PDB-6v3m: Crystal structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphate ...

ID or keywords:

Entry

Database: PDB / ID: 6v3m

Title

Crystal structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (IspF) Burkholderia pseudomallei in compomplex with ligand HGN-0961 (BSI110840)

Components

2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase

Keywords

LYASE / SSGCID / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / Burkholderia pseudomallei / 2-C-methyl-D-erythritol 2 / 4-cyclodiphosphate synthase / HGN-0961

Function / homology

Function and homology information

2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase / 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase activity / terpenoid biosynthetic process / isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway / metal ion binding
Similarity search - Function

Biological species

Burkholderia pseudomallei (bacteria)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 1.55 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Citation

Journal: to be published
Title: Crystal structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (IspF) Burkholderia pseudomallei in compomplex with ligand HGN-0961 (BSI110840)
Authors: Abendroth, J. / Yano, J.K. / Pierce, P.G. / Horn, J.R. / Hagen, T.J. / Horanyi, P.S. / Lorimer, D.D. / Edwards, T.E.

History

Deposition	Nov 26, 2019	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 9, 2020	Provider: repository / Type: Initial release
Revision 1.1	Oct 11, 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	6v3m.cif.gz	252.6 KB	Display	PDBx/mmCIF format
PDB format	pdb6v3m.ent.gz	167.7 KB	Display	PDB format
PDBx/mmJSON format	6v3m.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	6v3m_validation.pdf.gz	436.6 KB	Display	wwPDB validaton report
Full document	6v3m_full_validation.pdf.gz	438.4 KB	Display
Data in XML	6v3m_validation.xml.gz	2 KB	Display
Data in CIF	6v3m_validation.cif.gz	9.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/v3/6v3m ftp://data.pdbj.org/pub/pdb/validation_reports/v3/6v3m	HTTPS FTP

-
Related structure data

Related structure data	3qhdS S: Starting model for refinement
Similar structure data	6mwj-d 3f0f-d 6mwf-d 3qhd-d 6mwi-d 3q8h-d 3p10-d 3jvh-d 3k2x-d 6mwk-d 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: BupsA.00122.a

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#154 - Oct 2012 Citric Acid Cycle similarity (1) #21 - Sep 2001 Antibodies similarity (1)

Deposited unit

A: 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase

B: 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase

C: 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase

hetero molecules

60.2 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	117.310, 67.550, 60.570
Angle α, β, γ (deg.)	90.000, 96.317, 90.000
Int Tables number	5
Space group name H-M	C121
Space group name Hall	C2y
Symmetry operation	#1: x,y,z #2: -x,y,-z #3: x+1/2,y+1/2,z #4: -x+1/2,y+1/2,-z

Components on special symmetry positions

ID	Model	Components
1	1	A-427- HOH
2	1	A-431- HOH
3	1	A-467- HOH
4	1	B-327- HOH

-
Protein , 1 types, 3 molecules ABC

#1: Protein	2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase / MECPS Mass: 19487.109 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Burkholderia pseudomallei (strain 1710b) (bacteria) Strain: 1710b / Gene: ispF, BURPS1710b_2511 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) Strain (production host): BL21(DE3) References: UniProt: Q3JRA0, 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase

#1: Protein

2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase / MECPS

Mass: 19487.109 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Burkholderia pseudomallei (strain 1710b) (bacteria)
Strain: 1710b / Gene: ispF, BURPS1710b_2511
Production host:

Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): BL21(DE3)
References: UniProt: Q3JRA0, 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase

-
Non-polymers , 6 types, 480 molecules

#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Chemical	ChemComp-QOG / 5-{[(propan-2-yl)carbamoyl]amino}-1,3,4-thiadiazole-2-sulfonamide Mass: 265.313 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₆H₁₁N₅O₃S₂ / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-DMS / DIMETHYL SULFOXIDE Mass: 78.133 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₂H₆OS / Comment: DMSO, precipitant*YM
#5: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₂H₆O₂
#6: Chemical	ChemComp-MLT / D-MALATE / (2R)-2-HYDROXYBUTANEDIOIC ACID / 2-HYDROXY-SUCCINIC ACID Mass: 134.087 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C₄H₆O₅
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 465 / Source method: isolated from a natural source / Formula: H₂O

