PDB-4mkr: Structure of the apo form of a Zingiber officinale double bond re...

ID or keywords:

Entry

Database: PDB / ID: 4mkr

Title

Structure of the apo form of a Zingiber officinale double bond reductase

Components

Zingiber officinale double bond reductase

Keywords

PLANT PROTEIN / Rossmann fold / twisted b-barrel / curcuminoid reductase / NADPH

Function / homology

Function and homology information

2-alkenal reductase [NAD(P)H] activity / nucleotide binding
Similarity search - Function

Biological species

Zingiber officinale (ginger)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2.58 Å

Authors

Buratto, J. / Langlois d'Estaintot, B. / Granier, T. / Gallois, B. / Willis, M.A. / Sang, Y. / Flores-Sanchez, I.J. / Gang, D.R.

Citation

Journal: To be Published
Title: Structure of Zingiber officinale double bond reductase
Authors: Buratto, J. / Langlois d'Estaintot, B. / Granier, T. / Gallois, B. / Willis, M.A. / Sang, Y. / Flores-Sanchez, I.J. / Gang, D.R.

History

Deposition	Sep 5, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 10, 2014	Provider: repository / Type: Initial release
Revision 1.1	Sep 20, 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 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	4mkr.cif.gz	464.1 KB	Display	PDBx/mmCIF format
PDB format	pdb4mkr.ent.gz	383.5 KB	Display	PDB format
PDBx/mmJSON format	4mkr.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/mk/4mkr ftp://data.pdbj.org/pub/pdb/validation_reports/mk/4mkr	HTTPS FTP

-
Related structure data

Related structure data	4hfnS S: Starting model for refinement
Similar structure data	6sny-d 3kbo-1 1vb5-d 3kbo-2 1hku-1 2ome-3 2ome-1 2fji-1 6v8a-1 4u6q-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	#13 - Jan 2001 Alcohol Dehydrogenase similarity (5) #32 - Aug 2002 Chaperones similarity (1)

Deposited unit

A: Zingiber officinale double bond reductase

B: Zingiber officinale double bond reductase

C: Zingiber officinale double bond reductase

D: Zingiber officinale double bond reductase

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

1

A: Zingiber officinale double bond reductase

B: Zingiber officinale double bond reductase

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

2

C: Zingiber officinale double bond reductase

D: Zingiber officinale double bond reductase

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

Unit cell

Length a, b, c (Å)	50.930, 76.340, 93.450
Angle α, β, γ (deg.)	80.150, 89.970, 85.660
Int Tables number	1
Space group name H-M	P1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Refine code	Auth asym-ID	Auth seq-ID
1	1	1	2	A	8 - 21
2	1	1	2	C	8 - 21
3	1	1	2	D	8 - 21
1	1	2	2	A	28 - 33
2	1	2	2	C	28 - 33
3	1	2	2	D	28 - 33
1	1	3	2	A	50 - 57
2	1	3	2	C	50 - 57
3	1	3	2	D	50 - 57
4	1	3	2	B	50 - 57
1	1	4	2	A	78 - 93
2	1	4	2	C	78 - 93
3	1	4	2	D	78 - 93
4	1	4	2	B	78 - 93
1	1	5	2	A	105 - 111
2	1	5	2	C	105 - 111
3	1	5	2	D	105 - 111
4	1	5	2	B	105 - 111
1	1	6	2	A	136 - 197
2	1	6	2	C	136 - 197
3	1	6	2	D	136 - 197
4	1	6	2	B	136 - 197
1	1	7	2	A	220 - 261
2	1	7	2	C	220 - 261
3	1	7	2	D	220 - 261
4	1	7	2	B	220 - 261
1	1	8	2	A	274 - 296
2	1	8	2	C	274 - 296
3	1	8	2	D	274 - 296
4	1	8	2	B	274 - 296
1	1	9	2	A	299 - 324
2	1	9	2	C	299 - 324
3	1	9	2	D	299 - 324
1	1	10	2	A	326 - 335
2	1	10	2	C	326 - 335
3	1	10	2	D	326 - 335

NCS ensembles :

