PDB-5v6q: Crystal structure of NADPH-dependent glyoxylate/hydroxypyruvate r...

ID or keywords:

Entry

Database: PDB / ID: 5v6q

Title

Crystal structure of NADPH-dependent glyoxylate/hydroxypyruvate reductase SMc04462 (SmGhrB) from Sinorhizobium meliloti in complex with NADP and malonate

Components

NADPH-dependent glyoxylate/hydroxypyruvate reductase

Keywords

OXIDOREDUCTASE / NADPH-dependent glyoxylate/hydroxypyruvate reductase / NADP / NYSGRC / Sinorhizobium meliloti / Structural Genomics / PSI-Biology / New York Structural Genomics Research Consortium

Function / homology

Function and homology information

hydroxypyruvate reductase [NAD(P)H] activity / glyoxylate reductase (NADPH) activity / NAD binding / metal ion binding / cytosol
Similarity search - Function

Biological species

Rhizobium meliloti (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.95 Å

Authors

Shabalin, I.G. / Handing, K.B. / Miezaniec, A.P. / Gasiorowska, O.A. / Bonanno, J. / Almo, S.C. / Minor, W. / New York Structural Genomics Research Consortium (NYSGRC)

Funding support

United States, 3items

Organization	Grant number	Country
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	GM094662	United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	GM117080	United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)	HG008424	United States

Citation

Journal: Biochemistry / Year: 2018
Title: Structural, Biochemical, and Evolutionary Characterizations of Glyoxylate/Hydroxypyruvate Reductases Show Their Division into Two Distinct Subfamilies.
Authors: Kutner, J. / Shabalin, I.G. / Matelska, D. / Handing, K.B. / Gasiorowska, O. / Sroka, P. / Gorna, M.W. / Ginalski, K. / Wozniak, K. / Minor, W.

History

Deposition	Mar 17, 2017	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 29, 2017	Provider: repository / Type: Initial release
Revision 1.1	Sep 13, 2017	Group: Author supporting evidence / Refinement description / Category: pdbx_audit_support / software / Item: _pdbx_audit_support.funding_organization
Revision 1.2	May 16, 2018	Group: Data collection / Database references / Structure summary Category: citation / citation_author / entity Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 / _entity.pdbx_ec
Revision 1.3	Nov 27, 2019	Group: Author supporting evidence / Category: pdbx_audit_support
Revision 1.4	Oct 4, 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 / struct_conn / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_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_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	5v6q.cif.gz	491.8 KB	Display	PDBx/mmCIF format
PDB format	pdb5v6q.ent.gz	406.7 KB	Display	PDB format
PDBx/mmJSON format	5v6q.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	5v6q_validation.pdf.gz	1.5 MB	Display	wwPDB validaton report
Full document	5v6q_full_validation.pdf.gz	1.5 MB	Display
Data in XML	5v6q_validation.xml.gz	52.5 KB	Display
Data in CIF	5v6q_validation.cif.gz	76.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/v6/5v6q ftp://data.pdbj.org/pub/pdb/validation_reports/v6/5v6q	HTTPS FTP

-
Related structure data

Related structure data	4weqC 4z0pC 5j23SC 5unnC 5uogC 5v72C 5v7gC 5v7nC C: citing same article (ref.) S: Starting model for refinement
Similar structure data	5v7g-2 5v7g-1 5j23-1 3ba1-1 4lcj-3 6p2i-d 5v7n-2 4lcj-1 2hu2-1 6v89-1 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
Other databases	TargetTrack: NYSGRC-012132

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#254 - Feb 2021 Cellulose Synthase similarity (1)

Deposited unit

A: NADPH-dependent glyoxylate/hydroxypyruvate reductase

B: NADPH-dependent glyoxylate/hydroxypyruvate reductase

C: NADPH-dependent glyoxylate/hydroxypyruvate reductase

D: NADPH-dependent glyoxylate/hydroxypyruvate reductase

hetero molecules

141 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: NADPH-dependent glyoxylate/hydroxypyruvate reductase

B: NADPH-dependent glyoxylate/hydroxypyruvate reductase

hetero molecules

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

2

C: NADPH-dependent glyoxylate/hydroxypyruvate reductase

D: NADPH-dependent glyoxylate/hydroxypyruvate reductase

hetero molecules

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

Unit cell

Length a, b, c (Å)	176.484, 176.484, 135.857
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	146
Space group name H-M	H3

