PDB-8ofh: Streptococcus pneumoniae CdaA

ID or keywords:

Entry

Database: PDB / ID: 8ofh

Title

Streptococcus pneumoniae CdaA

Components

Diadenylate cyclase

Keywords

TRANSFERASE / diadenylate cyclase

Function / homology

Function and homology information

: / diadenylate cyclase activity / diadenylate cyclase / cAMP biosynthetic process / adenylate cyclase activity / ATP binding / plasma membrane
Similarity search - Function

Biological species

Streptococcus pneumoniae R6 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.64 Å

Authors

Garbers, T.B. / Neumann, P. / Ficner, R.

Funding support

Germany, 1items

Citation

Journal: To Be Published
Title: Streptococcus pneumoniae CdaA
Authors: Garbers, T.B. / Neumann, P. / Ficner, R.

History

Deposition	Mar 15, 2023	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jun 21, 2023	Provider: repository / Type: Initial release
Revision 1.1	Jun 19, 2024	Group: Data collection / Category: chem_comp_atom / chem_comp_bond

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	8ofh.cif.gz	453.9 KB	Display	PDBx/mmCIF format
PDB format	pdb8ofh.ent.gz	310.2 KB	Display	PDB format
PDBx/mmJSON format	8ofh.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	8ofh_validation.pdf.gz	463.6 KB	Display	wwPDB validaton report
Full document	8ofh_full_validation.pdf.gz	469.2 KB	Display
Data in XML	8ofh_validation.xml.gz	38 KB	Display
Data in CIF	8ofh_validation.cif.gz	54.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/of/8ofh ftp://data.pdbj.org/pub/pdb/validation_reports/of/8ofh	HTTPS FTP

-
Related structure data

Related structure data	8ofjC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Diadenylate cyclase

B: Diadenylate cyclase

C: Diadenylate cyclase

D: Diadenylate cyclase

E: Diadenylate cyclase

F: Diadenylate cyclase

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

1

A: Diadenylate cyclase

B: Diadenylate cyclase

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

2

C: Diadenylate cyclase

F: Diadenylate cyclase

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

3

D: Diadenylate cyclase

E: Diadenylate cyclase

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

Unit cell

Length a, b, c (Å)	62.730, 102.400, 89.790
Angle α, β, γ (deg.)	90.000, 98.330, 90.000
Int Tables number	4
Space group name H-M	P12₁1
Space group name Hall	P2yb
Symmetry operation	#1: x,y,z #2: -x,y+1/2,-z

#1: Protein	Diadenylate cyclase Mass: 20121.164 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pneumoniae R6 (bacteria) / Gene: dacA / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8DP14
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 611 / 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: 2.31 Å³/Da / Density % sol: 46.67 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 15% (v/v) PEG3350 0.2 M KSCN, 0.1M Bis-Tris propane pH 7.5 PH range: 7.5

-
Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

PETRA III, EMBL c/o DESY

/ Beamline: P13 (MX1) / Wavelength: 0.97626 Å

Detector

Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 14, 2022

Radiation

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

Radiation wavelength

Wavelength: 0.97626 Å / Relative weight: 1

Reflection

Resolution: 1.64→50 Å / Num. obs: 130851 / % possible obs: 95.4 % / Redundancy: 6.5 % / B_iso Wilson estimate: 28.72 Å² / CC_1/2: 1 / R_merge(I) obs: 0.056 / R_rim(I) all: 0.06 / Net I/σ(I): 15.74

Reflection shell

Resolution (Å)	R_merge(I) obs	Num. unique obs	CC_1/2	R_rim(I) all	Diffraction-ID
1.64-1.7	1.85	9553	0.396	2.074	1
1.7-1.75	1.427	9594	0.509	1.584	1
1.75-1.86	1.09	18189	0.736	1.184	1
1.86-8	0.051	92297	0.999	0.055	1
8-14	0.019	984	1	0.021	1
14-17	0.021	110	1	0.022	1
17-50	0.024	124	0.999	0.026	1

-
Processing

Software

Name	Version	Classification
PHENIX	1.20.1_4487	refinement
XSCALE		data scaling
XDS		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.64→48.28 Å / SU ML: 0.2424 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.4775
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2232	6538	5 %
R_work	0.1915	124239	-
obs	0.193	130777	95.38 %

Solvent computation

Shrinkage radii: 1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 41.82 Å²

Refinement step

Cycle: LAST / Resolution: 1.64→48.28 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7035	0	0	611	7646