ID
1
2
3
4
5
6
7
8
9
10

#1: Protein	Zingiber officinale double bond reductase Mass: 39988.969 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Zingiber officinale (ginger) / Plasmid: pEXP5-CT / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) CodonPlus-RP / References: UniProt: A0A096LNF0*PLUS
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 119 / 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: 2.23 Å³/Da / Density % sol: 44.88 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 60 mM KCN, 28% PEG 2000 MME, 3 mM NaN3, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

-
Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

ESRF

/ Beamline: ID23-2 / Wavelength: 0.873 Å

Detector

Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 15, 2013 / Details: Pt coated Si mirrors

Radiation

Monochromator: horizontally side diffracting Silicon 111 crystal
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.873 Å / Relative weight: 1

Reflection

Resolution: 2.58→46.03 Å / Num. all: 42573 / Num. obs: 42573 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.3 % / B_iso Wilson estimate: 49.681 Å² / R_merge(I) obs: 0.072 / Net I/σ(I): 12.88

Reflection shell

Resolution (Å)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. unique obs	Diffraction-ID	% possible all
2.58-2.65	0.539	2.19	8576	2792	1	86.3
2.65-2.72	0.432	2.86	9946	3104	1	98.3
2.72-2.8	0.364	3.44	10074	3041	1	98.6
2.8-2.88	0.3	4.19	9566	2878	1	98.3
2.88-2.98	0.258	4.92	9470	2859	1	98.6
2.98-3.08	0.188	6.61	8955	2697	1	98.6
3.08-3.2	0.146	8.16	8829	2686	1	98.6
3.2-3.33	0.116	10.07	8444	2550	1	98.9
3.33-3.48	0.091	12.34	7979	2426	1	98.8
3.48-3.65	0.074	14.81	7766	2370	1	98.9
3.65-3.85	0.059	17.61	7263	2213	1	98.4
3.85-4.08	0.05	20.55	6859	2089	1	98.9
4.08-4.36	0.042	23.85	6369	1944	1	98.4
4.36-4.71	0.038	25.75	6097	1864	1	98.8
4.71-5.16	0.039	25.71	5523	1684	1	98.6
5.16-5.77	0.042	24.05	5026	1532	1	99.1
5.77-6.66	0.041	24.69	4457	1353	1	99.1
6.66-8.16	0.036	27.89	3732	1143	1	98.6
8.16-11.54	0.027	32.98	2821	860	1	97.7
11.54-46.03	0.024	33.71	1554	488	1	98.2

-
Phasing

Phasing

Method:

molecular replacement

Phasing MR

Model details: Phaser MODE: MR_AUTO

	Highest resolution	Lowest resolution
Rotation	2.6 Å	46.03 Å
Translation	2.6 Å	46.03 Å

-
Processing

Software

Name	Version	Classification
XSCALE		data scaling
PHASER	2.5.2	phasing
REFMAC		refinement
PDB_EXTRACT	3.11	data extraction
MxCuBE		data collection
XDS		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: model generated by Robetta server with structure 4HFN as target

4hfn

Resolution: 2.58→46.03 Å / Cor.coef. F_o:F_c: 0.918 / Cor.coef. F_o:F_c free: 0.876 / WR_factor R_free: 0.2719 / WR_factor R_work: 0.221 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.7858 / SU B: 26.098 / SU ML: 0.275 / SU R Cruickshank DPI: 0.9857 / SU R_free: 0.3563 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.986 / ESU R Free: 0.356 / Stereochemistry target values: Engh & Huber
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: RESIDUAL ONLY

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2817	2131	5 %	RANDOM
R_work	0.2281	-	-	-
all	0.2309	42573	-	-
obs	0.2309	42573	97.63 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso max: 166.76 Å² / B_iso mean: 47.4358 Å² / B_iso min: 13.34 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.44 Å²	0.15 Å²	0.4 Å²
2-	-	-0.36 Å²	0.75 Å²
3-	-	-	0.06 Å²

Refine analyze

Luzzati coordinate error obs: 0.374 Å

Refinement step

Cycle: LAST / Resolution: 2.58→46.03 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9119	0	0	119	9238

