RAY DIFFRACTION	r_mcangle_it	2.971	4.66	13076
X-RAY DIFFRACTION	r_mcangle_other	2.971	4.66	13077
X-RAY DIFFRACTION	r_scbond_it	2.487	3.404	10327
X-RAY DIFFRACTION	r_scbond_other	2.487	3.404	10327
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	3.908	4.98	15164
X-RAY DIFFRACTION	r_long_range_B_refined	6.322	37.579	24174
X-RAY DIFFRACTION	r_long_range_B_other	6.322	37.58	24175
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 / Type: interatomic distance / Weight position: 0.05

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	A	27960	0.08
1	2	B	27960	0.08
2	1	A	27714	0.08
2	2	C	27714	0.08
3	1	A	27840	0.08
3	2	D	27840	0.08
4	1	A	27494	0.09
4	2	E	27494	0.09
5	1	A	27714	0.08
5	2	F	27714	0.08
6	1	B	28102	0.08
6	2	C	28102	0.08
7	1	B	28114	0.07
7	2	D	28114	0.07
8	1	B	27654	0.09
8	2	E	27654	0.09
9	1	B	28000	0.07
9	2	F	28000	0.07
10	1	C	27760	0.08
10	2	D	27760	0.08
11	1	C	27520	0.09
11	2	E	27520	0.09
12	1	C	27736	0.08
12	2	F	27736	0.08
13	1	D	27454	0.09
13	2	E	27454	0.09
14	1	D	27840	0.07
14	2	F	27840	0.07
15	1	E	27544	0.09
15	2	F	27544	0.09

LS refinement shell

Resolution: 2.05→2.103 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.27	596	-
R_work	0.253	11731	-
obs	-	-	98.25 %

