[English] 日本語

Yorodumi

- PDB-7mtx: Crystal Structure of the Catalytic Domain of the Inosine Monophos... -

+
Open data

-
Basic information

Entry

Database: PDB / ID: 7mtx

Title

Crystal Structure of the Catalytic Domain of the Inosine Monophosphate Dehydrogenase from Bacillus anthracis in the complex with IMP and the inhibitor P176

Components

Inosine-5'-monophosphate dehydrogenase

Keywords

OXIDOREDUCTASE / IMPDH /

TIM barrel / delta CBS /

Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex

Function / homology

Function and homology information

IMP dehydrogenase activity /

IMP dehydrogenase / GMP biosynthetic process /

nucleotide binding /

metal ion binding
Similarity search - Function

Biological species

Bacillus anthracis (anthrax bacterium)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.44 Å

Authors

Kim, Y. / Maltseva, N. / Makowska-Grzyska, M. / Gu, M. / Gollapalli, D. / Hedstrom, L. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases / Center for Structural Genomics of Infectious Diseases (CSGID)

Funding support

United States, 1items

Citation

Journal: To Be Published
Title: Crystal Structure of the Catalytic Domain of the Inosine Monophosphate Dehydrogenase from Bacillus anthracis in the complex with IMP and the inhibitor P176
Authors: Kim, Y. / Maltseva, N. / Makowska-Grzyska, M. / Gu, M. / Gollapalli, D. / Hedstrom, L. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)

History

Deposition	May 13, 2021	Deposition site: RCSB / Processing site: RCSB
Supersession	Jun 9, 2021	ID: 5URR
Revision 1.0	Jun 9, 2021	Provider: repository / Type: Initial release
Revision 1.1	Oct 18, 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 / refine_hist Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_high

-
Structure visualization

Structure viewer	Molecule: MolmilJmol/JSmol

-
Downloads & links

-
Download

PDBx/mmCIF format	7mtx.cif.gz	1.2 MB	Display	PDBx/mmCIF format
PDB format	pdb7mtx.ent.gz	871.6 KB	Display	PDB format
PDBx/mmJSON format	7mtx.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/mt/7mtx ftp://data.pdbj.org/pub/pdb/validation_reports/mt/7mtx	HTTPS FTP

-
Related structure data

Related structure data	4mjmS 3tsb 3tsd 3usb 4my1 4my8 4my9 4mya 4myx 4qm1 5urs 7mtu S: Starting model for refinement
Similar structure data	7mtx-2 4mya-2 7mtu-1 5urs-2 4my1-2 4mya-1 5uzs-d 5urs-1 5uuv-d 4fo4-2 5upy-1 4myx-2 6mgu-2 4myx-1 7mtu-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
Other databases	TargetTrack: CSGID-IDP01178

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#140 - Aug 2011 Rhomboid Protease GlpG similarity (4)

-
Assembly

Deposited unit

A: Inosine-5'-monophosphate dehydrogenase

B: Inosine-5'-monophosphate dehydrogenase

C: Inosine-5'-monophosphate dehydrogenase

D: Inosine-5'-monophosphate dehydrogenase

E: Inosine-5'-monophosphate dehydrogenase

F: Inosine-5'-monophosphate dehydrogenase

G: Inosine-5'-monophosphate dehydrogenase

H: Inosine-5'-monophosphate dehydrogenase

hetero molecules

333 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

A: Inosine-5'-monophosphate dehydrogenase

B: Inosine-5'-monophosphate dehydrogenase

C: Inosine-5'-monophosphate dehydrogenase

D: Inosine-5'-monophosphate dehydrogenase

hetero molecules

defined by author&software
Evidence: gel filtration
166 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

E: Inosine-5'-monophosphate dehydrogenase

F: Inosine-5'-monophosphate dehydrogenase

G: Inosine-5'-monophosphate dehydrogenase

H: Inosine-5'-monophosphate dehydrogenase

hetero molecules

defined by author&software
166 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	85.390, 89.921, 104.856
Angle α, β, γ (deg.)	81.413, 90.030, 83.443
Int Tables number	1
Space group name H-M	P1
Space group name Hall	P1
Symmetry operation	#1: x,y,z

-
Components

#1: Protein	Inosine-5'-monophosphate dehydrogenase / IMP dehydrogenase / IMPD / IMPDH Mass: 40709.574 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) Gene: guaB, BA_0008, A9486_01210, ABW01_29210, BVG01_30935, COL95_27530 Plasmid: pMCSG7 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): Gold / References: UniProt: A0A6H3A7R4, IMP dehydrogenase
#2: Chemical	ChemComp-IMP / INOSINIC ACID / Inosinic acid Mass: 348.206 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₁₀H₁₃N₄O₈P
#3: Chemical	ChemComp-ZO4 / N-{2-chloro-5-[({2-[3-(prop-1-en-2-yl)phenyl]propan-2-yl}carbamoyl)amino]phenyl}-beta-D-ribopyranosylamine Mass: 475.965 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₂₄H₃₀ClN₃O₅ / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-K / POTASSIUM ION Mass: 39.098 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: K
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 429 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

-
Experimental details

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.43 Å³/Da / Density % sol: 49.34 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.2 Details: 10 % (W/V) PEG8000, 0.1 M SODIUM/POTASSIUM PHOSPHATE PH 6.2, 0.2 M SODIUM CHLORIDE