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
1	2	A
2	2	C
1	3	A
2	3	D
1	4	B
2	4	C
1	5	B
2	5	D
1	6	C
2	6	D

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	ARG	ARG	ARG	ARG	A	A	3 - 318	4 - 319
2	1	ARG	ARG	ARG	ARG	B	B	3 - 318	4 - 319
1	2	ARG	ARG	ALA	ALA	A	A	3 - 319	4 - 320
2	2	ARG	ARG	ALA	ALA	C	C	3 - 319	4 - 320
1	3	ARG	ARG	ILE	ILE	A	A	3 - 320	4 - 321
2	3	ARG	ARG	ILE	ILE	D	D	3 - 320	4 - 321
1	4	SER	SER	ARG	ARG	B	B	2 - 318	3 - 319
2	4	SER	SER	ARG	ARG	C	C	2 - 318	3 - 319
1	5	ARG	ARG	ARG	ARG	B	B	3 - 318	4 - 319
2	5	ARG	ARG	ARG	ARG	D	D	3 - 318	4 - 319
1	6	ARG	ARG	ALA	ALA	C	C	3 - 319	4 - 320
2	6	ARG	ARG	ALA	ALA	D	D	3 - 319	4 - 320

NCS ensembles :

ID
1
2
3
4
5
6

#1: Protein	NADPH-dependent glyoxylate/hydroxypyruvate reductase Mass: 34358.496 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhizobium meliloti (strain 1021) (bacteria) Strain: 1021 / Gene: SMc04462 / Plasmid: pSGC-His / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3)-RIPL / References: UniProt: Q92LZ4, hydroxypyruvate reductase
#2: Chemical	ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE Mass: 743.405 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂₁H₂₈N₇O₁₇P₃
#3: Chemical	ChemComp-MLA / MALONIC ACID / DICARBOXYLIC ACID C3 / PROPANEDIOLIC ACID / METHANEDICARBOXYLIC ACID Mass: 104.061 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₃H₄O₄
#4: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 841 / 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: 2.96 Å³/Da / Density % sol: 58.48 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.2 uL 13 mg/mL protein in 20 mM HEPES, pH 7.5, 150 mM sodium chloride, 10% glycerol, 0.1% sodium azide, 0.5 mM TCEP, 5 mM NADP + 0.2 uL MCSG Suite II condition #20 (1.1 M malonic acid, 0. ...Details: 0.2 uL 13 mg/mL protein in 20 mM HEPES, pH 7.5, 150 mM sodium chloride, 10% glycerol, 0.1% sodium azide, 0.5 mM TCEP, 5 mM NADP + 0.2 uL MCSG Suite II condition #20 (1.1 M malonic acid, 0.072 M succinic acid, 0.15 M ammonium citrate tribasic, 0.18 M DL-malic acid, 0.096 M ammonium tartrate dibasic, 0.24 M sodium acetate, 0.3 M sodium formate, pH 7), equilibrated against 1.5 M sodium chloride in a 96-well, 3-drop crystallization plate (Swissci), incubated with 1/50 v/v 1 mg/mL rTEV at 289 K for 3 hours prior to crystallization

Crystal

Density Matthews: 2.96 Å³/Da / Density % sol: 58.48 %

Crystal grow

Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2 uL 13 mg/mL protein in 20 mM HEPES, pH 7.5, 150 mM sodium chloride, 10% glycerol, 0.1% sodium azide, 0.5 mM TCEP, 5 mM NADP + 0.2 uL MCSG Suite II condition #20 (1.1 M malonic acid, 0. ...

-
Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 21-ID-G / Wavelength: 0.97856 Å

Detector

Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 24, 2014 / Details: Beryllium Lenses

Radiation

Monochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97856 Å / Relative weight: 1

Reflection twin

Crystal-ID	ID	Operator	Domain-ID	Fraction
1	1	H, K, L	1	0.587
1	1	K, H, -L	2	0.413

Reflection

Resolution: 1.95→50 Å / Num. obs: 114355 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 4.6 % / B_iso Wilson estimate: 30 Å² / R_merge(I) obs: 0.105 / R_pim(I) all: 0.055 / R_rim(I) all: 0.119 / R_sym value: 0.105 / Χ²: 2.144 / Net I/av σ(I): 22.8 / Net I/σ(I): 7.6