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0092	7143
X-RAY DIFFRACTION	f_angle_d	0.9018	9670
X-RAY DIFFRACTION	f_chiral_restr	0.0704	1171
X-RAY DIFFRACTION	f_plane_restr	0.01	1224
X-RAY DIFFRACTION	f_dihedral_angle_d	6.4069	973

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 (%)
1.64-1.66	0.4169	162	0.4156	3050	X-RAY DIFFRACTION	70.47
1.66-1.68	0.4406	166	0.4137	3166	X-RAY DIFFRACTION	73.33
1.68-1.7	0.4103	182	0.3967	3441	X-RAY DIFFRACTION	78.9
1.7-1.72	0.3913	187	0.37	3571	X-RAY DIFFRACTION	82.79
1.72-1.74	0.3548	199	0.3407	3793	X-RAY DIFFRACTION	87.14
1.74-1.77	0.3524	205	0.3354	3893	X-RAY DIFFRACTION	90.72
1.77-1.79	0.3339	217	0.3234	4132	X-RAY DIFFRACTION	94.83
1.79-1.82	0.3398	224	0.3032	4259	X-RAY DIFFRACTION	99.09
1.82-1.85	0.3054	226	0.2839	4297	X-RAY DIFFRACTION	98.95
1.85-1.88	0.3272	227	0.2612	4293	X-RAY DIFFRACTION	99.47
1.88-1.91	0.2913	227	0.2553	4327	X-RAY DIFFRACTION	99.17
1.91-1.94	0.2819	225	0.2458	4266	X-RAY DIFFRACTION	99.4
1.94-1.98	0.2513	226	0.2339	4289	X-RAY DIFFRACTION	99.08
1.98-2.02	0.244	227	0.2144	4314	X-RAY DIFFRACTION	99.21
2.02-2.07	0.2412	225	0.2104	4264	X-RAY DIFFRACTION	99.05
2.07-2.11	0.2322	226	0.2046	4298	X-RAY DIFFRACTION	99.32
2.11-2.17	0.2834	229	0.1962	4347	X-RAY DIFFRACTION	99.41
2.17-2.23	0.2168	225	0.1869	4304	X-RAY DIFFRACTION	99.3
2.23-2.29	0.225	226	0.1834	4289	X-RAY DIFFRACTION	99.41
2.29-2.37	0.2228	226	0.183	4317	X-RAY DIFFRACTION	99.37
2.37-2.45	0.2222	227	0.1944	4313	X-RAY DIFFRACTION	99.3
2.45-2.55	0.2707	228	0.2096	4324	X-RAY DIFFRACTION	99.45
2.55-2.66	0.2392	226	0.1978	4292	X-RAY DIFFRACTION	99.12
2.66-2.8	0.217	227	0.188	4307	X-RAY DIFFRACTION	99.06
2.8-2.98	0.2288	228	0.2007	4329	X-RAY DIFFRACTION	99.02
2.98-3.21	0.2466	226	0.2025	4300	X-RAY DIFFRACTION	99.47
3.21-3.53	0.2155	229	0.186	4348	X-RAY DIFFRACTION	99.13
3.53-4.04	0.2159	228	0.1608	4333	X-RAY DIFFRACTION	99.5
4.04-5.09	0.1593	229	0.1348	4374	X-RAY DIFFRACTION	99.55
5.09-48.28	0.1658	233	0.1648	4409	X-RAY DIFFRACTION	99.04