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97926 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 29, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97926 Å / Relative weight: 1
Reflection	Resolution: 2.44→50 Å / Num. obs: 111274 / % possible obs: 98.6 % / Redundancy: 2.6 % / B_iso Wilson estimate: 35.43 Å² / R_merge(I) obs: 0.122 / Net I/σ(I): 8.9
Reflection shell	Resolution: 2.44→2.49 Å / Redundancy: 2.5 % / R_merge(I) obs: 0.73 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 5504 / % possible all: 97.9

-
Processing

Software

Name	Version	Classification
PHENIX	1.19_4092	refinement
HKL-3000		data reduction
HKL-3000		data scaling
HKL-3000		phasing
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4MJM

4mjm

Resolution: 2.44→40.08 Å / SU ML: 0.2833 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 24.0567
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2223	5152	4.93 %
R_work	0.1779	99338	-
obs	0.1801	104490	91.24 %

Solvent computation

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

Displacement parameters

B_iso mean: 42.21 Å²

Refinement step

Cycle: LAST / Resolution: 2.44→40.08 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	20621	0	456	429	21506

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0016	21431
X-RAY DIFFRACTION	f_angle_d	0.5403	29026
X-RAY DIFFRACTION	f_chiral_restr	0.0418	3387
X-RAY DIFFRACTION	f_plane_restr	0.003	3706
X-RAY DIFFRACTION	f_dihedral_angle_d	12.8072	7850

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 (%)
2.44-2.46	0.3031	66	0.2096	1214	X-RAY DIFFRACTION	33.94
2.46-2.49	0.2585	112	0.2248	2636	X-RAY DIFFRACTION	71.62
2.49-2.52	0.3074	143	0.2303	2639	X-RAY DIFFRACTION	73.44
2.52-2.55	0.2895	142	0.2293	2797	X-RAY DIFFRACTION	76.26
2.55-2.59	0.2932	146	0.2238	2868	X-RAY DIFFRACTION	78.57
2.59-2.62	0.2774	135	0.2325	2906	X-RAY DIFFRACTION	80.43
2.62-2.66	0.3357	179	0.2323	3008	X-RAY DIFFRACTION	82.76
2.66-2.7	0.2844	164	0.2224	3109	X-RAY DIFFRACTION	86.29
2.7-2.74	0.3206	181	0.2213	3257	X-RAY DIFFRACTION	90.09
2.74-2.79	0.2344	162	0.2196	3377	X-RAY DIFFRACTION	92.86
2.79-2.84	0.3081	190	0.2158	3520	X-RAY DIFFRACTION	95.84
2.84-2.89	0.2704	158	0.2081	3496	X-RAY DIFFRACTION	97.16
2.89-2.94	0.2756	186	0.1983	3584	X-RAY DIFFRACTION	98.2
2.94-3	0.2617	180	0.2149	3573	X-RAY DIFFRACTION	98.19
3-3.07	0.2494	188	0.2149	3575	X-RAY DIFFRACTION	98.4
3.07-3.14	0.2697	192	0.2171	3565	X-RAY DIFFRACTION	98.53
3.14-3.22	0.281	182	0.2037	3568	X-RAY DIFFRACTION	98.43
3.22-3.31	0.2364	177	0.2004	3601	X-RAY DIFFRACTION	98.69
3.31-3.4	0.249	200	0.1969	3555	X-RAY DIFFRACTION	98.66
3.4-3.51	0.2271	179	0.1879	3601	X-RAY DIFFRACTION	98.8
3.51-3.64	0.2092	203	0.1848	3586	X-RAY DIFFRACTION	98.93
3.64-3.78	0.2376	189	0.1725	3560	X-RAY DIFFRACTION	98.87
3.78-3.96	0.2018	181	0.1613	3599	X-RAY DIFFRACTION	98.88
3.96-4.16	0.1946	206	0.142	3561	X-RAY DIFFRACTION	99.05
4.16-4.42	0.1655	181	0.1401	3609	X-RAY DIFFRACTION	98.98
4.42-4.77	0.1773	193	0.1354	3621	X-RAY DIFFRACTION	99.06
4.77-5.24	0.1608	186	0.1324	3587	X-RAY DIFFRACTION	99.26
5.24-6	0.1857	210	0.1642	3570	X-RAY DIFFRACTION	99.37
6-7.55	0.1833	183	0.1578	3624	X-RAY DIFFRACTION	99.37
7.55-40.08	0.173	158	0.1521	3572	X-RAY DIFFRACTION	97.59