-
Details

Has ligand of interest	Y

-
Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

Crystal	Density Matthews: 2.04 Å³/Da / Density % sol: 39.8 %
Crystal grow	Temperature: 290 K / Method: vapor diffusion, sitting drop Details: Bups122_opt3 screen: 100mM HEPES free acid / NaOH pH 7.4, 200mM ammonium acetate, 27% (w/V) PEG 3350: BupsA.00122.a.A1.PW28612 at 14.33mg/ml plus 1mM ZnCl2 and 10mM compound HGN- ...Details: Bups122_opt3 screen: 100mM HEPES free acid / NaOH pH 7.4, 200mM ammonium acetate, 27% (w/V) PEG 3350: BupsA.00122.a.A1.PW28612 at 14.33mg/ml plus 1mM ZnCl2 and 10mM compound HGN-0961/BSI110840: soaked over night with reservoir and 25mM compound: cryo: 20% EG + soak buffer: tray 310506a10: puck bno0-4. The ligand description was generated from a smiles string using phenix elbow. The ligand structure was minimized using GAMESS with the 3-21G basis. Restraints were extracted using phenix.elbow

Crystal

Density Matthews: 2.04 Å³/Da / Density % sol: 39.8 %

Crystal grow

Temperature: 290 K / Method: vapor diffusion, sitting drop
Details: Bups122_opt3 screen: 100mM HEPES free acid / NaOH pH 7.4, 200mM ammonium acetate, 27% (w/V) PEG 3350: BupsA.00122.a.A1.PW28612 at 14.33mg/ml plus 1mM ZnCl2 and 10mM compound HGN- ...

-
Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å

Detector

Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Nov 7, 2019

Radiation

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

Radiation wavelength

Wavelength: 1.5418 Å / Relative weight: 1

Reflection

Resolution: 1.55→50 Å / Num. obs: 67221 / % possible obs: 98.5 % / Redundancy: 11.388 % / B_iso Wilson estimate: 23.959 Å² / CC_1/2: 1 / R_merge(I) obs: 0.026 / R_rim(I) all: 0.027 / Χ²: 1.019 / Net I/σ(I): 49.7

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique obs	CC_1/2	R_rim(I) all	% possible all
1.55-1.59	4.565	0.32	4.47	4704	0.941	0.36	93.2
1.59-1.63	7.721	0.276	7.16	4620	0.977	0.295	94.7
1.63-1.68	8.213	0.224	9.04	4581	0.986	0.239	95.9
1.68-1.73	8.488	0.191	10.54	4519	0.99	0.203	97.5
1.73-1.79	8.808	0.148	13.63	4407	0.994	0.157	98.4
1.79-1.85	9.189	0.118	17.51	4308	0.996	0.124	99.4
1.85-1.92	9.556	0.092	22.26	4201	0.997	0.097	99.8
1.92-2	9.973	0.07	29.49	4001	0.999	0.074	99.9
2-2.09	10.399	0.055	38.56	3873	0.999	0.057	100
2.09-2.19	10.714	0.045	47.36	3706	0.999	0.047	99.9
2.19-2.31	11.579	0.04	55.81	3526	1	0.042	100
2.31-2.45	12.691	0.035	66.79	3335	1	0.036	99.9
2.45-2.62	13.395	0.03	79.26	3146	1	0.031	99.9
2.62-2.83	14.596	0.027	89.29	2937	1	0.028	100
2.83-3.1	16.229	0.023	104.88	2681	1	0.024	99.8
3.1-3.47	19.241	0.021	129	2437	1	0.021	100
3.47-4	22.016	0.018	152.99	2174	1	0.019	100
4-4.9	21.884	0.017	164.59	1820	1	0.017	99.9
4.9-6.93	21.663	0.017	161.53	1439	1	0.018	100
6.93-50	20.552	0.016	167	806	0.999	0.016	99.6

-
Processing

Software

Name	Version	Classification
PHENIX	1.17.1	refinement
XDS		data reduction
XSCALE		data scaling
PDB_EXTRACT	3.25	data extraction
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 3qhd

3qhd

Resolution: 1.55→44.39 Å / SU ML: 0.1343 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.4689
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1693	1897	2.82 %	0
R_work	0.1447	65311	-	-
obs	0.1454	67208	98.47 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 23.76 Å²

Refinement step

Cycle: LAST / Resolution: 1.55→44.39 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3519	0	92	465	4076