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	6.15659740545	-1.27847513372	-0.558980790561	6.93279400122	-0.267959111169	8.16733063189	0.166609538807	0.587578392752	0.341423774146	-0.564464652774	-0.0773323679115	-0.189140218088	-0.407240012052	0.17316324671	-0.074730441741	0.183601282466	-0.00767695273375	0.00524026786624	0.297386971409	-0.0147901153303	0.220816063887	-10.3577578366	24.7430008499	-30.1341026045
2	9.66372554891	-4.07380988047	2.73362069275	8.44409781251	-4.11461945763	8.49350802539	0.000454909788433	-1.01213027481	0.827331785562	0.209749295205	0.054076167842	0.489975914722	-0.246600405753	-0.555141103917	-0.0275104791676	0.288173787592	-0.0169945245331	0.0248987943422	0.339136659412	-0.114293354273	0.385713142943	-16.3052633002	33.3318217138	-13.123490771
3	5.76410191506	-0.902240050174	-0.408186570127	3.33914453616	0.694224170519	5.76969034595	0.0213555510315	0.0538446512109	0.0893695963144	-0.133565470503	-0.025096815657	-0.242337384426	-0.164411641837	0.26415239413	0.0433987012392	0.186041022285	-0.000267824283646	0.00756651283877	0.20711649578	-0.00600993923125	0.299628045508	-3.1510984014	27.3784730435	-22.6958123713
4	8.17295985391	-2.65435412046	0.483558730215	5.92994677333	1.46996743987	5.30007030004	-0.173896244254	-0.418483564146	-1.28611708147	0.55193648783	-0.174350650515	0.203325011563	0.797980131578	-0.0421923555976	0.1233810284	0.271774852217	-0.006664234147	0.0118771034684	0.270153267613	0.0302585138367	0.426828357955	-3.5610052948	17.5226485397	-17.3828156525
5	5.94520903057	3.20880049895	-2.90979967953	7.99282065313	-2.20347570259	8.83177488038	-0.0357421638078	-0.109938045472	0.451153153617	0.138842144561	0.161974269259	0.946210536333	-0.0408138341094	-0.765528388061	-0.229594583621	0.168363795046	0.0395478343294	0.00397830125136	0.270400123675	-0.027626276809	0.292088131181	-13.5921733358	27.7171774947	-15.8220176518
6	8.71832147487	6.60281989913	-5.61191436206	2.00076733486	-5.05966431074	8.53398462328	-0.492371540807	-0.175685250798	-2.15903489503	0.648157436461	-0.50063232279	2.40640667629	3.46893938521	-1.48457219422	1.0132764013	1.2216609243	-0.214110248685	-0.0423660582927	0.640680845412	-0.0455189437001	1.47235942868	-24.7252352401	10.5699859698	-18.2181133024
7	2.08410045938	-4.4148594828	-2.70010321636	2.06803124901	4.16975725268	7.16331581267	-0.283065543702	-0.618760779435	-0.415054504792	0.65728506385	-0.00257707817008	0.77546151513	0.588104501187	-0.200389406113	0.263474574385	0.276780487771	0.000856726412145	0.0816073437724	0.319616604904	0.0411000114332	0.432291960522	-21.2912667882	20.7473203524	-15.5062054328
8	7.82511318526	-3.01475199139	-2.2553809936	8.24415533013	4.03122302459	6.28799836557	0.0365753021935	0.0704020085259	-0.41813849917	-0.00117255315168	-0.171819447264	0.584821145379	0.191149291844	-0.289353367282	0.109896479603	0.160895178606	-0.024494254252	0.0055950850213	0.260671973446	-0.0479830323689	0.286081156045	-18.6882162773	20.6619705029	-23.4901811894
9	2.33966913774	1.59607343504	-3.57068522654	4.75001892925	0.75974435156	5.36639729201	0.0701632776582	0.720950980765	0.0266312920304	-0.400307583175	-0.13620610795	0.311311820913	-0.266602099725	-0.583357781093	0.0687755426087	0.241699754655	0.0629431855163	-0.0522081414003	0.444448681159	-0.0223457284103	0.370145192099	-22.3672961649	24.5360919598	-30.728650952
10	4.7391656391	1.39763859921	0.448411208384	5.30748416253	-1.37649143118	6.27041971694	0.0473127158845	-0.356782909199	0.263321379271	0.552086991953	0.040840457971	0.5036636561	-0.443042174858	-0.252863372887	-0.0642292585024	0.211984358872	0.0309651602997	0.0231031063043	0.228513768917	0.0377142577358	0.228405128809	11.7423485414	25.708511297	-12.3631936892
