PDB-6xdk: Crystal structure of Phosphoserine aminotransferase (SerC) from S...

ID or keywords:

Entry

Database: PDB / ID: 6xdk

Title

Crystal structure of Phosphoserine aminotransferase (SerC) from Stenotrophomonas maltophilia K279a

Components

Phosphoserine aminotransferase

Phosphoserine transaminase

Keywords

TRANSFERASE / SSGCID /

Stenotrophomonas maltophilia /

Phosphoserine aminotransferase / serC /

Structural Genomics / Seattle Structural Genomics Center for Infectious Disease

Function / homology

Function and homology information

phosphoserine transaminase /

O-phospho-L-serine:2-oxoglutarate aminotransferase activity / pyridoxine biosynthetic process / L-serine biosynthetic process /

pyridoxal phosphate binding /

cytoplasm
Similarity search - Function

Biological species

Stenotrophomonas maltophilia (bacteria)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 1.6 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Citation

Journal: to be published
Title: Crystal structure of Phosphoserine aminotransferase (SerC) from Stenotrophomonas maltophilia K279a
Authors: Abendroth, J. / Horanyi, P.S. / Lorimer, D.D. / Edwards, T.E.

History

Deposition	Jun 10, 2020	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 24, 2020	Provider: repository / Type: Initial release
Revision 1.1	Oct 18, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	6xdk.cif.gz	738.1 KB	Display	PDBx/mmCIF format
PDB format	pdb6xdk.ent.gz	500.7 KB	Display	PDB format
PDBx/mmJSON format	6xdk.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/xd/6xdk ftp://data.pdbj.org/pub/pdb/validation_reports/xd/6xdk	HTTPS FTP

-
Related structure data

Related structure data	4xk1S S: Starting model for refinement
Similar structure data	1w3u-1 6czy-2 5yb0-1 2vi8-1 5u21-1 2vmn-1 2bhx-d 2vmv-1 2vms-1 5u21-2 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: StmaA.00980.a

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Phosphoserine aminotransferase

B: Phosphoserine aminotransferase

C: Phosphoserine aminotransferase

D: Phosphoserine aminotransferase

hetero molecules

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

1

A: Phosphoserine aminotransferase

B: Phosphoserine aminotransferase

hetero molecules

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

2

C: Phosphoserine aminotransferase

D: Phosphoserine aminotransferase

hetero molecules

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

Unit cell

Length a, b, c (Å)	64.350, 71.620, 89.860
Angle α, β, γ (deg.)	84.985, 88.816, 63.369
Int Tables number	1
Space group name H-M	P1
Space group name Hall	P1
Symmetry operation	#1: x,y,z

-
Protein , 1 types, 4 molecules ABCD

#1: Protein	Phosphoserine aminotransferase / Phosphoserine transaminase / Phosphohydroxythreonine aminotransferase / PSAT Mass: 40110.289 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Stenotrophomonas maltophilia (strain K279a) (bacteria) Strain: K279a / Gene: serC, Smlt3098 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) Strain (production host): BL21(DE3) / References: UniProt: B2FKF0, phosphoserine transaminase

#1: Protein

Phosphoserine aminotransferase /

Phosphoserine transaminase / Phosphohydroxythreonine aminotransferase / PSAT

Mass: 40110.289 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Stenotrophomonas maltophilia (strain K279a) (bacteria)
Strain: K279a / Gene: serC, Smlt3098
Production host:

Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): BL21(DE3) / References: UniProt: B2FKF0,

phosphoserine transaminase

-
Non-polymers , 5 types, 1949 molecules

#2: Chemical	ChemComp-CL / CHLORIDE ION / Chloride Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Chemical	ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate / Pyridoxal phosphate Mass: 247.142 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C₈H₁₀NO₆P / Feature type: SUBJECT OF INVESTIGATION
#6: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 1938 / Source method: isolated from a natural source / Formula: H₂O

-
Details

Has ligand of interest	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.3 Å³/Da / Density % sol: 46.5 %
Crystal grow	Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: Molecular Dimensions Morpheus screen condition A2: 10% (w/V) 8000, 20% (V/V) ethylene glycol: 30mM of each magnesium chloride, calcium chloride: 100mM MES / imidazole pH 6.5: StmaA.00980.a. ...Details: Molecular Dimensions Morpheus screen condition A2: 10% (w/V) 8000, 20% (V/V) ethylene glycol: 30mM of each magnesium chloride, calcium chloride: 100mM MES / imidazole pH 6.5: StmaA.00980.a.B1.PW38764 at 25.7mg/ml: tray: 314406a2: cryo: reservoir + 5% 50mM PLP in DMSO: puck mcj9-7

