PDB-7l32: Molybdopterin biosynthesis MoaE protein from Burkholderia ambifar...

ID or keywords:

Entry

Database: PDB / ID: 7l32

Title

Molybdopterin biosynthesis MoaE protein from Burkholderia ambifaria MC40-6

Components

MPT synthase subunit 2

Keywords

BIOSYNTHETIC PROTEIN / SSGCID / Molybdopterin biosynthesis / moaE / Burkholderia ambifaria / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease

Function / homology

molybdopterin synthase activity / molybdopterin synthase / Molybdopterin biosynthesis MoaE / Molybdopterin biosynthesis MoaE subunit superfamily / MoaE protein / Mo-molybdopterin cofactor biosynthetic process / cytosol / BROMIDE ION / Molybdopterin synthase catalytic subunit

Function and homology information

Biological species

Burkholderia ambifaria (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.9 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Citation

Journal: to be published
Title: Molybdopterin biosynthesis MoaE protein from Burkholderia ambifaria MC40-6
Authors: Sroge, C.D. / Abendroth, J. / Horanyi, P.S. / Lorimer, D.D. / Edwards, T.E.

History

Deposition	Dec 17, 2020	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 30, 2020	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 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2	Oct 30, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	7l32.cif.gz	230.2 KB	Display	PDBx/mmCIF format
PDB format	pdb7l32.ent.gz	153.2 KB	Display	PDB format
PDBx/mmJSON format	7l32.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	7l32_validation.pdf.gz	448.5 KB	Display	wwPDB validaton report
Full document	7l32_full_validation.pdf.gz	453.6 KB	Display
Data in XML	7l32_validation.xml.gz	21.9 KB	Display
Data in CIF	7l32_validation.cif.gz	31.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/l3/7l32 ftp://data.pdbj.org/pub/pdb/validation_reports/l3/7l32	HTTPS FTP

-
Related structure data

Related structure data	2qieS S: Starting model for refinement
Similar structure data	3ddd-d 3bx7-d 6hn6-d 3wx6-d 5brk-d 5jsf-d 1i3s-3 5js6-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#122 - Feb 2010 Enhanceosome similarity (1) #220 - Apr 2018 Dehalogenases similarity (1)

Deposited unit

A: MPT synthase subunit 2

B: MPT synthase subunit 2

C: MPT synthase subunit 2

hetero molecules

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

1

A: MPT synthase subunit 2

hetero molecules

A: MPT synthase subunit 2

hetero molecules

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

2

B: MPT synthase subunit 2

C: MPT synthase subunit 2

hetero molecules

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

Unit cell

Length a, b, c (Å)	111.680, 93.290, 65.250
Angle α, β, γ (deg.)	90.000, 90.103, 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-404- HOH

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
d_1	ens_1	(chain "A" and (resid 2 through 20 or resid 22...
d_2	ens_1	(chain "B" and (resid 2 through 20 or resid 22...
d_3	ens_1	(chain "C" and (resid 2 through 20 or resid 22...

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Beg label comp-ID	End label comp-ID	Label asym-ID	Label seq-ID
d_1	1	ens_1	ALA	LEU	A	1 - 19
d_1	2	ens_1	ALA	ALA	A	21 - 30
d_1	3	ens_1	PHE	THR	A	32 - 90
d_1	4	ens_1	ALA	THR	A	92 - 120
d_1	5	ens_1	GLU	GLU	A	125 - 144
d_2	1	ens_1	ALA	LEU	B	2 - 20
d_2	2	ens_1	ALA	ALA	B	22 - 31
d_2	3	ens_1	PHE	LEU	B	33 - 40
d_2	4	ens_1	ALA	THR	B	43 - 93
d_2	5	ens_1	ALA	THR	B	95 - 123
d_2	6	ens_1	GLU	GLU	B	128 - 147
d_3	1	ens_1	ALA	LEU	C	1 - 19
d_3	2	ens_1	ALA	ALA	C	21 - 30
d_3	3	ens_1	PHE	THR	C	32 - 90
d_3	4	ens_1	ALA	GLU	C	92 - 140

NCS oper:

ID	Code	Matrix	Vector
1	given	(-0.177746461837, -0.984042510317, 0.00815678816071), (0.984005818881, -0.177628409971, 0.0134423353564), (-0.0117789521172, 0.0104156545619, 0.999876377572)	-21.6280278199, 30.9379761287, 5.82643920671
2	given	(0.187878131208, -0.982169722939, -0.00666656997871), (-0.982187585647, -0.18789402832, 0.00183867411661), (-0.00305849873607, 0.006202375615, -0.999976087775)	-21.3467122905, 31.313905014, 71.0627614894

#1: Protein	MPT synthase subunit 2 / Molybdenum cofactor biosynthesis protein E / Molybdopterin synthase catalytic subunit / ...Molybdenum cofactor biosynthesis protein E / Molybdopterin synthase catalytic subunit / Molybdopterin-converting factor large subunit / Molybdopterin-converting factor subunit 2 Mass: 18423.844 Da / Num. of mol.: 3 / Fragment: BuamA.00098.a.B1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Burkholderia ambifaria (strain MC40-6) (bacteria) Strain: MC40-6 / Gene: BamMC406_1760 / Plasmid: BuamA.00098.a.B1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B1YRH1, molybdopterin synthase
#2: Chemical	ChemComp-BR / BROMIDE ION Mass: 79.904 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Br
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 360 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N
Has protein modification	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 3.08 Å³/Da / Density % sol: 60.1 %
Crystal grow	Temperature: 287 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: Molecular Dimensions Morpheus screen, B5:10% w/v PEG 20 000, 20% v/v PEG MME 550 0.03 M of each sodium fluoride, sodium bromide, sodium iodide 0.1 M MOPS/HEPES-Na pH 7.5: BuamA.00098.a.B1. ...Details: Molecular Dimensions Morpheus screen, B5:10% w/v PEG 20 000, 20% v/v PEG MME 550 0.03 M of each sodium fluoride, sodium bromide, sodium iodide 0.1 M MOPS/HEPES-Na pH 7.5: BuamA.00098.a.B1.PS37913 at 49.6 mg/ml + 0.5% n-Octyl-??-D-glucopyranoside: cryo: direct: tray 317329b5, puck xxu3-9

Crystal

Density Matthews: 3.08 Å³/Da / Density % sol: 60.1 %

Crystal grow

Temperature: 287 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Molecular Dimensions Morpheus screen, B5:10% w/v PEG 20 000, 20% v/v PEG MME 550 0.03 M of each sodium fluoride, sodium bromide, sodium iodide 0.1 M MOPS/HEPES-Na pH 7.5: BuamA.00098.a.B1. ...

-
Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 21-ID-F / Wavelength: 0.97872 Å

Detector

Type: RAYONIX MX-300 / Detector: CCD / Date: Jul 30, 2020 / Details: Beryllium Lenses

Radiation

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

Radiation wavelength

Wavelength: 0.97872 Å / Relative weight: 1

Reflection

Resolution: 1.9→50 Å / Num. obs: 52076 / % possible obs: 98.8 % / Redundancy: 3.672 % / B_iso Wilson estimate: 37.499 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.048 / R_rim(I) all: 0.056 / Χ²: 0.939 / Net I/σ(I): 16.26

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
1.9-1.95	2.991	0.392	3.04	3372	0.915	0.474	87.4
1.95-2	3.331	0.372	3.65	3740	0.932	0.442	98.5
2-2.06	3.745	0.272	5.43	3660	0.957	0.319	99.9
2.06-2.12	3.781	0.22	6.46	3618	0.97	0.257	100
2.12-2.19	3.782	0.164	8.3	3460	0.983	0.191	100
2.19-2.27	3.775	0.129	10.25	3373	0.987	0.151	99.8
2.27-2.36	3.792	0.107	11.91	3187	0.99	0.125	99.7
2.36-2.45	3.791	0.092	13.32	3139	0.993	0.107	99.9
2.45-2.56	3.783	0.072	16.37	2956	0.994	0.084	99.8
2.56-2.69	3.778	0.061	18.49	2876	0.996	0.071	99.9
2.69-2.83	3.798	0.053	20.88	2709	0.997	0.062	99.8
2.83-3	3.782	0.047	24.06	2572	0.996	0.054	99.9
3-3.21	3.756	0.043	26.47	2427	0.997	0.051	99.8
3.21-3.47	3.73	0.04	29.33	2274	0.997	0.047	99.8
3.47-3.8	3.727	0.036	31.36	2073	0.998	0.042	99.8
3.8-4.25	3.712	0.034	32.57	1872	0.997	0.04	99.5
4.25-4.91	3.66	0.033	33.58	1650	0.998	0.039	99.8
4.91-6.01	3.6	0.034	32.87	1410	0.998	0.039	99.5
6.01-8.5	3.604	0.031	33.7	1094	0.998	0.036	99.5
8.5-50	3.393	0.03	33.77	614	0.998	0.035	97.9