11	4.3527715464	2.41126395708	4.04537383303	7.37923780215	5.40083570822	2.08244695601	-0.118731162012	0.391873265051	0.595065406838	-0.0656808851447	0.0653020571378	-0.0314416220247	-0.0429604380896	0.419710517693	0.0550286811582	0.325423376436	-0.0286629744888	0.032473520729	0.289159962484	0.0750856823392	0.352801705878	15.7490666446	38.9451992087	-26.9608383308
12	7.23300941567	0.459126495603	-2.066146734	6.10994510846	-2.973345888	5.53442751726	-0.297873131624	0.411819294554	-0.583126562412	-0.459734095416	0.0684481573445	0.301560589245	0.389179338832	-0.224695943099	0.219061080164	0.172232105744	-0.0354611401523	-0.0129246937483	0.203722706646	-0.018410964757	0.267689706475	5.53959367929	25.0447215133	-22.615710389
13	2.46688716135	-3.48054903989	-4.39245266588	6.7196378878	1.74277140143	7.68564539135	0.0758317640296	0.00246816410777	0.43371802666	-0.334864573871	0.303209243035	-0.548773820315	-0.0897368196087	0.340671469253	-0.190920636038	0.178500899198	-0.060424867569	-0.00172670224602	0.241021845672	-0.0300490647235	0.285587936876	14.2225542991	31.845081352	-26.0009305086
14	9.06197917226	-1.76502753968	-1.7348829373	8.17400963902	2.37855502146	4.89913510339	-0.132360455999	0.174453191967	-0.640255746269	-0.192978878909	0.190586917581	-1.11761730114	0.489961739616	0.171677548272	-0.0837705863626	0.224726241381	-0.00956278573926	0.0393164626926	0.285249837071	0.00486687363991	0.365937042814	25.6680391953	21.9318273667	-26.8961461891
15	6.32460254839	2.11674641548	-0.777774656755	7.27038964766	-3.58990483233	3.34836665896	-0.032971943952	0.0503964602506	-0.0922476117081	-0.331108209237	-0.0385521937944	-0.524814855434	0.173945987796	0.280018851825	0.0550994866562	0.20021701308	0.0241465239301	0.0159350687564	0.242354946485	0.00214728601142	0.252899016185	21.674455421	26.0227122689	-20.4257975547
16	6.15739099293	5.37575505802	-5.10688385619	6.20724314418	-7.33486478385	2.21366450772	0.0814972497921	-0.166153941694	0.000633764471327	0.0952261892897	-0.442984194879	-0.554288175047	-0.101380106146	0.447679375767	0.376460084484	0.302806041151	0.00059884326016	-0.000182204661415	0.38142067365	-0.0140714726896	0.377869176854	27.8506926604	25.3338017797	-16.2508332864
17	2.15461727923	-0.0319594259419	-0.0747112068163	8.95523574354	-3.50643903403	8.41693614902	0.0566463973088	-0.487661076926	0.494134949171	0.779078513935	-0.178630535485	-0.656930279305	-1.1855783919	0.63313224884	0.0218562065074	0.347632571979	-0.0713116886242	-0.0364707967219	0.332298631317	-0.0401686448147	0.353568643125	20.9683004634	30.7955879282	-7.72527314413
18	6.65895042734	-1.0537095482	-0.449161946199	2.19135237489	4.76996886707	8.46847067886	-0.289795140542	0.0719104464394	-0.86243334811	0.267590363841	0.44416569377	-0.0606929171915	0.726798483539	0.444396568435	-0.264823810026	0.278875253486	0.00709970613193	0.0214095013027	0.356562086056	-0.0152663041994	0.402976963558	-17.665006908	61.8681365804	-24.0278687783
19	4.57746072865	-0.936648005951	-3.59008162868	2.81622026324	1.65150139295	5.53088481376	0.0637092041528	-0.0853231184319	-0.236148831076	-0.0775764584656	-0.136572638384	-0.111124418763	0.206847911854	0.480109359597	0.0902216350027	0.232756456243	0.025111676864	0.0189139869751	0.301856188748	-0.0128226517705	0.265101822978	-1.61320609411	66.5030059234	-20.6332617974
20	6.18046113643	1.64405563248	0.706143007787	1.62792461352	-0.469605035093	4.89619698619	0.0845250447316	-0.042766062293	0.148356436376	0.291171555964	-0.0566504121422	0.12441468557	-0.00111747664856	0.0178684705768	-0.0171929852507	0.212867997752	0.0547756721413	0.0260346562363	0.237779768513	0.00837294049456	0.203907260575	-11.5760640299	64.15896219	-12.0414212806