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	2.82201080847	2.56010199435	0.764944580196	4.35589105526	1.34151657742	1.12245158493	-0.206631714446	-0.354566318215	-0.0820621193523	-0.196259579652	0.0321560042265	0.0495971930147	-0.114961421095	-0.0416530112475	0.174471776798	0.26624364198	0.0705241039784	0.0113576852854	0.328216568106	0.024306440127	0.266023590078	-15.1421006673	4.33705664986	6.04000245979
2	1.6072302296	-0.101752145764	0.0965439665979	2.79981118294	-0.527219826181	2.5903301659	-0.0359168276889	0.22857874722	0.18647188638	-0.306778969978	-0.0216410552839	0.347263661993	-0.159620977591	-0.211411326376	0.0311041604753	0.277167329266	0.0473749245113	-0.122260919245	0.30372734653	0.0386278265709	0.401379433225	-31.5707523951	12.62911256	-18.9875785949
3	1.47784865006	0.151922523506	0.868286386337	0.126758191899	0.0962713054325	2.44631031081	0.0125049388601	0.180034427752	0.187181901282	0.0336156816177	0.181761882115	0.445166256082	-0.377138942607	-0.0670625923809	-0.185891631861	0.44840695251	0.108157605974	-0.0734542402653	0.346132375834	0.035048108544	0.56905320799	-30.7814859395	24.7406631116	-13.3665475074
4	1.05181676188	0.236323801567	0.46913875743	0.844308236682	-0.034957151472	0.723034870635	-0.0427435980305	-0.1088234295	0.210762572747	-0.00960034498506	-0.0208269638708	0.309311465932	-0.142299701053	-0.175122253356	0.0613514359352	0.286484305311	0.0783436844696	0.0157090386092	0.239941055086	0.00897530937047	0.312926067657	-24.5389911718	15.0048061929	-3.47511113324
5	3.95818411828	0.0114704348781	-0.64858243369	1.93865224532	1.36030802733	1.28063417837	-0.210846676329	0.565842607053	-0.429031682623	-0.475904616292	0.155387800269	-0.226271506587	-0.04476673332	0.305524661759	0.0382560014228	0.398022646823	0.0116442490055	0.0405576727287	0.429165292772	-0.0139115326808	0.303356753526	-14.5206697193	6.93029095309	-27.24799261
6	3.41335232808	1.11476174557	0.871653197851	3.72896257572	2.37572043249	3.22615843394	-0.203558198727	0.465198950007	0.561110807472	-0.451271956455	0.303753749326	0.133031351382	-0.658848133725	0.194948606309	-0.063783773835	0.409582721345	0.0321963435582	-0.0440417609936	0.264860656763	0.0713318943244	0.297948465039	-11.4165424313	17.5191277903	-21.3437428028
7	2.89389744962	-0.330546915681	-1.15047951789	2.54604297886	-0.223014837364	3.05367826432	-0.226392946808	0.481721545	-0.443537199523	-0.108364494325	-0.224559508419	0.242426071259	0.0677971854253	-0.372847172835	0.365856768028	0.271686939809	-0.0147417567398	-0.10580274231	0.253894253661	-0.0262957696804	0.335211333495	-26.1274957174	-5.82428715535	-13.3488992299
8	1.73468296282	-0.390523976701	0.559122471997	2.38455448574	0.325851931847	1.86344657383	0.00256469291861	0.0336553843022	0.0652618646696	-0.0883230903153	0.0603439682103	0.0905407007044	0.0123488492812	-0.0347739322881	-0.0430012558432	0.250797097614	-0.00772758281945	0.0218869893905	0.235191311418	0.0750109393564	0.266099639595	-16.4558910956	-6.87451364624	-5.92098296002
9	4.88150966316	-2.39013975229	0.392981206542	2.12373197966	-0.220934443885	1.30476487466	0.17251447084	-0.130594371079	-0.286634875467	0.0222337337595	-0.083158094173	0.42183986997	-0.157768790778	-0.0719314495998	-0.0994340577696	0.334148250733	-0.00283234309992	0.0158069216699	0.218793375827	-0.00423852108275	0.29314591756	-7.80640805486	-10.9038585413	10.3380380535
10	2.20904342541	0.0546092243763	1.05795355985	1.83607312535	0.229217584029	2.90305972589	0.0025501346414	0.042989407215	-0.137776495364	-0.0860949424496	-0.0205606905484	0.166651435689	0.44268358012	-0.110378217378	0.0150377303195	0.368861245203	0.000825155922613	-0.00317307588683	0.206895909614	0.0142699405076	0.317467623209	-11.4894625565	-36.4668631718	-6.80300694939
11	0.702470297266	0.0665800605909	0.0393893908877	1.70852449247	0.234678619099	1.08599407038	0.0161180938585	-0.109285995599	-0.0836900392977	0.122533906849	-0.00482108604507	0.371320412668	0.0917551972534	-0.250765895637	-0.00450059958713	0.273680795983	-0.00982944688527	0.0264059387801	0.256139888026	0.0370413579977	0.340445019328	-18.8282604592	-25.2590306591	1.18609309863