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0104	3747
X-RAY DIFFRACTION	f_angle_d	1.1692	5105
X-RAY DIFFRACTION	f_chiral_restr	0.0764	583
X-RAY DIFFRACTION	f_plane_restr	0.0066	684
X-RAY DIFFRACTION	f_dihedral_angle_d	20.1948	1356

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.55-1.59	0.2236	135	0.1964	4394	X-RAY DIFFRACTION	93.06
1.59-1.63	0.2186	123	0.1659	4452	X-RAY DIFFRACTION	94.66
1.63-1.68	0.1688	137	0.1534	4530	X-RAY DIFFRACTION	95.87
1.68-1.73	0.1765	135	0.1572	4593	X-RAY DIFFRACTION	97.4
1.73-1.8	0.19	122	0.1517	4638	X-RAY DIFFRACTION	98.49
1.8-1.87	0.1757	147	0.151	4682	X-RAY DIFFRACTION	99.44
1.87-1.95	0.1928	137	0.1532	4726	X-RAY DIFFRACTION	99.92
1.95-2.06	0.1642	136	0.1489	4739	X-RAY DIFFRACTION	100
2.06-2.18	0.179	144	0.143	4722	X-RAY DIFFRACTION	99.96
2.18-2.35	0.1624	128	0.1457	4709	X-RAY DIFFRACTION	99.98
2.35-2.59	0.1635	145	0.1449	4738	X-RAY DIFFRACTION	99.88
2.59-2.96	0.159	145	0.1477	4744	X-RAY DIFFRACTION	99.98
2.96-3.73	0.1673	120	0.1365	4801	X-RAY DIFFRACTION	100
3.74-44.39	0.1582	143	0.1334	4843	X-RAY DIFFRACTION	99.88