21	6.26320997454	5.94833888669	-1.71147900674	6.02454513658	-2.05019089335	2.40401761507	0.0186540418995	0.121715011827	-0.225006168956	-0.104061965041	0.0884904487224	-0.361441633892	0.102727170531	0.189005882698	-0.120785470057	0.256667597197	0.0926943422344	0.0166539789388	0.402493532658	-0.00378988029641	0.278104515563	-2.11625986237	67.1247556128	-18.7791360872
22	0.104968426848	0.382460303258	0.33226918618	3.38244737107	-1.0269685326	3.37460075167	0.203419292292	0.335849351806	2.29752778473	-0.294756659575	-0.184008632922	0.387386943344	-0.926748622189	-0.405932481292	-0.105421939896	0.427086208025	0.11878468712	0.0995920064341	0.474611487963	0.0958276023513	1.01184166419	-8.36738670626	86.0078353933	-24.5398941253
23	6.33637350019	0.342367265614	-0.00621862017451	1.78821023444	-1.64324173347	1.6688502763	0.17633119043	0.076477352841	0.746818049505	0.0469614685276	-0.0428707049742	-0.140838192649	-0.184648680736	0.0396664680645	-0.150598845842	0.205688301093	0.016117324177	0.0272884462871	0.264433919302	-0.019793340819	0.33609209935	-7.17681709643	74.5009221135	-24.1752658783
24	7.51679605493	-0.0187654468478	1.50440713206	9.04492184055	1.50012725665	4.67095462561	0.14498833434	1.13297667661	-0.207086107403	-0.89144667915	-0.0902665094985	-0.723754749112	0.129452685953	0.337489872096	-0.0473613706282	0.266786709136	0.0509123994455	0.0481781823206	0.473980863728	-0.021774615373	0.269607520757	-12.3721334811	69.0636070114	-32.9904946206
25	2.26934163257	-0.804014595389	-4.40069225336	6.70773021779	1.75659527374	2.50310798289	0.202806204178	0.170732934683	-0.490024376995	-0.55568826188	-0.102507795245	-0.202094781799	-0.0742898020779	0.14056169157	-0.114716844728	0.241753851875	0.0184091240514	-0.0548238810011	0.378828751429	0.0245507093982	0.258641427883	-12.5298271886	18.2591605339	-69.6943041437
26	8.15739999728	2.72960427655	-0.91792061188	4.3722153186	-0.197558635138	3.27936399704	0.401826264845	-0.349091119326	0.725116491253	0.181351644017	-0.140443638349	0.328943901568	-0.0684090666751	-0.00891118903634	-0.2388884192	0.165757363929	0.00615309628581	0.000185427827356	0.206927970117	0.022180975774	0.235699468287	-15.7028762154	25.1017013678	-60.755272825
27	4.39903219076	-0.0219476064909	-1.9897112419	3.87293254712	-3.01170661407	2.06907320154	-0.0715280451221	0.291431487317	0.553473250977	0.169498223083	0.0419737512971	-0.246324962663	-0.649006474278	-0.33534651865	0.146242460726	0.237399778149	0.0058175309276	0.0328360808951	0.26462316325	-0.000748584910221	0.407116031922	1.5723270459	32.8712902006	-62.2351255821
28	3.87569330005	2.35665042383	2.26568703483	6.02426192834	1.52342916049	6.5963686745	0.0262071615937	0.0270710309677	-0.323910171154	-0.0147828445961	0.135431349259	-0.46280901882	-0.00327334738376	0.360325434029	-0.170917858736	0.184102282975	0.0136365549372	-0.00976132814602	0.21210834384	0.0170232245423	0.223967456498	-6.78161827986	17.822783994	-59.0364306483
29	2.04932644105	6.20816011799	-1.60908513776	2.04580940341	-6.8656749758	8.31240462242	0.555747596032	-0.455309138135	0.998814522435	0.935631160927	-0.161689358714	1.11777214675	-0.714162006646	-0.205312006268	-0.363436516339	0.298040204157	0.0465499219209	0.0905810440382	0.334459432172	-0.0481394812705	0.38797392727	-12.9445888339	22.9366453661	-51.126871315
30	7.4921776587	-2.41783018187	0.419212016382	7.85175507531	-2.24644283581	5.2623728524	0.0351031476653	0.0994702743969	0.805568322862	0.150656835544	0.184940095311	-0.355846745761	-0.661968667289	-0.0907426289349	-0.157664137993	0.205511069432	-0.0200714966343	0.0166642187683	0.184769145091	0.00847958524057	0.297487111467	-4.21586443666	29.8669547214	-60.1399506877
31	2.6721738043	-0.576068048983	4.32871227613	8.84282962256	0.543095545828	7.30754648991	-0.574421795291	-0.383891071627	2.02245778274	0.340189141763	-0.202481851998	1.63047866591	-1.01026437455	-0.93948391006	0.711411186392	0.602074601445	0.164619057439	0.179339775002	0.673031188592	0.119957436614	1.36013810465	-21.9233804588	41.2157611351	-61.1454706834