12	2.03600110168	-0.69513122104	-0.0600406833554	2.29186573235	0.192531415029	1.86963972827	0.0875556355508	0.383419691032	-0.102078694095	-0.614079694043	-0.0735109834792	0.0466583763793	0.166311777614	-0.0874055706121	-0.00809463199982	0.330535704155	-0.0300238622998	-0.00600164535763	0.248820388856	-0.0148139876559	0.250287592266	-8.2450325106	-22.4715924745	-16.0845077965
13	0.98140844619	-0.567643961471	0.135900083341	1.68782451758	0.651839783179	1.19924722718	0.0341911275382	0.0480882852477	-0.0216626077171	0.039298925308	0.0157059361607	-0.0778570593884	0.519611734105	0.0557637385728	-0.0318410451034	0.304796374112	-0.00166555709901	0.0108389511448	0.210323613168	0.0139146261879	0.282521866123	3.48142614129	-27.5717739186	-5.80346228535
14	2.67723233494	0.937302759334	-0.619166607804	1.94438605204	-0.451381190949	1.98412357827	-0.0598584712599	-0.0898049841635	-0.092148348876	-0.00963340003064	-0.0167583156201	-0.0320634047526	0.197479500562	0.245140887516	0.0719788107057	0.28202747584	0.0627337130861	-0.0436336693619	0.185969785513	-0.000208913873752	0.22886476269	5.95772034247	-17.6392721328	4.03065249564
15	5.32001431921	-0.437826538393	1.72405623737	2.56977604003	-0.892272811907	4.7011170398	-0.171254631122	-0.286135880815	-0.596106932471	0.683909057192	0.385191444549	0.290751167805	-0.205562045708	-0.048799308865	0.00155849034623	0.453783680412	0.05478374002	0.0196084924733	0.223778189374	-0.0292551931086	0.222333006211	9.90100266122	3.88923894554	22.0769842475
16	2.90272017945	1.29169472737	-0.667082314421	1.15462274513	0.0140108560526	1.38588441603	0.198537050535	0.0484926523954	0.267244028203	0.0432615704255	-0.0728386684535	-0.0307688427056	-0.359981367328	0.144063743613	-0.128699935045	0.379179664261	0.000641250075021	-0.014259932627	0.207636327584	-0.00301783936543	0.345592479665	10.9761566599	33.5421730674	-2.25838308023
17	0.779352512644	0.369572616903	-0.770799108712	3.27442842368	-1.26923370855	2.22500546987	-0.0993412808829	-0.128361912038	0.268599928327	0.132735999872	0.00238791579108	-0.579865740889	-0.306881875978	0.50704741589	0.0686918148228	0.438525837041	-0.103793573856	-0.0936318240727	0.420830033303	-0.0860735314388	0.476549334276	23.5913461036	33.4376897592	6.84192186238
18	1.06361831585	0.263856179855	0.304296061991	1.52711141783	0.200217939061	0.885017973118	-0.0417512424293	-0.212973889254	0.18783791476	0.282690906746	-0.0492107967351	0.0165113620532	-0.24256710413	0.084762001352	0.0884203110921	0.35424960237	-0.00978784072824	-0.0234549564094	0.236947085206	-0.0244407007871	0.24986724774	12.0770066746	24.3526438411	10.2091832943
19	1.37235099897	-0.748936985967	-0.350206487556	1.58549782375	0.0674059270038	3.61823499223	0.0283687288222	0.0986204212194	0.088813905041	-0.128516907106	-0.16131606212	-0.226206999266	-0.0105187879038	0.303581996274	0.124772964783	0.248530377532	-0.0395826276018	0.00821091568003	0.193760318371	0.00949318990928	0.209300979606	17.3808409409	20.6918546636	-10.5092709277
20	5.48814940113	0.631223998148	-2.71002820302	0.903916033537	-0.633391208946	2.79248051153	0.297072258091	-0.0159664929884	0.357239273469	0.372772606376	0.036811766706	-0.0700967117664	-0.582788792122	-0.270267876346	-0.321000188205	0.385883081138	0.0568965716255	-0.0300615964333	0.190856246489	-0.0187506831786	0.34604854978	-3.30710687279	28.8150120019	-7.42767284986
21	1.83585989742	-0.172339880431	-0.245194457175	1.493200368	-0.186003862942	2.57013522204	0.0046767246061	-0.032521390581	0.00629716597286	-0.0041942259947	0.0380153936508	0.0829730206154	0.0303914123553	0.0237725885844	-0.0583552379974	0.267022814344	0.0353474518852	-0.00578807286693	0.208000188229	0.0103870984487	0.347037134448	-6.00096194862	17.4473523144	-3.98335809995
22	1.94381920564	2.05800592357	0.639817521655	3.41055914525	0.45400580471	0.820235793503	-0.186552741584	0.00324220846304	0.209459090249	0.0717573781327	0.101759880554	0.325388453567	-0.151457199681	-0.0667996981868	0.0805559523177	0.299237573349	0.088545498641	-0.0150596160338	0.243659322995	-0.0292739110118	0.214038732189	6.29676732603	-3.0331219777	15.4794753612
23	1.55326774675	-0.201827473301	0.0138279308862	2.98180483328	-0.217653079175	1.98027163806	-0.0559600119846	-0.0966786316129	-0.172330465314	0.115152887872	-0.0209902075351	-0.496751837529	0.287032385288	0.538455607481	0.0668568563807	0.289645728454	0.123330823531	-0.0549132928814	0.473275969772	-0.00974285890552	0.375134204122	35.2350181317	-15.3809603766	10.2212096844