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.014	0.019	9334
X-RAY DIFFRACTION	r_bond_other_d	0	0.02	8759
X-RAY DIFFRACTION	r_angle_refined_deg	1.674	1.963	12653
X-RAY DIFFRACTION	r_angle_other_deg	3.771	3	20075
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.411	5	1198
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.075	23.925	372
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.032	15	1429
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	21.788	15	31
X-RAY DIFFRACTION	r_chiral_restr	0.086	0.2	1417
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.021	10602
X-RAY DIFFRACTION	r_gen_planes_other	0.008	0.02	2121
X-RAY DIFFRACTION	r_mcbond_it	1.065	1.947	4837
X-RAY DIFFRACTION	r_mcbond_other	1.065	1.947	4836
X-RAY DIFFRACTION	r_mcangle_it	1.804	2.912	6017

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	58	TIGHT POSITIONAL	0.03	0.05
1	2	C	58	TIGHT POSITIONAL	0.03	0.05
1	3	D	58	TIGHT POSITIONAL	0.03	0.05
1	1	A	144	MEDIUM POSITIONAL	0.05	0.5
1	2	C	144	MEDIUM POSITIONAL	0.05	0.5
1	3	D	144	MEDIUM POSITIONAL	0.09	0.5
1	1	A	83	TIGHT THERMAL	1.93	0.5
1	2	C	83	TIGHT THERMAL	7.59	0.5
1	3	D	83	TIGHT THERMAL	8.01	0.5
1	1	A	144	MEDIUM THERMAL	1.95	2
1	2	C	144	MEDIUM THERMAL	8.06	2
1	3	D	144	MEDIUM THERMAL	8.83	2
2	1	A	56	MEDIUM POSITIONAL	0.04	0.5
2	2	C	56	MEDIUM POSITIONAL	0.03	0.5
2	3	D	56	MEDIUM POSITIONAL	0.03	0.5
2	1	A	36	TIGHT THERMAL	1.63	0.5
2	2	C	36	TIGHT THERMAL	4.85	0.5
2	3	D	36	TIGHT THERMAL	6.33	0.5
2	1	A	56	MEDIUM THERMAL	1.81	2
2	2	C	56	MEDIUM THERMAL	5.01	2
2	3	D	56	MEDIUM THERMAL	6.72	2
3	1	A	70	MEDIUM POSITIONAL	0.06	0.5
3	2	C	70	MEDIUM POSITIONAL	0.07	0.5
3	3	D	70	MEDIUM POSITIONAL	0.06	0.5
3	4	B	70	MEDIUM POSITIONAL	0.16	0.5
3	1	A	48	TIGHT THERMAL	6.74	0.5
3	2	C	48	TIGHT THERMAL	9.51	0.5
3	3	D	48	TIGHT THERMAL	11.25	0.5
3	4	B	48	TIGHT THERMAL	5.13	0.5
3	1	A	70	MEDIUM THERMAL	7.58	2
3	2	C	70	MEDIUM THERMAL	10.27	2
3	3	D	70	MEDIUM THERMAL	15.09	2
3	4	B	70	MEDIUM THERMAL	4.1	2
4	1	A	52	MEDIUM POSITIONAL	0.03	0.5
4	2	C	52	MEDIUM POSITIONAL	0.03	0.5
4	3	D	52	MEDIUM POSITIONAL	0.03	0.5
4	4	B	52	MEDIUM POSITIONAL	0.04	0.5
4	1	A	45	TIGHT THERMAL	4.6	0.5
4	2	C	45	TIGHT THERMAL	7.15	0.5
4	3	D	45	TIGHT THERMAL	7.86	0.5
4	4	B	45	TIGHT THERMAL	4.09	0.5
4	1	A	52	MEDIUM THERMAL	4.72	2
4	2	C	52	MEDIUM THERMAL	7.43	2