-
Processing

Software

Name	Version	Classification
XDS		data reduction
XSCALE		data scaling
PHENIX	1.19RC4-4035	refinement
PDB_EXTRACT	3.27	data extraction
MoRDa		phasing
PHENIX		model building
Coot		model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: pdb entry 2qie as per Morda

2qie

Resolution: 1.9→48.25 Å / SU ML: 0.2188 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.8287
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2031	1986	3.82 %	0
R_work	0.1792	50069	-	-
obs	0.1801	52055	98.76 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 41.9 Å²

Refinement step

Cycle: LAST / Resolution: 1.9→48.25 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3279	0	8	362	3649

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0079	3380
X-RAY DIFFRACTION	f_angle_d	0.8472	4601
X-RAY DIFFRACTION	f_chiral_restr	0.0607	523
X-RAY DIFFRACTION	f_plane_restr	0.0083	598
X-RAY DIFFRACTION	f_dihedral_angle_d	12.3228	1206

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)
ens_1	d_2	A	X-RAY DIFFRACTION	Torsion NCS	0.560993342605
ens_1	d_3	A	X-RAY DIFFRACTION	Torsion NCS	1.24405046506

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 (%)
1.9-1.95	0.3176	132	0.264	3114	X-RAY DIFFRACTION	87.21
1.95-2	0.2568	125	0.2398	3577	X-RAY DIFFRACTION	98.01
2-2.06	0.2512	162	0.2085	3541	X-RAY DIFFRACTION	99.87
2.06-2.13	0.2394	142	0.1915	3656	X-RAY DIFFRACTION	99.95
2.13-2.2	0.2148	155	0.1814	3592	X-RAY DIFFRACTION	99.95
2.2-2.29	0.182	133	0.173	3583	X-RAY DIFFRACTION	99.79
2.29-2.39	0.2004	144	0.1817	3622	X-RAY DIFFRACTION	99.68
2.39-2.52	0.2357	171	0.1798	3581	X-RAY DIFFRACTION	99.84
2.52-2.68	0.2091	136	0.1807	3610	X-RAY DIFFRACTION	99.89
2.68-2.88	0.2142	148	0.1871	3601	X-RAY DIFFRACTION	99.84
2.88-3.17	0.2065	138	0.1879	3628	X-RAY DIFFRACTION	99.81
3.17-3.63	0.1893	128	0.1758	3670	X-RAY DIFFRACTION	99.82
3.63-4.58	0.1931	128	0.1552	3614	X-RAY DIFFRACTION	99.6
4.58-48.25	0.1778	144	0.1751	3680	X-RAY DIFFRACTION	99.3