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	1.60355407613	-0.0260696639046	-0.117157275495	0.940617871673	0.417003393852	1.88816037739	0.0410750933111	0.189115607647	0.0983221110336	-0.428005750947	-0.070564586196	-0.0637102407607	-0.221246477573	-0.015477930473	-0.0180410406033	0.0841043883491	0.00629076581968	-0.00927961269106	0.0968708783433	0.025509856252	0.0849556717347	12.7275270157	-37.7974532968	-14.8959939068
2	1.03780026672	-0.0430820445987	-0.544118168557	3.19836001007	1.28551928614	0.87380990532	0.142329617168	-0.288700426948	0.777782019512	0.217638436003	-0.176284787874	0.426770905035	-0.193855691722	0.0253014076024	0.0390250578661	0.158122648427	-0.00865809580708	0.0238544363801	0.0931229357813	-0.0435088962038	0.276888468561	7.6722258619	-26.5090592466	-0.0892480579613
3	1.78616932806	0.0740646682382	0.0329926722211	1.9581694421	0.972826811149	1.57058459401	-0.0546061296219	0.15712454648	0.305355537902	-0.116139450394	0.016879193236	0.0897629828752	-0.199653625531	0.0036873346874	0.0507684704306	0.107938936888	0.00300542487547	0.00463613174479	0.0896894228029	0.0508943371582	0.117394524619	7.89920669307	-31.7576783338	-11.625550213
4	5.15420078596	-0.584520491846	0.315773610334	7.92654706095	-0.607618922508	5.49547067888	0.010158767566	0.455757365635	0.621608662161	-0.00635978405436	-0.0104819410603	0.0625605549088	-0.757658962731	-0.320914786814	0.0285030332839	0.213131998828	0.0131852457043	0.0092790145862	0.272502643899	0.0798911827418	0.153666304752	3.19503087741	-33.0846975498	-21.7067013655
5	1.05297570547	-2.26267621797	1.18511491769	4.92122224974	-2.43414451852	3.6973127162	-0.123470335237	0.853323831658	0.784294165129	-0.82701120683	0.180823186848	1.19584193673	-0.479567915318	-1.21155213924	-0.144808157835	0.399772821474	0.0962709545794	-0.0930789711774	0.397029192538	0.18238496858	0.448756117517	-2.98317448486	-25.6122439485	-12.962169147
6	1.82583565247	0.267767285285	-0.0563142912198	1.22114545747	0.224938495445	1.07023262948	0.0520983647593	0.127608663909	0.0278295243225	-0.0240017224311	0.00786228417215	-0.0424240401566	0.0271409701283	-0.103251817786	-0.0510075210715	0.0880018286817	-0.00239916328237	0.0049630963126	0.0650162882191	0.0197007186323	0.0442694608097	6.80867349097	-40.4663869268	-10.5129449138
7	2.17672432171	0.552909407104	0.176927865354	2.56624367109	0.862023419327	2.07594271981	0.044113439154	-0.127670520436	-0.114374125379	0.194226420145	0.0455120350335	-0.185179519849	0.0627435285673	0.172193394234	-0.0924340899797	0.12997858085	0.0141345090385	0.00324344121186	0.100163489482	0.00753824017954	0.096464498007	7.56920184045	-40.7414742953	-0.206371428539
8	4.74778380835	1.56766727618	-0.734353751302	6.49356620057	0.0568778222929	3.13029003416	0.0385138938446	-0.140471371473	-0.447274686777	0.144073411863	0.113551987519	0.137344218397	0.397914150723	-0.134565763114	-0.0979464687184	0.177499254826	-0.0129313590601	0.0115912412145	0.0746020504915	0.018040749963	0.108963555412	5.79521080153	-50.958315024	-4.31121108797
9	4.57968890826	4.37936041576	-0.593999069579	5.85941965486	-0.668478828693	1.07970456271	0.125677707752	-0.195416795559	0.00453555061418	0.18541677817	-0.188108533847	-0.220544472216	-0.0771374904434	0.167186381456	0.0193959116061	0.115289908261	-0.00117217394129	-0.0194261870749	0.0785376184754	-0.00213694789416	0.126844802155	22.0028204564	-35.5885175543	-3.08960477776
10	2.90665508692	1.75373430328	0.19263186404	3.52948302717	-0.299337178236	2.67250914845	-0.00944147184137	0.0175362048767	0.627596056018	-0.0305724522022	-0.0120667868151	0.386107707278	-0.380354851568	0.229591028146	0.00529848603032	0.164371150731	-0.0353394066904	-0.0163933552259	0.111854919245	0.020377156681	0.265706603522	23.038940368	-22.6207811063	-6.98836977416
11	2.12192713714	-0.185500717418	-0.185849023916	4.71255834436	0.687392013845	2.55886776896	0.0496603285721	0.287496267993	-0.0916071739649	-0.16542083262	0.0379779368981	-0.107751172343	0.154263217423	-0.0837626547214	-0.105202087353	0.0837336113798	0.00720158726545	0.000635796328797	0.0880675245238	0.00731336924559	0.0451808745805	11.6840961356	-43.4710954959	-14.3419882911
12	1.42123953057	0.558886358925	0.263906060236	3.14060598442	-0.412421758374	1.78429562063	-0.168548514673	0.739175304971	0.0919248249211	-0.0210522101458	0.248135172274	-0.493605398525	-0.219257102177	0.168858011392	0.141098507114	0.0900761830431	-0.0490584722758	0.0785807608182	0.374512411904	0.105538975636	0.104464176883	23.8355071691	-36.5319683521	-27.3587903385
13	3.20980919264	-0.314495576153	0.414635178631	4.05539033629	-0.259143238126	1.32301329938	-0.0690880534196	0.862380545167	0.575249543969	-0.24811787294	-0.0770604567355	-0.394468680635	-0.200030396575	0.336318485751	0.117738227943	0.167792235075	-0.0202686894408	0.0188702643722	0.485735081995	0.106540030772	0.198573444005	25.7567650381	-34.7858093571	-29.6503827013
14	2.99578420102	0.686796078366	-1.92945202858	3.23170750498	-0.973929964476	4.00107418717	-0.0127177917226	0.694964041964	0.201320492025	-0.330937649478	-0.0313477544541	-0.684147051982	-0.232861886648	0.566532955747	0.0459354229619	0.233415326316	0.00656624662662	0.0682087504291	0.482104521819	-0.00433699445879	0.282120029867	35.5868515708	-45.5211630123	-28.4681434513