24	3.713723906	0.0270102409788	0.687113146131	1.01564431553	0.451291908923	1.00100991578	0.105191847024	0.0298673428627	-0.409927667749	0.0615795306432	-0.064243064528	-0.0234024445179	0.464763735542	0.368051883111	-0.0292045580685	0.441273935363	0.114902777053	-0.0930794866281	0.312739013698	0.0596515204264	0.35464277559	25.1616072854	-24.6142639209	18.9312591882
25	0.976417454485	-0.435099393796	0.143724719191	1.57121230925	-0.297003838315	1.32554856569	-0.031882427983	-0.0170736883542	-0.11210936039	0.122425139754	-0.039942570902	-0.130373038366	0.0620495541902	0.160592237728	0.0700303211826	0.307116673761	0.035630135135	-0.0406156673779	0.293963022481	0.0165275824155	0.242286672835	18.0194617512	-12.0525759144	15.5228871331
26	1.57953966224	1.20126774422	-0.296941716442	2.34564591851	0.0737038661399	2.77535628595	-0.160739455365	0.502946843688	-0.17832188675	-0.348327783039	0.265317748777	-0.291606775391	-0.0151228137575	0.162557475971	-0.164792090476	0.279660537403	0.00181921067252	-0.0475979090069	0.441521537348	0.00410359360336	0.345052603032	27.6375642508	-9.55291010767	-4.11282917176
27	1.4050309997	0.228994033278	-0.628171874353	0.561262000271	-0.0375122789301	1.7726671885	-0.187406323458	0.0589263573937	-0.13284550992	-0.0293096251969	0.10615695233	-0.143003894329	0.123942877941	0.249127793731	0.0226508467613	0.270382783267	0.036095704109	-0.0551455458307	0.318165351455	0.0313695339616	0.256557152551	24.7372778728	-9.16784887508	0.163764283069
28	2.13829915533	-0.134709808897	-0.291791290427	1.84416731918	-0.96487823153	1.98925847971	0.0490802724206	0.00240454582313	-0.176308885668	0.0219281021208	-0.0674851914788	-0.0514461767925	-0.181891541037	0.0366574250306	0.0361898503319	0.276415060148	-0.0041521452017	-0.0484976990418	0.126838815009	-0.0133219163593	0.222558903452	16.3642258305	6.91093687414	5.71288906243
29	0.917539295218	0.280929226858	0.0183985992014	1.24872230998	-0.0155650764135	0.434401945731	0.0694304893627	-0.077314810042	0.00307436055759	0.223255263605	-0.0106466445317	0.120710361763	0.00335193491123	-0.016882493749	-0.0740023735573	0.321883376302	-0.034485128981	0.0500082829295	0.398057819592	-0.0443594749304	0.212538061088	20.4951063451	17.8130332443	63.9249317459
30	2.29853060639	-0.37649881424	0.202427610037	3.6037555913	-0.230849379812	2.84955423456	-0.0971589120914	0.0587111962168	0.313106308069	-0.258518884227	-0.100427536992	0.512918008891	-0.284008418726	-0.647958382675	0.172175375235	0.28577250132	0.0876058784935	-0.024647458293	0.460517105152	-0.0907549642559	0.371754813438	1.87154334373	31.0053432535	54.2444356426
31	3.89602511788	0.183230023962	-0.946610730363	0.308691669229	-0.423705761053	0.908024098975	0.0757885385347	-0.207696429242	0.290333361793	-0.0818130495693	-0.213619825053	0.0996169782065	-0.368692223824	-0.190557614179	0.119636179356	0.354206056675	0.0270972309219	0.0320637839462	0.362594765989	-0.123091733038	0.394063927963	13.4762053792	38.0965715322	62.3872479967
32	6.04778203141	-2.85865188727	-1.35398449199	2.60888289045	0.304593153914	2.34543408528	0.212218431317	0.0766452084348	0.161021683863	0.311151511224	-0.209352409961	0.215297320268	-0.220411839325	-0.353652286696	0.0171951907489	0.342659543646	-0.0151336552596	0.0664808713663	0.387522003936	-0.14692337042	0.339755916203	16.8036304538	33.6296462675	67.0815410832
33	0.467843125956	-0.280050927125	-0.586476526261	0.552380454923	0.179559324885	1.27731429995	-0.0217582230893	-0.137007809328	0.0571716537764	0.0650108552336	-0.118500839808	0.282996679267	-0.00739275438834	-0.1739827955	0.12632859151	0.301435337813	-0.0231915270919	0.0259217656581	0.376563084863	-0.0693524245312	0.287116325095	20.9780485346	21.3513235634	60.5881675493
34	1.13751221578	1.16534123579	-0.421937840084	1.93544198848	1.23083547746	4.27263232891	-0.31132823035	0.926790661704	-0.138956648748	-0.961700714281	0.250889994861	0.180557226389	0.498118595855	-0.445647052887	0.0696753907417	0.534223032237	-0.0680269316872	-0.0578990138242	0.601356968952	-0.108351484164	0.31708714389	9.7697310372	16.4007570218	38.1316305141
35	4.47959330613	2.47449084189	-0.777553936539	3.61032981505	-0.137361815569	1.95845132859	-0.245046290723	0.34446588287	0.589022101903	-0.309789106424	0.0880161862162	0.69146462538	-0.229631267568	-0.204610074689	0.110315719432	0.273929438367	0.00579281713346	-0.0413659246929	0.324257870378	0.00341635804184	0.232882177243	17.2555006778	26.8940376394	40.9306906265