4	3	D	52	MEDIUM THERMAL	8.61	2
4	4	B	52	MEDIUM THERMAL	3.58	2
5	1	A	49	MEDIUM POSITIONAL	0.07	0.5
5	2	C	49	MEDIUM POSITIONAL	0.06	0.5
5	3	D	49	MEDIUM POSITIONAL	0.07	0.5
5	4	B	49	MEDIUM POSITIONAL	0.18	0.5
5	1	A	40	TIGHT THERMAL	6.35	0.5
5	2	C	40	TIGHT THERMAL	8.84	0.5
5	3	D	40	TIGHT THERMAL	6.4	0.5
5	4	B	40	TIGHT THERMAL	8.91	0.5
5	1	A	49	MEDIUM THERMAL	6.5	2
5	2	C	49	MEDIUM THERMAL	8.65	2
5	3	D	49	MEDIUM THERMAL	6.45	2
5	4	B	49	MEDIUM THERMAL	8.75	2
6	1	A	447	MEDIUM POSITIONAL	0.07	0.5
6	2	C	447	MEDIUM POSITIONAL	0.08	0.5
6	3	D	447	MEDIUM POSITIONAL	0.07	0.5
6	4	B	447	MEDIUM POSITIONAL	0.1	0.5
6	1	A	360	TIGHT THERMAL	6.97	0.5
6	2	C	360	TIGHT THERMAL	4.49	0.5
6	3	D	360	TIGHT THERMAL	4.33	0.5
6	4	B	360	TIGHT THERMAL	7.09	0.5
6	1	A	447	MEDIUM THERMAL	7.27	2
6	2	C	447	MEDIUM THERMAL	5.16	2
6	3	D	447	MEDIUM THERMAL	4.35	2
6	4	B	447	MEDIUM THERMAL	8.08	2
7	1	A	393	MEDIUM POSITIONAL	0.04	0.5
7	2	C	393	MEDIUM POSITIONAL	0.06	0.5
7	3	D	393	MEDIUM POSITIONAL	0.04	0.5
7	4	B	393	MEDIUM POSITIONAL	0.04	0.5
7	1	A	245	TIGHT THERMAL	3.69	0.5
7	2	C	245	TIGHT THERMAL	2.31	0.5
7	3	D	245	TIGHT THERMAL	1.95	0.5
7	4	B	245	TIGHT THERMAL	4.33	0.5
7	1	A	393	MEDIUM THERMAL	4.01	2
7	2	C	393	MEDIUM THERMAL	2.72	2
7	3	D	393	MEDIUM THERMAL	2.31	2
7	4	B	393	MEDIUM THERMAL	4.79	2
8	1	A	240	MEDIUM POSITIONAL	0.1	0.5
8	2	C	240	MEDIUM POSITIONAL	0.06	0.5
8	3	D	240	MEDIUM POSITIONAL	0.06	0.5
8	4	B	240	MEDIUM POSITIONAL	0.09	0.5
8	1	A	135	TIGHT THERMAL	3.32	0.5
8	2	C	135	TIGHT THERMAL	1.9	0.5
8	3	D	135	TIGHT THERMAL	2.48	0.5
8	4	B	135	TIGHT THERMAL	4.39	0.5
8	1	A	240	MEDIUM THERMAL	4.06	2
8	2	C	240	MEDIUM THERMAL	2.51	2
8	3	D	240	MEDIUM THERMAL	3.18	2
8	4	B	240	MEDIUM THERMAL	5.81	2
9	1	A	185	MEDIUM POSITIONAL	0.11	0.5
9	2	C	185	MEDIUM POSITIONAL	0.1	0.5
9	3	D	185	MEDIUM POSITIONAL	0.17	0.5
9	1	A	152	TIGHT THERMAL	6.64	0.5
9	2	C	152	TIGHT THERMAL	5.04	0.5
9	3	D	152	TIGHT THERMAL	11.49	0.5
9	1	A	185	MEDIUM THERMAL	6.69	2
9	2	C	185	MEDIUM THERMAL	5.01	2
9	3	D	185	MEDIUM THERMAL	11.32	2
10	1	A	84	MEDIUM POSITIONAL	0.03	0.5
10	2	C	84	MEDIUM POSITIONAL	0.03	0.5
10	3	D	84	MEDIUM POSITIONAL	0.03	0.5
10	1	A	58	TIGHT THERMAL	1.24	0.5
10	2	C	58	TIGHT THERMAL	5.09	0.5
10	3	D	58	TIGHT THERMAL	5.51	0.5
10	1	A	84	MEDIUM THERMAL	1.89	2
10	2	C	84	MEDIUM THERMAL	5.43	2
10	3	D	84	MEDIUM THERMAL	6.61	2