32	2.0423455484	3.31988398757	-0.446083426069	8.79212114858	-3.60385669135	6.46405138726	0.423455105306	-0.0632974892828	1.46000210414	0.959178812335	-0.0113043548465	0.722937099619	-1.02823125237	-0.213465565039	-0.306546383837	0.38061137791	0.0326315196443	0.0689961084092	0.288740683127	-0.0132564082831	0.551357424267	-11.9429598139	37.4370885276	-61.0874542316
33	7.57948288532	2.49937970345	1.33307664432	6.45732444452	-1.82937715326	4.42536949928	-0.0356686865907	0.433066279581	0.900368769533	0.0308456007012	0.223866452815	0.298834252255	-0.402778506389	-0.252334806142	-0.220191050822	0.240103195667	0.035443743034	0.0310945793524	0.250101259158	0.051103568311	0.395192583317	-15.0212315342	32.9296808546	-67.4195909301
34	7.76773865042	2.77429692431	-1.75687165427	2.11172277342	0.308107752421	8.27084288986	-0.0818602145356	1.55334798785	0.37282754589	-0.929073102055	0.194800517337	-0.373057338678	0.105430774891	0.139564012775	-0.137648361929	0.369064788328	0.0269763929192	0.0369021199238	0.495833191187	0.109619322449	0.380095753812	-13.0579194472	25.7941862194	-76.7203615111
35	3.06210115495	2.24631762531	-2.38368448682	5.01833740231	-3.87350765998	6.03096987481	-0.0616715195005	0.240691960877	0.191380879631	-0.0910052769259	0.273925702811	0.579793066791	-0.0473623815139	-0.403116346344	-0.166674476979	0.195674904726	-0.00569441925991	0.0101284736449	0.17144803425	-0.0190176821093	0.249202297213	13.9103112564	57.8554304169	-41.6279548687
36	3.67154966236	1.7694296868	0.309169541758	5.99817404249	-0.752951017167	3.26780496958	-0.161075754901	0.168454282234	-0.515094622073	-0.260145300771	0.10425039364	-0.377428339323	0.421771582999	0.10654095926	0.0634159722048	0.230034445922	-0.00225241272579	0.0374348138842	0.223244849201	-0.00428502311778	0.194469501553	19.8353527235	55.3341032513	-37.1849274543
37	5.39167429076	6.25126830469	-4.51105001544	9.98351397418	-4.80053583959	9.05214644641	-0.459051516171	0.0187523023719	-0.826543084647	-0.463647609619	-0.0182672721262	-0.651976736014	0.924366071888	0.245336032328	0.451377619929	0.359348409219	0.0160344032673	0.0793889682131	0.227258932143	0.0157282505665	0.309409409834	19.1281193081	48.5516116315	-44.2652717174
38	8.34869074893	0.0989408978073	-4.13784109244	7.73837810079	-3.02914676757	8.60252354123	-0.50158123552	0.441220007903	-0.799835959085	-0.983064096203	0.230022160782	0.842884034437	1.02555179659	-1.11388006219	0.311849710479	0.472768898152	-0.161216199068	-0.0165398151035	0.452636962626	-0.0389392556028	0.322161814993	11.6916461673	52.752314686	-52.2558531068
39	2.68727864718	-0.707867776873	-0.695135136223	5.39681994739	0.236561018521	4.42227774906	0.141911213817	0.164486000663	-0.330560257694	-0.260647335614	-0.131395315096	-0.127989612642	0.418170816939	0.0547474167765	-0.00742314316022	0.238792221231	0.00104238400081	0.00415110131354	0.185104259835	-0.0411223725052	0.226403526092	-13.6380404184	54.7162844624	-1.66519254031
40	8.09519468315	3.12372636169	-2.59220248292	7.74160471201	-2.72835887086	8.60821663058	0.132950838684	-0.225223532285	0.119461055979	0.23638958162	0.0425773076404	0.8622051434	0.452625339313	-0.810430144906	-0.126881340626	0.327117666389	-0.0543566338601	-0.0524491711617	0.225149103853	-0.043645022086	0.374639472379	-23.0655897146	48.2796727144	1.86398853087
41	3.19585600176	2.37669870921	0.0928217703086	8.71367467874	1.13487517507	4.83226095732	0.136763129719	-0.29977642846	-0.442948387721	0.715180795272	-0.066420799157	0.0161490500567	0.606481586739	0.0186906621457	-0.0564445555697	0.33032579218	-0.0349612379657	0.00630417463425	0.216370427588	0.0162134286388	0.232184687635	-15.5673677968	50.5544657148	10.5647331617