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique all	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all	R_sym value	Χ²	% possible all
1.95-1.98	4.5	0.691	2.1	5653	5653	0.686	0.366	0.784	0.691	0.868	98.6
1.98-2.02	4.5	0.615				0.723	0.326	0.698		0.899	98.7
2.02-2.06	4.5	0.518				0.801	0.273	0.587		0.967	98.6
2.06-2.1	4.6	0.435				0.859	0.228	0.493		1.043	98.9
2.1-2.15	4.6	0.365				0.889	0.191	0.413		1.136	99
2.15-2.2	4.6	0.324				0.919	0.169	0.366		1.244	99.3
2.2-2.25	4.6	0.305				0.927	0.158	0.344		1.356	99.5
2.25-2.31	4.6	0.263				0.938	0.136	0.297		1.409	99.7
2.31-2.38	4.7	0.245				0.951	0.126	0.276		1.493	99.8
2.38-2.46	4.7	0.222				0.96	0.114	0.251		1.627	100
2.46-2.54	4.7	0.196				0.964	0.1	0.221		1.869	100
2.54-2.65	4.7	0.179				0.973	0.092	0.202		2.003	100
2.65-2.77	4.7	0.157				0.977	0.08	0.176		2.352	100
2.77-2.91	4.7	0.136				0.982	0.07	0.153		2.799	100
2.91-3.1	4.6	0.119				0.986	0.062	0.134		3.207	100
3.1-3.33	4.6	0.1				0.989	0.052	0.113		3.53	99.9
3.33-3.67	4.4	0.084				0.992	0.044	0.095		3.885	100
3.67-4.2	4.4	0.072				0.994	0.038	0.082		4.016	100
4.2-5.29	4.3	0.065				0.994	0.034	0.073		3.919	100
5.29-50	4.4	0.057				0.996	0.03	0.065		3.488	99.5

-
Processing

Software

Name	Version	Classification
MD2		data collection
HKL-3000		data scaling
MOLREP		phasing
REFMAC	5.8.0135	refinement
PDB_EXTRACT	3.22	data extraction
HKL-3000		data reduction
DENZO		data reduction
SCALEPACK		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 5J23

5j23

Resolution: 1.95→40.29 Å / Cor.coef. F_o:F_c: 0.978 / Cor.coef. F_o:F_c free: 0.973 / SU B: 3.603 / SU ML: 0.061 / SU R Cruickshank DPI: 0.024 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.024 / ESU R Free: 0.02
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1565	5559	4.9 %	RANDOM
R_work	0.1438	-	-	-
obs	0.1444	108794	99.54 %	-

Solvent computation

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

Displacement parameters

B_iso max: 77.88 Å² / B_iso mean: 33.875 Å² / B_iso min: 18.25 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-2.22 Å²	-0 Å²	-0 Å²
2-	-	-2.22 Å²	-0 Å²
3-	-	-	4.43 Å²

Refinement step

Cycle: final / Resolution: 1.95→40.29 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9446	0	223	841	10510
B_iso mean	-	-	31.46	38.92	-
Num. residues	-	-	-	-	1274

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.019	9850
X-RAY DIFFRACTION	r_bond_other_d	0.004	0.02	9654
X-RAY DIFFRACTION	r_angle_refined_deg	1.34	2.003	13492
X-RAY DIFFRACTION	r_angle_other_deg	1.1	3	22057
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.94	5	1270
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.507	22.402	358
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.866	15	1484
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	20.3	15	96
X-RAY DIFFRACTION	r_chiral_restr	0.069	0.2	1642
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.021	11030
X-RAY DIFFRACTION	r_gen_planes_other	0.003	0.02	2142

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	39102	0.05
1	2	B	39102	0.05
2	1	A	39650	0.04
2	2	C	39650	0.04
3	1	A	39244	0.04
3	2	D	39244	0.04
4	1	B	39232	0.04
4	2	C	39232	0.04
5	1	B	39540	0.02
5	2	D	39540	0.02
6	1	C	39310	0.04
6	2	D	39310	0.04

LS refinement shell

Resolution: 1.951→2.001 Å / R_factor R_free error: 0 / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.257	422	-
R_work	0.216	7946	-
all	-	8368	-
obs	-	-	98.22 %