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	0.8062	-0.8001	-0.2083	3.7517	0.3253	0.6721	-0.1564	-0.1593	-0.0628	0.4127	0.0491	0.0227	0.0637	0.0291	0.1074	0.1388	0.0306	0.0026	0.1199	0.0042	0.0722	22.676	8.833	-47.545
2	0.529	-0.1066	-0.0543	0.5455	0.1874	0.4535	-0.0507	0.0186	-0.0772	0.0213	0.0503	-0.0491	0.0607	0.0197	0.0003	0.1414	-0.0066	0.0409	0.1358	-0.0122	0.1469	25.852	3.279	-68.747
3	1.6105	0.9082	-0.8974	1.138	-0.9904	1.8234	0.0645	0.1111	0.1126	0.1637	-0.0088	0.0385	-0.1639	-0.0372	-0.0556	0.1185	0.0041	0.0281	0.1398	0.0083	0.1405	44.012	23.567	-72.711
4	0.339	-0.0075	-0.0118	0.6575	0.1305	0.1324	-0.1158	-0.0344	-0.0057	0.0605	0.0397	-0.0433	0.0323	-0.0026	0.0761	0.135	0.0105	0.0193	0.1639	-0.0132	0.1456	18.976	14.862	-60.775
5	1.0862	-0.8101	0.5627	1.4758	-0.681	1.112	-0.1955	-0.0511	0.1916	0.2012	0.0793	-0.1436	-0.1603	-0.0333	0.1162	0.1378	0.0141	-0.0037	0.1245	-0.0334	0.1	11.245	35.272	-58.614
6	0.5319	-0.1219	-0.0845	0.5039	-0.1868	0.4536	-0.0207	0.0527	-0.003	-0.0504	0.0403	0.0166	0.0049	-0.0984	-0.0196	0.1203	-0.0147	0.0106	0.1786	-0.0036	0.117	-0.739	22.657	-72.088
7	0.4675	0.0141	-0.1282	2.0569	-0.8631	1.2635	-0.1082	0.0281	-0.0086	0.0979	0.2193	0.1448	0.0273	-0.1271	-0.111	0.0922	0.0224	0.0181	0.1888	0.0356	0.1263	-15.401	10.064	-50.629
8	0.1468	0.0418	-0.2309	0.1138	-0.1498	0.5106	-0.0405	0.0669	0.0185	0.0467	0.08	-0.0088	0.0606	-0.0761	-0.0394	0.1647	0.0024	-0.0079	0.1877	-0.0107	0.1519	2.774	17.388	-58.985
9	0.882	0.5121	-0.8656	1.7337	-0.6712	1.8123	-0.0641	0.1514	-0.1497	-0.3896	0.0265	0.0742	0.3305	0.0554	0.0376	0.1818	-0.0011	-0.0816	0.2089	-0.0422	0.0988	-14.621	25.546	-119.776
10	0.6781	-0.0643	0.0004	0.4877	-0.0354	0.9474	0.0413	0.0272	-0.0577	-0.0277	0.0212	0.104	0.0249	-0.0697	-0.0626	0.1149	-0.0108	-0.0087	0.1581	0.0115	0.124	-22.014	36.674	-101.796
11	1.1692	-0.2571	0.1542	2.7277	-0.1956	1.9188	-0.0057	0.1544	0.1361	-0.3128	0.0947	0.166	-0.1544	-0.0383	-0.0889	0.1283	0.0153	-0.0217	0.1483	0.071	0.1205	-34.267	56.32	-117.102
12	0.8731	-0.009	-0.1235	0.4814	-0.2084	0.998	0.0131	0.1237	-0.0552	-0.134	0.0222	0.0735	-0.0093	0.0208	-0.0354	0.157	-0.0067	-0.0159	0.198	-0.0149	0.0842	-10.867	36.776	-113.404
13	0.5518	0.1409	0.1236	0.6101	0.0253	0.8371	0.0026	0.1178	0.0597	-0.0723	0.0267	-0.0749	-0.1173	0.1833	-0.0294	0.1412	-0.0527	0.0238	0.2046	0.0025	0.0844	7.227	49.611	-108.958
14	0.8054	0.7895	-0.0187	4.2307	-2.2246	6.2899	-0.2502	-0.0401	-0.2668	-0.3926	0.0051	-0.2114	0.9581	-0.0011	0.2452	0.3643	0.0382	0.0639	0.1161	-0.0338	0.1844	19.694	19.539	-102.623
15	0.59	-0.1147	0.327	3.4378	-0.4876	3.7644	0.0127	0.1086	0.0305	-0.2959	-0.1385	-0.5013	0.5956	0.0236	0.1258	0.2188	0.0613	0.0651	0.2143	-0.0286	0.1467	21.609	28.009	-108.348
16	0.4838	-0.0427	0.4837	0.614	0.5855	1.2458	0.0586	0.1174	0.0311	-0.0817	-0.0219	-0.0485	0.0693	0.102	-0.0366	0.1428	-0.0177	0.0137	0.2025	0.02	0.0758	-1.295	41.61	-113.348
17	2.0034	-1.2815	-1.5757	2.8552	1.5326	2.7028	-0.2151	-0.4614	-0.3198	0.489	0.1585	0.0631	0.3863	0.1558	0.0567	0.3103	0.1147	-0.0482	0.3318	0.115	0.135	-9.948	27.156	-8.392
18	1.388	-0.2551	-0.1186	0.5094	0.3659	0.8434	0.0115	-0.1926	-0.0237	0.129	0.1485	-0.1057	0.0353	0.1655	-0.1601	0.1607	0.0599	-0.0102	0.1653	-0.035	0.1088	-2.383	35.407	-27.709
19	0.4368	0.0794	-0.6278	4.2099	0.5082	1.0185	0.2773	-0.3037	0.2104	0.3753	0.0629	-0.371	-0.3204	0.4444	-0.3402	0.3166	-0.0984	0.0405	0.3369	-0.276	0.2632	9.633	59.095	-15.634
20	1.307	-0.2556	-0.4463	0.2217	0.1514	0.7657	0.0094	-0.3518	0.0995	0.1444	0.2041	-0.0706	-0.1025	0.1097	-0.2135	0.2793	0.0581	0.0095	0.256	-0.0361	0.1418	-6.696	43.067	-18.57
21	1.046	-0.3293	-0.0331	0.9911	0.0636	0.9232	-0.0445	-0.1969	0.0123	0.1281	0.1161	0.1937	-0.0928	-0.105	-0.0717	0.1419	0.0529	0.0549	0.128	0.047	0.1297	-31.29	49.164	-23.651
22	3.3231	2.0067	0.7759	4.1326	-1.4888	3.2536	-0.147	-0.0475	-0.5987	0.1496	0.0661	0.2091	0.1303	0.2244	0.0808	0.12	0.0649	0.1639	0.0575	0.152	0.6102	-42.332	19.803	-21.014
23	2.9151	0.8805	0.2931	4.1847	-0.3574	1.2723	-0.1539	-0.1855	-0.4054	0.135	0.0769	0.9407	0.2486	-0.0976	0.077	0.1349	-0.0036	0.123	0.1019	0.1319	0.5465	-47.152	28.96	-21.886
24	0.5898	-0.1217	0.155	1.6711	-0.0241	1.1568	-0.1078	-0.2854	-0.0336	0.2545	0.1323	0.1863	-0.0128	-0	-0.0245	0.1698	0.061	0.056	0.2084	0.0241	0.0596	-22.223	42.72	-16.907

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	30 - 74
2	X-RAY DIFFRACTION	2	A	75 - 304
3	X-RAY DIFFRACTION	3	A	305 - 422
4	X-RAY DIFFRACTION	4	A	423 - 464
5	X-RAY DIFFRACTION	5	B	30 - 75
6	X-RAY DIFFRACTION	6	B	76 - 304
7	X-RAY DIFFRACTION	7	B	305 - 395
8	X-RAY DIFFRACTION	8	B	396 - 464
9	X-RAY DIFFRACTION	9	C	30 - 77
10	X-RAY DIFFRACTION	10	C	78 - 304
11	X-RAY DIFFRACTION	11	C	305 - 424
12	X-RAY DIFFRACTION	12	C	425 - 464
13	X-RAY DIFFRACTION	13	D	30 - 304
14	X-RAY DIFFRACTION	14	D	305 - 340
15	X-RAY DIFFRACTION	15	D	341 - 420
16	X-RAY DIFFRACTION	16	D	421 - 464
17	X-RAY DIFFRACTION	17	E	31 - 75
18	X-RAY DIFFRACTION	18	E	76 - 310
19	X-RAY DIFFRACTION	19	E	311 - 399
20	X-RAY DIFFRACTION	20	E	400 - 464
21	X-RAY DIFFRACTION	21	F	31 - 304
22	X-RAY DIFFRACTION	22	F	305 - 357
23	X-RAY DIFFRACTION	23	F	358 - 422
24	X-RAY DIFFRACTION	24	F	423 - 464

-
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