15	1.91576646833	0.03353592014	0.466123221397	1.47682391284	-0.0137332385177	1.31755463004	-0.0225850832604	0.683986920399	0.108113840691	-0.23153566307	0.0312539443695	-0.0154994943635	-0.0150529389182	0.23418596143	-0.0362380470141	0.137606340654	-0.00123532744075	0.0386135578141	0.386486549427	0.042635590042	0.0780655132941	19.7080787407	-39.5252000308	-29.4243580132
16	3.67990917488	0.992530576813	-0.159855975288	4.42086434033	-2.07174910727	2.59513809031	0.0607805382734	0.425693237827	-0.197585906503	-0.0393732971717	-0.0229140318842	0.21104456717	0.184078117664	0.258856069859	-0.0109834521808	0.0946890824382	0.0257491086322	-0.00256000585786	0.226487312553	-0.0259784994047	0.0569745773867	21.168205601	-45.9462945986	-23.1836267293
17	2.57707930737	0.88002644487	-0.411682093499	4.11815552564	-0.0125790790866	0.805664154648	0.066352302157	-0.101066060731	0.195592400408	0.152234705066	-0.073761956989	-0.43874572046	-0.0258417993094	0.196270619508	-0.0125807510883	0.13364136131	0.0128351574751	-0.0257119795478	0.111847484907	0.00741130733232	0.0945082317255	33.5551521219	-40.6927355229	-7.48239961888
18	5.16469620628	2.77488363544	-2.02568107705	4.06817234694	-1.51315220037	1.01542461965	0.256674087961	-0.389235337478	0.173547991334	0.363755745943	-0.208719904642	-0.193090171886	-0.106976940613	0.223862012936	-0.0838298802129	0.157696002941	0.0310889813577	-0.0230292477031	0.12758149738	-0.0176908875329	0.138668443692	29.7459724215	-43.4446427023	-3.62433193559
19	8.42454557357	4.13657042694	1.64893322846	6.15954939948	0.704151069414	5.13347352389	-0.0767032224436	-0.473665230422	0.497055374596	0.423281238952	0.00316861094484	0.00656122037385	-0.29262388663	0.29391522167	0.0192146570438	0.22632127466	0.0334401764758	-0.0241114730174	0.145393364348	-0.0140975853158	0.159778438556	20.2947803651	-45.5344059634	1.65603226544
20	1.716974153	1.21392092036	0.176236619071	2.27389846725	-0.298089799752	3.19594958592	0.16850389028	-1.81953535439	0.285226761787	1.39671002604	-0.21128871442	-0.291057543538	-0.315072563044	0.545519388868	-0.0408600545519	0.550785117591	-0.0134639422142	-0.111374466583	0.570369255369	-0.0762848118788	0.449644075943	31.7391926437	-46.1273068348	8.83113896186
21	1.30632033668	0.122018647886	0.0114013981581	2.00653744592	-0.477122476957	1.09810846496	-0.017423430645	0.156619806349	-0.111919167352	-0.0953624240904	-0.00868887383876	-0.227121494637	0.0796183016312	0.155634543756	0.0392528823266	0.113761399134	0.0318137328544	0.00113175289227	0.123667974604	-0.0113718176426	0.13534262496	32.2837451886	-46.9003235185	-11.1760329816
22	6.81921842779	4.6997736373	1.19609956614	6.64700210094	1.07169649181	2.40720015545	-0.102997983863	0.137726846505	-0.253584517508	-0.0504015958384	0.157030017844	-0.0818260052216	0.149263206298	-0.0424028489061	-0.0532938808404	0.0695105444609	0.0454600194026	0.00647440195863	0.061938702205	-0.0160428199638	0.0852797936857	23.3193165274	-48.4234358403	-10.4844359046

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 0 through 16 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 17 through 30 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 31 through 53 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 54 through 67 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 68 through 74 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 75 through 107 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 108 through 122 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 123 through 128 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 129 through 139 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 140 through 146 )
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 147 through 159 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 0 through 27 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 28 through 53 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 54 through 67 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 68 through 146 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 147 through 159 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 0 through 33 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 34 through 53 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 54 through 62 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 63 through 74 )
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 75 through 146 )
22	X-RAY DIFFRACTION	22	chain 'C' and (resid 147 through 159 )

-
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

-
Protein , 1 types, 3 molecules ABC

-
Non-polymers , 6 types, 480 molecules

-
Details

-
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

-Protein , 1 types, 3 molecules ABC

-Non-polymers , 6 types, 480 molecules

-Details

-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

-
Protein , 1 types, 3 molecules ABC

-
Non-polymers , 6 types, 480 molecules

-
Details

-
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