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	1.7409	-0.8201	-0.1654	3.8198	-0.0718	2.9604	0.2094	0.1324	0.1828	-0.3255	0.0492	-0.2629	-0.2773	0.4067	-0.2586	0.1135	-0.0761	0.1281	0.1654	-0.0673	0.171	67.132	82.57	37.735
2	0.83	0.124	0.4325	1.7868	0.2049	2.1072	0.0141	-0.0354	0.0276	0.1437	0.1639	-0.1604	-0.0218	0.4622	-0.1779	0.0748	-0.0345	0.0762	0.2014	-0.1108	0.1495	67.6	79.66	50.363
3	0.049	0.0737	0.007	1.2426	0.2817	0.5825	0.0667	0.0042	-0.0042	0.1354	-0.0422	0.0014	0.0037	-0.0077	-0.0244	0.0988	-0.0245	0.0154	0.131	-0.0513	0.1345	63.526	46.411	35.673
4	2.1421	-0.2913	-1.31	2.5421	1.2377	4.8786	0.0946	0.0745	-0.0487	0.5088	-0.1279	0.7715	0.1921	-0.5794	0.0334	0.1537	-0.0588	0.1819	0.1394	-0.021	0.2817	47.831	50.236	49.265
5	0.7933	0.2897	-0.493	1.9487	0.0362	1.512	-0.0199	-0.114	0.0028	0.6422	0.031	-0.123	0.1348	0.0222	-0.0111	0.2682	-0.0042	-0.0155	0.0798	-0.043	0.0487	66.527	48.758	51.228
6	0.3437	-0.7656	-0.3097	2.0183	0.8254	0.5515	0.0859	0.0068	0.0656	-0.0196	-0.0275	-0.0528	-0.0424	-0.0248	-0.0584	0.1284	-0.0277	0.0765	0.1193	-0.0487	0.1554	58.867	74.857	42.478
7	4.4899	0.3919	0.2501	3.2995	0.2757	2.9319	0.1016	-0.2228	-0.3523	0.1348	0.0132	-0.069	0.2678	0.1529	-0.1148	0.0943	0.0426	-0.0906	0.1199	0.0103	0.1725	62.429	13.345	26.917
8	0.3603	0.4549	0.2371	1.4592	0.435	0.2949	0.0619	0.0368	-0.0839	-0.1059	0.0385	-0.0889	0.0001	0.0685	-0.1004	0.1018	0.0045	-0.0398	0.1288	-0.0414	0.1299	63.186	27.006	19.092
9	4.977	3.2574	2.4247	6.1553	-0.0865	1.878	-0.0033	0.134	0.0677	-0.2194	-0.1585	-0.2534	0.0839	0.1714	0.1617	0.0972	-0.0028	-0.01	0.09	-0.0467	0.23	80.502	58.473	38.378
10	0.2047	0.2003	0.4595	1.8785	0.3974	1.388	0.0474	-0.0247	0.022	-0.1303	-0.0381	0.2319	-0.0531	-0.1777	-0.0093	0.1114	0.0349	0.0007	0.1531	-0.0399	0.1374	54.428	51.85	24.52
11	1.5096	0.6974	0.1102	3.1605	0.8011	1.5651	-0.0048	0.0963	0.0253	-0.3411	-0.013	0.5176	-0.0536	-0.1572	0.0178	0.168	0.0166	-0.1146	0.135	-0.0219	0.1308	51.263	47.099	12.497
12	0.3633	0.2812	0.0632	1.4578	0.2142	0.2766	0.0522	0.0007	-0.0289	-0.2369	-0.0026	-0.0549	-0.038	0.045	-0.0496	0.1187	0.0043	-0.0146	0.1225	-0.0436	0.0929	62.149	37.23	18.057
13	5.3342	-0.7118	0.6991	2.1946	-0.7052	2.7606	0.1087	0.2531	-0.3237	-0.0927	0.0458	-0.0077	0.0854	-0.0079	-0.1546	0.1553	-0.0057	-0.0712	0.0434	-0.0662	0.1558	36.521	1.754	57.225
14	0.9406	-0.1149	0.3838	0.2623	-0.0553	0.1685	0.0383	-0.0633	-0.0999	0.0346	0.0375	-0.0109	0.0352	-0.0337	-0.0758	0.1389	-0.005	-0.0688	0.1021	-0.0119	0.1377	26.107	9.248	61.779
15	1.3605	-0.4672	0.7167	0.2942	0.0761	1.4809	-0.0657	-0.06	0.1294	0.0483	0.0886	-0.06	-0.1186	0.0366	-0.0229	0.1775	0.0184	-0.0571	0.0883	0.0043	0.1431	10.695	29.974	58.534
16	4.0819	-0.2592	0.1085	2.3148	0.7144	1.2782	-0.1342	-0.2986	0.3449	0.2308	0.1872	-0.1266	-0.0669	0.048	-0.0531	0.1807	0.0473	-0.0754	0.1542	-0.0911	0.0872	17.26	33.424	70.622
17	1.279	-0.574	-0.1125	1.1491	0.5704	0.8723	-0.0937	-0.3832	-0.1879	0.2157	0.1747	0.0736	0.0061	-0.1172	-0.0809	0.1362	0.0467	-0.0258	0.2008	0.0737	0.0887	8.392	18.184	69.799
18	2.1598	-0.6632	0.9332	0.4014	-0.1977	0.4532	0.0081	0.0415	-0.0436	0.0268	0.0489	-0.0447	-0.0083	0.0498	-0.0569	0.1312	-0.0006	-0.0608	0.0976	-0.0303	0.1343	35.259	13.604	60.88
19	2.5412	0.0504	-0.1352	2.3445	-0.3939	2.5987	0.14	-0.1171	0.0233	0.1287	-0.0696	0.1536	0.1153	-0.3366	-0.0703	0.0665	-0.0159	0.036	0.1447	0.0707	0.1569	-20.216	38.179	43.367
20	0.7093	-0.4332	0.1902	0.528	-0.2613	0.2195	0.073	0.0959	-0.0156	-0.0182	0.0015	0.038	0.0239	-0.0192	-0.0745	0.1131	0.0128	-0.0153	0.1132	0.0486	0.1304	-6.231	32.105	38.619
21	1.1211	-0.7746	0.058	1.0008	-0.6214	0.945	0.083	0.085	0.0373	0.0218	-0.0405	-0.0363	-0.0382	0.1187	-0.0425	0.099	-0.001	-0.0469	0.1325	0.013	0.126	16.297	23.64	46.094
22	2.1706	-0.6895	0.6839	2.2408	-0.5493	2.7536	0.168	0.327	0.2794	-0.0926	-0.1465	-0.2288	-0.1076	0.1816	-0.0216	0.0952	0.0098	0.0363	0.1678	0.0929	0.0833	15.625	33.99	31.864
23	1.0093	-0.7297	0.0011	1.1653	-0.0598	0.3969	0.1225	0.1586	-0.0745	-0.0609	-0.0551	0.0611	0.0685	0.0122	-0.0674	0.1182	0.0138	-0.0419	0.1207	0.022	0.0898	2.197	27.034	36.977
24	0.0453	0.3444	-0.1843	3.4026	0.2593	4.6258	0.0233	0.0101	0.0146	0.1375	0.0873	0.0132	-0.1998	-0.1171	-0.1106	0.1024	0.016	0.0085	0.1623	0.0733	0.174	-11.851	53.194	31.128