Crystal

Density Matthews: 2.3 Å³/Da / Density % sol: 46.5 %

Crystal grow

Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Molecular Dimensions Morpheus screen condition A2: 10% (w/V) 8000, 20% (V/V) ethylene glycol: 30mM of each magnesium chloride, calcium chloride: 100mM MES / imidazole pH 6.5: StmaA.00980.a. ...

-
Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

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

Detector

Type: RIGAKU SATURN 944+ / Detector: CCD / Date: May 6, 2020

Radiation

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

Radiation wavelength

Wavelength: 1.5418 Å / Relative weight: 1

Reflection

Resolution: 1.6→50 Å / Num. obs: 183658 / % possible obs: 97.4 % / Redundancy: 8.238 % / B_iso Wilson estimate: 23.637 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.055 / R_rim(I) all: 0.058 / Χ²: 0.927 / Net I/σ(I): 21.99

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
1.6-1.64	5.776	0.609	2.71	12478	0.807	0.665	89.3
1.64-1.69	5.913	0.501	3.35	12378	0.874	0.545	91.1
1.69-1.74	6.054	0.415	4.06	12333	0.909	0.451	93.1
1.74-1.79	6.197	0.338	5.03	12239	0.939	0.367	95
1.79-1.85	6.365	0.283	6.02	12016	0.957	0.307	96.8
1.85-1.91	6.542	0.225	7.62	11833	0.975	0.244	98.5
1.91-1.98	6.742	0.169	10.15	11587	0.987	0.182	99.8
1.98-2.07	7	0.136	13.23	11217	0.991	0.147	99.9
2.07-2.16	7.256	0.111	16.86	10694	0.994	0.119	100
2.16-2.26	7.624	0.093	20.39	10225	0.996	0.099	99.9
2.26-2.39	8.381	0.079	25.14	9782	0.997	0.084	100
2.39-2.53	8.94	0.069	28.84	9181	0.998	0.073	100
2.53-2.7	9.503	0.061	32.89	8659	0.998	0.065	100
2.7-2.92	10.138	0.052	38.66	8058	0.999	0.055	100
2.92-3.2	11.322	0.045	46.54	7411	0.999	0.047	100
3.2-3.58	13.794	0.038	60.04	6740	0.999	0.04	100
3.58-4.13	14.619	0.035	68.79	5883	1	0.036	99.9
4.13-5.06	14.451	0.034	71.14	4985	0.999	0.036	100
5.06-7.16	14.898	0.035	66.98	3873	1	0.036	100
7.16-50	14.652	0.029	75.97	2086	1	0.03	99.5

-
Processing

Software

Name	Version	Classification
PHENIX	1.18.2	refinement
XDS		data reduction
XSCALE		data scaling
PDB_EXTRACT	3.25	data extraction
MoRDa		phasing
Coot		model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 4xk1 in two domains per MoRDa

4xk1

Resolution: 1.6→48.85 Å / SU ML: 0.1465 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 18.6861
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1811	2019	1.1 %	0
R_work	0.156	181624	-	-
obs	0.1563	183643	97.4 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 21.19 Å²

Refinement step

Cycle: LAST / Resolution: 1.6→48.85 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10783	0	54	1938	12775

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0102	11813
X-RAY DIFFRACTION	f_angle_d	1.0845	16205
X-RAY DIFFRACTION	f_chiral_restr	0.066	1772
X-RAY DIFFRACTION	f_plane_restr	0.0073	2170
X-RAY DIFFRACTION	f_dihedral_angle_d	16.2485	4340