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	4.58086719933	0.135024700758	2.98224049287	5.77361287823	2.05088868962	8.59581852755	0.0752608085515	0.207365766174	0.571880863558	0.109378865014	0.112537198168	0.36429816461	-1.38449968581	-0.304879985873	-0.199522667358	0.408548668391	0.0359451896362	0.0302273566248	0.203131079285	0.0808149564764	0.27031212632	-4.11088334072	24.3232291806	19.5843706653
2	3.78671713738	0.494800082471	0.236598454985	1.86807267763	-0.865583604229	4.06247113744	0.0151794090306	-0.355124634203	0.459902217946	0.0914464047939	0.112057076879	0.117485558916	-0.591299414899	-0.104490153345	-0.0762974156007	0.283730633452	0.0891835093694	0.0252524034351	0.231449906832	-0.0619577375472	0.279289045757	-10.8198489942	21.8591867205	32.8659347451
3	2.94730570832	0.460726669379	0.643464298237	1.43686711759	-0.442125271079	4.043461022	-0.0132622719416	0.595185065144	0.185349553095	-0.261102168127	-0.0169137593491	-0.293239182483	-0.428612561038	0.834076818869	0.0463375251486	0.246485878818	-0.0253075701888	0.0401717796546	0.330800552064	0.0356334694339	0.291895701379	3.85396771078	17.9472014572	18.3961119258
4	4.5185822541	3.43431301175	-2.44788954865	6.50045344708	-4.22951639421	7.25545156311	-0.154859272368	0.622648438258	0.194845003185	-0.53547833452	0.319891432775	0.274393404721	-0.00528936656361	-0.413071021672	-0.196310258303	0.170458230118	0.000827713924971	-0.0279706796955	0.255785113189	0.00611926271538	0.199321985242	-10.813377831	9.51201943133	17.4625647149
5	3.05579633965	1.37402972467	-0.281203610949	2.80985124289	-1.40897234816	4.35808249071	-0.0130554749427	0.11463529711	0.155259727585	0.0284799016768	-0.0545708591127	0.0181337451836	-0.50466386069	0.235915143461	0.00211159510572	0.179812344869	0.0191100778921	-0.00370987373743	0.141741599793	0.00114445538481	0.177318955335	-2.2841686852	17.5124531787	24.0396860196
6	3.04537909597	1.47425350814	-1.8147903971	2.45351602535	-2.27063797934	2.45850118807	-0.116032596773	0.225084525415	-0.120378827061	-0.284174915115	0.0379308642139	-0.0896465445029	0.19987231571	-0.157021828129	0.049328991709	0.141848970226	0.00360452033401	-0.005562518543	0.156404475208	-0.0140593622272	0.224234060523	-3.30595076019	7.66483907318	25.6770540936
7	6.36550108057	2.50402624385	-5.42515008505	4.49300347603	-1.97368343464	7.1569826512	-0.16481813558	0.0519706036186	0.113791308922	-0.0282710439009	0.0777344463274	-0.659350536764	0.0952718364933	1.84259203357	0.354597151926	0.295696775091	-0.0898018579844	0.00383515572892	0.745604055938	0.0368864014137	0.276466110222	5.95567792174	14.7882434563	7.48532408314
8	4.04648232527	-0.263272084448	-1.16783462771	2.63043005255	-1.76072503203	2.29204575786	-0.254101322542	0.739199633297	-0.574865314988	-0.338170130948	-0.316533181531	-0.785264068875	0.337686322847	1.1827033617	0.566384957281	0.476708361866	0.021910420552	0.0776640442411	0.858919945495	-0.041525483286	0.375071431069	8.75106159162	11.3617554137	5.49408244233
9	5.12888307309	1.97252505801	-4.74377708307	9.70478561101	-6.53018792583	8.05599024899	-0.532361611648	1.5691888291	-0.451902245751	-1.00507802199	-0.193357618068	-0.596154445347	0.882508271507	0.595769361887	0.560553352235	0.270249959514	0.0233248277869	0.00765756935025	0.35158405232	-0.0302402549853	0.418893285526	-1.07893621118	-2.31216303652	22.2244633194
10	3.46853506079	-0.584280810545	0.800155832143	4.33606744977	-1.81885152807	7.92468463884	0.0492437831207	0.0193418795706	-0.602629311096	-0.0385521783538	0.152293608403	0.682992991076	0.355691174091	-0.601263152091	-0.147577377777	0.234735133204	-0.0103235281578	-0.0239009367319	0.272832266636	-0.0339124712693	0.481457507677	-43.9450685941	21.1788040798	30.7031462859
11	2.95216418493	-0.200710467975	0.212477832428	5.81326502427	-1.6702348628	5.88265251581	-0.157614025932	-0.0983266288575	-0.521362380284	0.13643022669	0.097185520568	0.245632298689	0.670061252315	-0.121356210763	-0.0742961136586	0.265806508178	0.0753804001746	0.0544246002194	0.235649469815	0.0185118072891	0.321805658355	-37.1631426957	21.0169624412	38.2448534703
12	0.574496951701	0.912281471587	1.07912486189	6.8984606322	1.06435989016	2.75096845005	0.0233745396639	-0.343798344066	0.183688763951	2.11997200798	-0.508190698901	-0.750055942659	0.137435124401	0.259093734391	0.394698463397	0.919789831619	0.155727854667	-0.0466599464108	0.60726008685	0.0573313619598	0.895390820387	-43.2334786984	43.6038375111	24.2506364887