LS refinement shell

Resolution: 2.58→2.647 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.41	151	-
R_work	0.323	2632	-
all	-	2783	-
obs	-	2783	86.05 %

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	2.5145	-0.1439	-0.058	2.4154	0.3743	0.6922	0.0743	-0.0216	-0.2728	0.062	-0.03	-0.1771	-0.0417	0.1026	-0.0443	0.1903	0.0221	-0.0325	0.2362	0.0016	0.2449	63.643	20.678	100.768
2	1.0298	0.8537	-0.619	2.2422	0.4733	2.7005	-0.1334	0.0322	-0.0843	-0.1214	-0.0234	0.1018	-0.0086	-0.2398	0.1568	0.1969	0.0262	0.0028	0.1903	-0.0267	0.2549	40.252	12.503	83.309
3	5.0679	-2.6168	0.9945	2.228	0.8769	3.1968	0.0701	-0.2021	-0.3711	0.0954	-0.2327	0.2162	0.2037	-0.3148	0.1626	0.2383	-0.0403	0.0107	0.2141	0.0678	0.3257	48.521	16.608	102.176
4	20.3243	-0.2903	9.799	1.7488	-3.5636	11.4669	1.581	0.271	-0.9406	0.6056	-0.1414	0.5009	-0.5105	0.2869	-1.4397	1.066	-0.0199	0.0076	0.3338	0.0305	0.2107	32.873	17.313	39.41
5	2.1968	-0.043	-0.3268	1.9747	0.2846	2.9494	-0.3648	0.1405	-0.2546	-0.5925	0.2079	-0.1837	-0.1735	0.0984	0.1569	0.4558	-0.1129	0.1134	0.1455	-0.0842	0.1222	56.047	12.367	59.12
6	12.2603	-6.4821	16.4145	4.6001	-7.4714	23.2495	-0.3024	0.3686	0.046	0.5121	0.1145	0.0245	-0.2012	0.7085	0.1879	0.801	-0.2749	-0.0879	0.3488	-0.0138	0.2617	42.244	18.948	43.793
7	1.6497	-0.1951	-0.2588	1.9374	0.6371	0.9336	0.0525	-0.0621	0.0993	-0.096	0.0229	-0.1508	0.033	0.1094	-0.0754	0.2251	0.0251	0.0409	0.2534	-0.0156	0.208	38.143	38.564	13.948
8	1.3205	-0.9753	-0.2114	1.4573	0.1289	2.4148	0.031	0.1802	0.1174	0.1844	-0.1081	0.0783	-0.0622	-0.273	0.0771	0.1762	-0.0191	0.0467	0.2849	-0.0199	0.2024	14.958	47.071	31.537
9	4.6345	3.6605	-0.9764	4.6233	0.167	2.5588	0.0714	0.2596	0.3815	-0.1301	-0.07	0.4308	-0.1535	-0.2945	-0.0014	0.1523	0.0866	0.0318	0.1963	0.0272	0.257	22.898	42.673	12.445
10	2.8716	-0.892	-0.0039	1.5324	-0.4347	2.2097	0.2775	-0.2357	0.1551	-0.2092	-0.0837	0.0775	0.1229	-0.0723	-0.1938	0.4211	-0.0218	0.0928	0.1249	-0.0093	0.1208	4.413	48.425	73.076
11	3.1538	-0.045	-1.9101	1.0786	-0.4331	3.2783	-0.3498	-0.1704	0.1272	0.3048	0.2075	-0.0513	0.2667	0.3381	0.1423	0.3896	0.0908	-0.0006	0.1834	-0.0828	0.166	29.044	44.443	57.676
12	6.1855	3.8525	-0.7483	3.7531	1.3107	2.4992	0.7229	-0.7427	0.0319	0.2137	-0.2572	-0.4192	-0.5198	0.2877	-0.4657	0.5548	0.0577	0.0808	0.2337	-0.1301	0.4548	17.004	55.915	75.28

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	7 - 142
2	X-RAY DIFFRACTION	2	A	143 - 302
3	X-RAY DIFFRACTION	3	A	303 - 349
4	X-RAY DIFFRACTION	4	B	49 - 134
5	X-RAY DIFFRACTION	5	B	135 - 293
6	X-RAY DIFFRACTION	6	B	294 - 349
7	X-RAY DIFFRACTION	7	C	7 - 142
8	X-RAY DIFFRACTION	8	C	143 - 302
9	X-RAY DIFFRACTION	9	C	303 - 349
10	X-RAY DIFFRACTION	10	D	7 - 139
11	X-RAY DIFFRACTION	11	D	140 - 320
12	X-RAY DIFFRACTION	12	D	321 - 349

-
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

-
Phasing

-
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

-Phasing

-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

-
Phasing

-
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