36	1.80553859604	-1.03193026963	1.16727794833	2.25356663978	-1.81453103695	3.8721951346	0.0219319887684	-0.201125510875	-0.00843485919556	0.105799104733	-0.0640128839465	0.288607393226	0.226930013181	-0.521543577278	0.0212880894869	0.243423757168	-0.0848007117818	0.0308272896346	0.391238212806	-0.0381395392866	0.31923189678	10.8109404965	5.95302321699	59.9485797211
37	3.25571718453	0.356150639974	0.318391537013	1.90751029333	0.41537363173	2.00369021329	0.145098302962	-0.0877726989435	0.197786067468	0.000445783833582	-0.0463730542362	-0.00316033998269	0.0838175367117	0.0391852166029	-0.0655515539845	0.280090769143	-0.0466259951193	0.0466708403751	0.292385566226	0.0352479071615	0.251172725425	22.8228095409	4.21689957934	59.0819050491
38	2.56040038125	-0.534750519547	1.63199997151	7.22633431538	2.44734660873	3.27360477456	-0.234699763587	-0.339301709237	0.435607845667	1.18416406723	0.0285190263655	-0.239801087614	0.18929220998	-0.24546875525	0.234774392815	0.392645462941	-0.0383877102019	-0.0452544482345	0.382674699682	0.00769461149206	0.230754180947	29.3249414967	12.0346210922	74.0998227915
39	2.77157274419	0.848897174958	-0.129609929123	1.54984491993	0.00766297234856	1.44845429794	0.0311463729356	-0.277525980567	-0.461493343031	0.11546864105	-0.0698321430318	0.177541782695	0.301383138976	-0.128158585842	0.04051388788	0.347497426854	-0.0118141170027	-0.00490212656292	0.312935307745	0.0510007445937	0.350317071564	26.7968177686	-23.7722324205	60.4238568473
40	0.723939702507	1.08548847796	0.203422893829	5.13290814124	-0.346599327968	0.32238440383	0.232902772944	-0.353217422224	-0.32030214901	0.557643412048	-0.44676072571	0.255548513425	0.308142770693	-0.234305757871	0.245573668788	0.387865869281	-0.0538362097596	0.0772855874693	0.474106687921	0.0901712556386	0.389735122083	17.3746757102	-16.7916944276	72.5726106619
41	1.3366355143	-0.114205258766	-0.753005818007	0.926387785674	-0.846301447521	1.12230577501	-0.0763010811197	-0.274975241444	-0.124277515855	0.208660381151	-0.0405531766826	-0.0859612672361	0.137856878528	-0.0209052334299	0.0963838477142	0.359773986211	-0.0547105717554	-0.0121859587766	0.357520973817	0.03160077746	0.257703959957	29.7755695646	-10.9010265536	65.9311222019
42	4.00906954838	-1.40633221073	-1.51801377372	0.651289640361	0.700282956902	6.75351207609	-0.112934437849	0.72906956208	-0.26857687385	-0.14952889799	-0.0704153666482	0.340298215449	-0.13996835996	-0.424113681488	0.151578964733	0.334829739205	-0.0283034604175	-0.0558867307677	0.378379025606	-0.0541878451792	0.328475696857	23.1543434034	-16.753151627	40.4595367313
43	2.46210411947	-1.6826062559	-1.59102508851	5.05805824246	1.84081141118	3.36492878385	-0.0188263521964	-0.159318160062	-0.303816350948	0.164982281712	-0.25086263601	0.649793169591	-0.0156118203673	-0.554591983507	0.292212297079	0.222454039429	-0.0440724056313	-0.0176794915863	0.374418731327	-0.0422860081874	0.299813129451	15.643593823	-9.78402526521	50.001672905
44	4.92184643206	1.59176709535	2.96203966832	1.50976314271	1.18680288028	2.54878945829	0.264752254276	-0.0333809946892	-0.46792534044	0.00131032574506	0.0242936381147	-0.0876219903477	0.460067412938	0.158787276065	-0.293437798947	0.373752181955	-0.00399924077038	-0.0182151328083	0.291323211487	0.0477405281613	0.309460287183	42.881794727	-20.2579563733	53.0382280286
45	2.29805487257	-0.0393056214018	-0.642357994766	2.05606442849	0.719596726147	2.33749487243	-0.0345049107431	-0.0219335355451	0.00906605892377	0.0283413446268	0.0574524838853	0.0509117351861	0.0580774377945	0.161597607348	-0.042927875269	0.179213397183	0.0143254673786	-0.0139037516313	0.313101694602	0.0330625332094	0.307162891553	45.3179793792	-8.3495635746	52.883331366
46	4.64060745283	-3.67488240733	-0.0081348404228	3.82454272981	0.708464046234	0.834859692129	0.0203079132359	0.241082399172	0.021910243797	0.311849317891	-0.166959099242	-0.069012014529	-0.0409397458248	0.100366275927	0.162320818807	0.275140025381	-0.075252102432	0.0449553581746	0.287996813894	0.00838380049256	0.246790177625	46.6265262593	23.1130263104	58.1105723034