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	3 - 24
2	X-RAY DIFFRACTION	2	A	25 - 93
3	X-RAY DIFFRACTION	3	A	94 - 161
4	X-RAY DIFFRACTION	4	A	162 - 187
5	X-RAY DIFFRACTION	5	A	188 - 271
6	X-RAY DIFFRACTION	6	A	272 - 320
7	X-RAY DIFFRACTION	7	B	1 - 26
8	X-RAY DIFFRACTION	8	B	27 - 121
9	X-RAY DIFFRACTION	9	B	122 - 132
10	X-RAY DIFFRACTION	10	B	133 - 170
11	X-RAY DIFFRACTION	11	B	171 - 209
12	X-RAY DIFFRACTION	12	B	210 - 319
13	X-RAY DIFFRACTION	13	C	2 - 18
14	X-RAY DIFFRACTION	14	C	19 - 128
15	X-RAY DIFFRACTION	15	C	129 - 171
16	X-RAY DIFFRACTION	16	C	172 - 200
17	X-RAY DIFFRACTION	17	C	201 - 271
18	X-RAY DIFFRACTION	18	C	272 - 320
19	X-RAY DIFFRACTION	19	D	3 - 33
20	X-RAY DIFFRACTION	20	D	34 - 126
21	X-RAY DIFFRACTION	21	D	127 - 165
22	X-RAY DIFFRACTION	22	D	166 - 209
23	X-RAY DIFFRACTION	23	D	210 - 311
24	X-RAY DIFFRACTION	24	D	312 - 320

-
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