13	4.42544052813	-0.601972486602	-2.67734121946	4.96522847972	3.46169210893	3.659206022	1.00078418373	1.21030302589	-0.122912847661	-1.3301794489	-0.887833811176	1.09487572671	0.229569369015	-0.485541654894	0.349371101933	0.682632135127	0.235149469631	-0.162430345396	0.516472117724	-0.118189727826	0.340996283668	-40.3209691974	28.5163863679	14.141865218
14	4.8223044163	-3.06467032489	2.27404501436	3.62232501284	-0.983264978668	4.45574093441	0.615546838387	0.45142887774	-0.626055389838	-0.746052849673	-0.303538589507	0.354954528512	0.789807833644	0.118387753105	-0.0775383884283	0.330142423852	0.196671568124	-0.0347913893432	0.32399947067	-0.0757886719128	0.250885959742	-28.6060395445	18.9046252789	24.2563865905
15	4.12470401424	-2.24055630492	0.977884710058	3.92498871256	-0.397441838022	3.80483531419	-0.149172648153	-0.147353892254	-0.188034347068	0.0496729992189	0.118610488559	0.286577745703	-0.108613168002	-0.435359381044	-0.0394522432158	0.207232097738	0.0622620607775	0.0158045144554	0.180193560212	-0.0343558893064	0.248964606762	-38.2746959004	25.8513395852	30.0962403368
16	4.02567176131	-2.85058272841	2.74840112529	3.40182179389	-1.57747714793	8.17898880673	0.121788701473	0.714036944685	0.271826041441	-0.656230463747	-0.394486217726	-0.261535763484	-0.397732400626	0.603166782736	0.190339955532	0.357067211351	0.0911066996589	0.0245358441957	0.322472769438	0.0253839225838	0.237178452105	-32.657237952	31.5064975604	21.3380207431
17	7.21772408255	-1.89044750225	5.04303151516	1.50388265286	-1.91258747459	3.79139174503	0.0529478425862	0.659916815062	1.9646027616	-0.579633820153	-0.265490804463	-0.58958538564	-0.60795105335	0.215171371004	0.344781596609	0.541034792953	0.0554104813282	0.11923914633	0.521322369023	0.047430025896	0.695961324801	-22.1759902972	31.5511385522	25.0553189897
18	2.93219152886	0.31836074607	1.46644601947	4.02340499853	1.13222887494	8.45740839448	-0.171331707759	-0.458692840614	0.110552371997	0.415061595715	0.299906598886	0.576523011982	-0.426799516302	-1.09291843587	-0.128709487781	0.407742122742	0.169235411538	0.159079013409	0.456350629652	0.0969697998196	0.345422179914	-46.1100408483	30.8281181642	51.8065870678
19	1.60098257255	-1.51353360017	0.130761947371	4.7778995498	-0.81798321751	1.36602154155	0.0229015684246	-0.0713705908775	-0.131845333192	-0.304283113022	-0.0374175974677	0.217948203582	0.302123271085	0.0701811101252	-0.00776983069167	0.213488754461	0.0464634058714	-0.0186103483804	0.235047849592	0.0154972867927	0.267408408203	-42.7451320079	34.9108259534	39.4618719787
20	2.01491004545	-0.439272984856	-0.633560968765	3.26515251541	-0.0559076703293	5.41834634978	-0.295002407028	-0.759268623421	-0.153586276054	1.19113875233	0.360097942247	0.154119494111	0.132377115823	0.144373940603	-0.0389573992856	0.434650528858	0.261546911708	0.00534179341731	0.519093505877	0.032182413026	0.309541679186	-35.5376148543	31.5717411535	55.9444052794
21	1.74682738466	-0.458277647817	-0.0699591718656	4.34883434231	-0.390311524552	3.67093759133	-0.293865174532	-0.347897424618	-0.12359729217	0.406742566294	0.269889490272	0.221646017792	0.475708085996	-0.0724911763801	-0.024711092744	0.293449877725	0.149375296844	0.046590702582	0.269687465214	0.0342176823508	0.222675688897	-39.1412456798	30.2161039591	47.1580143119
22	1.44271551231	-0.548093544564	-0.330185706046	3.46648760627	-1.95557474749	6.4674710824	-0.189697639807	-0.526795786442	-0.129590324172	0.727443795294	0.236825452174	-0.275700556698	0.441555563603	0.957710745221	0.250830018984	0.366622078717	0.197187888147	-0.0492124846993	0.422365639934	-0.0216697121541	0.288324558085	-30.7909664226	31.0919419777	49.9174749364
23	5.03064110779	-1.49110337385	0.999428235808	5.02110083906	-1.88041079366	7.87028231793	-0.0120802014139	-0.379314545042	-0.17090923999	1.09247158645	0.227436421709	-1.06706125913	0.0848281005258	0.905463598192	-0.0979220533868	1.00813575016	0.500125196272	-0.0516073647317	0.755876990362	0.040174220626	0.522419445598	-28.7198939728	23.2936913289	62.1360359017
24	5.88377966384	0.0863704169869	-1.84602707682	3.60804346496	-0.584167597841	6.68217253935	-0.151443726714	-0.290395072637	-0.759339912452	0.568524555232	-0.450732947155	-0.606738042355	0.12607688592	0.836024126289	0.0359395231315	0.303074061754	0.111151610682	-0.0304878129299	0.62589747197	-0.138529907189	0.882222087813	-20.5021858393	36.089168483	47.2711748405