47	2.87204246238	0.33422525753	-0.605394643129	1.21368737376	0.242189582211	1.94359371588	0.0175872076998	0.225037360167	0.272235730551	-0.272977327347	-0.0348313086619	-0.324874345031	-0.357159898562	0.323583977997	-0.00483745373894	0.466776481741	-0.0944610754519	0.0765656345539	0.381173726444	0.0721359126381	0.423076911465	51.7048432345	42.8043917622	33.8001211977
48	0.0415057502809	-0.240544991128	0.174154031721	5.38359226296	-1.76353900176	1.32024696697	0.11464780532	0.0747029734076	0.36415434319	0.227438675989	-0.130806810365	-0.206970921195	-0.3926925455	0.521575977182	-0.0198910415325	0.402603248752	-0.160934173548	0.0986034956737	0.523686978728	0.0333945147616	0.570704305164	65.1687093351	37.9467319536	41.3229591332
49	1.12378735116	0.0621699763783	-0.0600193766204	1.74173482753	-0.173345153245	0.936878045183	0.0647371399981	0.0715803679931	0.242189509135	0.0496520553183	-0.0287233815368	-0.213821332452	-0.223238069553	0.264558101096	-0.030097306236	0.268199338503	-0.111694686162	0.0301088162799	0.341201564001	-0.0106300936128	0.301022678519	51.7673468085	32.113988551	45.741984676
50	3.74846042356	-1.30727251437	1.43172751665	3.34547518865	-1.24810469809	1.54272783227	0.127145000159	0.242525582208	0.0669767696269	-0.443588883599	-0.0550113476159	-0.19931525339	0.115268314102	0.460837669783	-0.08525107216	0.346887833195	-0.0268211229806	0.0256187821441	0.429549330122	-0.0449618285071	0.205857138214	46.1996106002	23.410969775	26.4183849976
51	1.54046542543	0.00802502189427	-0.491964056322	1.06237763771	-0.42322007054	1.36337743931	-0.0625004256811	-0.0873738172523	0.0399722067813	-0.0899938761447	0.00084004551907	0.0651626413109	-0.0910821150792	-0.125821934205	0.0476597648954	0.293885761757	-0.0411523290248	0.0371308060929	0.265274954441	-0.0287493385062	0.247812128831	33.0720028971	30.1955924864	48.4459802535
52	1.3998104769	1.21688790528	-1.05864549904	2.82606528078	-1.53071091905	1.6580607473	-0.0564448496486	-0.211588198652	0.183299586876	0.0613389028703	-0.0834387327238	-0.236744605313	-0.0295883971952	0.136413222428	0.117454524999	0.218728814448	-0.0024566756291	-0.0447836013394	0.507397078927	-0.092801165577	0.332215859598	54.2660162387	7.33516163727	58.5554370052
53	1.01487904025	-0.504530263348	0.677888179421	2.75370187964	-0.150110485103	1.2681826445	0.0483446313643	0.112929039409	-0.155247828215	-0.194807042169	-0.0305749180778	-0.360120775584	0.138511065843	0.390688202419	-0.0329958611122	0.314668265615	0.0537603398373	0.110538566499	0.549428919565	-0.0550556858046	0.457798080674	70.8396923684	-7.73630119205	37.1297007018
54	2.62461018825	-0.143305517978	-2.10963335939	0.999209177987	0.0957864488921	3.28309273755	0.118341067375	-0.49187748051	-0.773189266271	-0.247530318797	-0.157045263589	-0.0107659310522	0.281093173018	0.53968798884	0.0112271538435	0.376227288604	0.13957615138	-0.0335086212557	0.581331873948	0.0583176409779	0.509642533273	70.2572686232	-17.6284925511	46.0584221499
55	0.268957506423	-0.0336002135325	-0.226480748102	1.23469574836	-0.0128927267412	0.830065427616	0.00520115415328	-0.208291522909	-0.0151220761106	0.124756131778	-0.0172090184531	-0.292338641934	0.119776424874	0.286992930271	0.0146179456414	0.266693995033	0.0285750706483	-0.0355094470824	0.471508538539	0.00943175189736	0.316302559281	63.7884012759	-5.47863178821	52.6621682687
56	3.02859790067	0.906010007033	0.0433789894127	2.63180149321	-1.00990605157	2.97683082733	-0.18180956592	0.652943508915	-0.255042737691	-0.77896627285	0.251737342432	-0.168244709019	0.586654248818	0.232098447206	-0.0540198752356	0.471964036973	-0.0111309428327	0.0061667528494	0.434387764777	-0.0258709578334	0.305522467631	53.3045602327	-7.94503505005	30.0164501201
57	1.84383492681	0.51089995141	-0.599836588775	1.40654576445	-0.0757414682828	1.23155207319	-0.0363291833767	0.215242095443	-0.195472264878	-0.282086778134	0.059377682298	-0.365724333523	0.0990212503268	0.212630518438	-0.019540737858	0.316300450675	0.0446775663915	0.0118965348962	0.452631126331	0.0211620925289	0.271197545293	58.2006189092	0.906743194556	36.0704224833
58	1.67204079669	-0.279518920591	0.132980895007	2.26132908408	-0.261992399945	2.62598292462	0.013796665937	-0.0825662039511	-0.12441086431	-0.0641407034596	0.00999995278487	-0.101943647973	-0.124309609651	0.147122058829	-0.047033616867	0.260610443058	-0.0585242556697	0.0530824048507	0.31674504803	-0.0583962067925	0.321505215008	55.4500027694	14.5916629989	43.7244412361