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 86 through 114 )	A	A	86 - 114	1 - 29
2	2	chain 'A' and (resid 115 through 126 )	A	A	115 - 126	30 - 41
3	3	chain 'A' and (resid 127 through 143 )	A	A	127 - 143	42 - 58
4	4	chain 'A' and (resid 144 through 153 )	A	A	144 - 153	59 - 68
5	5	chain 'A' and (resid 154 through 173 )	A	A	154 - 173	69 - 88
6	6	chain 'A' and (resid 174 through 181 )	A	A	174 - 181	89 - 96
7	7	chain 'A' and (resid 182 through 193 )	A	A	182 - 193	97 - 108
8	8	chain 'A' and (resid 194 through 212 )	A	A	194 - 212	109 - 127
9	9	chain 'A' and (resid 213 through 234 )	A	A	213 - 234	128 - 149
10	10	chain 'B' and (resid 85 through 114 )	B	B	85 - 114	1 - 30
11	11	chain 'B' and (resid 115 through 126 )	B	B	115 - 126	31 - 42
12	12	chain 'B' and (resid 127 through 153 )	B	B	127 - 153	43 - 69
13	13	chain 'B' and (resid 154 through 173 )	B	B	154 - 173	70 - 89
14	14	chain 'B' and (resid 174 through 191 )	B	B	174 - 191	90 - 107
15	15	chain 'B' and (resid 192 through 212 )	B	B	192 - 212	108 - 128
16	16	chain 'B' and (resid 213 through 221 )	B	B	213 - 221	129 - 137
17	17	chain 'B' and (resid 222 through 236 )	B	B	222 - 236	138 - 152
18	18	chain 'C' and (resid 86 through 106 )	C	C	86 - 106	1 - 21
19	19	chain 'C' and (resid 107 through 126 )	C	C	107 - 126	22 - 41
20	20	chain 'C' and (resid 127 through 153 )	C	C	127 - 153	42 - 68
21	21	chain 'C' and (resid 154 through 173 )	C	C	154 - 173	69 - 88
22	22	chain 'C' and (resid 174 through 181 )	C	C	174 - 181	89 - 96
23	23	chain 'C' and (resid 182 through 212 )	C	C	182 - 212	97 - 127
24	24	chain 'C' and (resid 213 through 235 )	C	C	213 - 235	128 - 150
25	25	chain 'D' and (resid 86 through 105 )	D	D	86 - 105	1 - 20
26	26	chain 'D' and (resid 106 through 114 )	D	D	106 - 114	21 - 29
27	27	chain 'D' and (resid 115 through 126 )	D	D	115 - 126	30 - 41
28	28	chain 'D' and (resid 127 through 143 )	D	D	127 - 143	42 - 58
29	29	chain 'D' and (resid 144 through 153 )	D	D	144 - 153	59 - 68
30	30	chain 'D' and (resid 154 through 173 )	D	D	154 - 173	69 - 88
31	31	chain 'D' and (resid 174 through 181 )	D	D	174 - 181	89 - 96
32	32	chain 'D' and (resid 182 through 192 )	D	D	182 - 192	97 - 107
33	33	chain 'D' and (resid 193 through 221 )	D	D	193 - 221	108 - 136
34	34	chain 'D' and (resid 222 through 235 )	D	D	222 - 235	137 - 150
35	35	chain 'E' and (resid 86 through 126 )	E	E	86 - 126	1 - 41
36	36	chain 'E' and (resid 127 through 181 )	E	E	127 - 181	42 - 96
37	37	chain 'E' and (resid 182 through 212 )	E	E	182 - 212	97 - 127
38	38	chain 'E' and (resid 213 through 235 )	E	E	213 - 235	128 - 150
39	39	chain 'F' and (resid 86 through 153 )	F	F	86 - 153	1 - 68
40	40	chain 'F' and (resid 154 through 192 )	F	F	154 - 192	69 - 107
41	41	chain 'F' and (resid 193 through 235 )	F	F	193 - 235	108 - 150

-
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://pdbjlvh1.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