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 2 through 12 )	A	A	2 - 12	1 - 11
2	2	chain 'A' and (resid 13 through 28 )	A	A	13 - 28	12 - 27
3	3	chain 'A' and (resid 29 through 56 )	A	A	29 - 56	28 - 48
4	4	chain 'A' and (resid 57 through 72 )	A	A	57 - 72	49 - 64
5	5	chain 'A' and (resid 73 through 102 )	A	A	73 - 102	65 - 94
6	6	chain 'A' and (resid 103 through 120 )	A	A	103 - 120	95 - 112
7	7	chain 'A' and (resid 121 through 128 )	A	A	121 - 128	113 - 120
8	8	chain 'A' and (resid 129 through 142 )	A	A	129 - 142	121 - 134
9	9	chain 'A' and (resid 143 through 152 )	A	A	143 - 152	135 - 144
10	10	chain 'B' and (resid 1 through 22 )	B	B	1 - 22	1 - 22
11	11	chain 'B' and (resid 23 through 36 )	B	B	23 - 36	23 - 36
12	12	chain 'B' and (resid 37 through 48 )	B	B	37 - 48	37 - 43
13	13	chain 'B' and (resid 49 through 56 )	B	B	49 - 56	44 - 51
14	14	chain 'B' and (resid 57 through 72 )	B	B	57 - 72	52 - 67
15	15	chain 'B' and (resid 73 through 102 )	B	B	73 - 102	68 - 97
16	16	chain 'B' and (resid 103 through 137 )	B	B	103 - 137	98 - 132
17	17	chain 'B' and (resid 138 through 152 )	B	B	138 - 152	133 - 147
18	18	chain 'C' and (resid 2 through 12 )	C	C	2 - 12	1 - 11
19	19	chain 'C' and (resid 13 through 36 )	C	C	13 - 36	12 - 35
20	20	chain 'C' and (resid 37 through 72 )	C	C	37 - 72	36 - 64
21	21	chain 'C' and (resid 73 through 102 )	C	C	73 - 102	65 - 94
22	22	chain 'C' and (resid 103 through 127 )	C	C	103 - 127	95 - 119
23	23	chain 'C' and (resid 128 through 144 )	C	C	128 - 144	120 - 132
24	24	chain 'C' and (resid 145 through 152 )	C	C	145 - 152	133 - 140

-
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