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

ID	Refine TLS-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	chain 'A' and (resid -1 through 26 )	A	A	-1 - 26	1 - 28
2	2	chain 'A' and (resid 27 through 232 )	A	A	27 - 232	29 - 107
3	3	chain 'A' and (resid 233 through 257 )	A	A	233 - 257	108 - 132
4	4	chain 'A' and (resid 258 through 363 )	A	A	258 - 363	133 - 238
5	5	chain 'A' and (resid 364 through 389 )	A	A	364 - 389	239 - 264
6	6	chain 'A' and (resid 390 through 427 )	A	A	390 - 427	265 - 291
7	7	chain 'A' and (resid 428 through 446 )	A	A	428 - 446	292 - 310
8	8	chain 'A' and (resid 447 through 486 )	A	A	447 - 486	311 - 350
9	9	chain 'B' and (resid -1 through 26 )	B	E	-1 - 26	1 - 28
10	10	chain 'B' and (resid 27 through 232 )	B	E	27 - 232	29 - 107
11	11	chain 'B' and (resid 233 through 355 )	B	E	233 - 355	108 - 230
12	12	chain 'B' and (resid 356 through 418 )	B	E	356 - 418	231 - 282
13	13	chain 'B' and (resid 419 through 445 )	B	E	419 - 445	283 - 309
14	14	chain 'B' and (resid 446 through 486 )	B	E	446 - 486	310 - 350
15	15	chain 'C' and (resid -4 through 12 )	C	I	-4 - 12	1 - 17
16	16	chain 'C' and (resid 13 through 232 )	C	I	13 - 232	18 - 110
17	17	chain 'C' and (resid 233 through 257 )	C	I	233 - 257	111 - 135
18	18	chain 'C' and (resid 258 through 355 )	C	I	258 - 355	136 - 233
19	19	chain 'C' and (resid 356 through 427 )	C	I	356 - 427	234 - 295
20	20	chain 'C' and (resid 428 through 446 )	C	I	428 - 446	296 - 314
21	21	chain 'C' and (resid 447 through 486 )	C	I	447 - 486	315 - 354
22	22	chain 'D' and (resid -2 through 26 )	D	M	-2 - 26	1 - 29
23	23	chain 'D' and (resid 27 through 242 )	D	M	27 - 242	30 - 118
24	24	chain 'D' and (resid 243 through 270 )	D	M	243 - 270	119 - 146
25	25	chain 'D' and (resid 271 through 355 )	D	M	271 - 355	147 - 231
26	26	chain 'D' and (resid 356 through 389 )	D	M	356 - 389	232 - 265
27	27	chain 'D' and (resid 390 through 446 )	D	M	390 - 446	266 - 311
28	28	chain 'D' and (resid 447 through 486 )	D	M	447 - 486	312 - 351
29	29	chain 'E' and (resid -3 through 56 )	E	Q	-3 - 56	1 - 60
30	30	chain 'E' and (resid 57 through 242 )	E	Q	57 - 242	61 - 119
31	31	chain 'E' and (resid 243 through 270 )	E	Q	243 - 270	120 - 147
32	32	chain 'E' and (resid 271 through 293 )	E	Q	271 - 293	148 - 170
33	33	chain 'E' and (resid 294 through 368 )	E	Q	294 - 368	171 - 245
34	34	chain 'E' and (resid 369 through 389 )	E	Q	369 - 389	246 - 266
35	35	chain 'E' and (resid 390 through 427 )	E	Q	390 - 427	267 - 293
36	36	chain 'E' and (resid 428 through 446 )	E	Q	428 - 446	294 - 312
37	37	chain 'E' and (resid 447 through 486 )	E	Q	447 - 486	313 - 352
38	38	chain 'F' and (resid -4 through 12 )	F	U	-4 - 12	1 - 17
39	39	chain 'F' and (resid 13 through 242 )	F	U	13 - 242	18 - 120
40	40	chain 'F' and (resid 243 through 270 )	F	U	243 - 270	121 - 148
41	41	chain 'F' and (resid 271 through 368 )	F	U	271 - 368	149 - 246
42	42	chain 'F' and (resid 369 through 389 )	F	U	369 - 389	247 - 267
43	43	chain 'F' and (resid 390 through 427 )	F	U	390 - 427	268 - 296
44	44	chain 'F' and (resid 428 through 446 )	F	U	428 - 446	297 - 315
45	45	chain 'F' and (resid 447 through 486 )	F	U	447 - 486	316 - 355
46	46	chain 'G' and (resid -1 through 26 )	G	Y	-1 - 26	1 - 28
47	47	chain 'G' and (resid 27 through 242 )	G	Y	27 - 242	29 - 117
48	48	chain 'G' and (resid 243 through 270 )	G	Y	243 - 270	118 - 145
49	49	chain 'G' and (resid 271 through 376 )	G	Y	271 - 376	146 - 251
50	50	chain 'G' and (resid 377 through 427 )	G	Y	377 - 427	252 - 290
51	51	chain 'G' and (resid 428 through 486 )	G	Y	428 - 486	291 - 349
52	52	chain 'H' and (resid -1 through 26 )	H	H	-1 - 26	1 - 28
53	53	chain 'H' and (resid 27 through 232 )	H	H	27 - 232	29 - 107
54	54	chain 'H' and (resid 233 through 257 )	H	H	233 - 257	108 - 132
55	55	chain 'H' and (resid 258 through 363 )	H	H	258 - 363	133 - 238
56	56	chain 'H' and (resid 364 through 398 )	H	H	364 - 398	239 - 273
57	57	chain 'H' and (resid 399 through 446 )	H	H	399 - 446	274 - 309
58	58	chain 'H' and (resid 447 through 486 )	H	H	447 - 486	310 - 349

+
About Yorodumi

-
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