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 (%)
1.6-1.64	0.2501	141	0.2194	11876	X-RAY DIFFRACTION	89.19
1.64-1.68	0.2444	109	0.1997	12154	X-RAY DIFFRACTION	91.07
1.68-1.73	0.2332	131	0.1924	12389	X-RAY DIFFRACTION	92.93
1.73-1.79	0.226	114	0.1808	12732	X-RAY DIFFRACTION	95.07
1.79-1.85	0.2168	142	0.1824	12849	X-RAY DIFFRACTION	96.9
1.85-1.93	0.2277	150	0.1704	13177	X-RAY DIFFRACTION	98.76
1.93-2.02	0.1774	158	0.1595	13266	X-RAY DIFFRACTION	99.88
2.02-2.12	0.191	167	0.1532	13256	X-RAY DIFFRACTION	100
2.12-2.26	0.203	146	0.1479	13369	X-RAY DIFFRACTION	100
2.26-2.43	0.1653	150	0.1485	13307	X-RAY DIFFRACTION	100
2.43-2.67	0.175	142	0.1526	13354	X-RAY DIFFRACTION	100
2.67-3.06	0.1993	164	0.1558	13292	X-RAY DIFFRACTION	100
3.06-3.86	0.1463	148	0.143	13299	X-RAY DIFFRACTION	99.99
3.86-48.85	0.1555	157	0.1436	13304	X-RAY DIFFRACTION	99.9

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	1.30482943232	0.0578345635922	-0.457238195833	1.49170464532	-0.0961069060981	2.06779767646	0.0401397071455	0.441663225936	0.11045057727	-0.500920832587	0.0571562724664	-0.0518737410815	-0.138371980495	-0.137367360192	-0.0729428695541	0.264627060708	-0.0561317822212	0.0274732958049	0.232083645954	0.0247816764876	0.113794902457	20.4915198522	35.8545804781	-15.3243871387
2	1.13089844173	1.71789718688	-1.1086324619	5.11772758877	-1.43677843278	1.07891148359	0.114308496806	-0.134763996612	-0.135713222673	0.586608521426	-0.0548613822559	-0.593986633364	0.0159970993329	0.323560756685	-0.0300823109163	0.241681015815	0.0361029833114	-0.0931124173098	0.221928263359	-0.0592631190928	0.214202168874	28.29617301	-6.34670598595	57.1316791266
3	1.16707261702	-0.791907603778	-1.50406003805	2.8532223284	1.35295893111	3.78564681888	0.207916935899	-0.14495638086	0.412207926823	-0.0985996587493	0.16751317165	-0.455247126501	-0.659321921844	0.200843021506	-0.406845289013	0.222302039925	-0.0344946796661	0.0453412848245	0.277138166472	-0.0291607527245	0.334198139751	29.2589154317	5.5489330435	42.0055025677
4	1.58067160921	-0.203982048756	0.319159032786	1.71480921874	-0.0643099833072	1.01812029436	0.00504882342579	-0.042484060479	-0.130284945926	-0.022410464247	0.0291037777872	0.129205889788	0.0494555184966	-0.0406912349576	-0.0425920563912	0.0723724628516	0.0105195833053	0.0141191845989	0.0943967330622	-0.0254303174766	0.0913492932497	8.40346832278	-18.28061615	36.757098585
5	1.39290879403	-0.32156368903	0.599831945725	1.28325888091	-0.16121972996	1.2392483029	-0.024945177519	0.00547015859582	-0.00908867925284	-0.0565416508631	0.0310549939477	-0.118849687804	-0.0436344752832	0.102308686109	0.00235410422442	0.0703133994392	0.00676058586975	0.0215045965696	0.0926430852488	-0.0251348926604	0.0965761032764	17.3067609288	-14.3991335168	36.3360622141
6	5.34549279405	-0.0888352093037	3.73344128456	0.209734610118	-0.130486442569	2.57171919608	-0.178956065508	0.0764097182179	0.158920877947	0.0437936292337	0.0212452489822	-0.0029000414631	-0.290522094195	0.101327929673	0.17986526755	0.154883655371	-0.00283474552238	0.0555470120915	0.118103411411	-0.00722932445422	0.155932711097	21.9180251494	-1.30204103586	39.9109217177
7	1.56781359238	-0.158225957502	0.621812733279	1.63542760394	0.210240711611	1.83883107888	0.00412270562266	-0.524090774754	-0.120352646793	0.666236583657	0.093088545096	-0.0956462423693	0.192746381918	-0.157058801523	-0.0675304293887	0.32233227311	0.06751252633	-0.0410154937731	0.247492220866	0.0266681522884	0.1449468811	22.2816466829	-25.0656020659	59.8431021326
8	0.367230386658	-0.0973046836311	0.267907579784	0.73905074318	-0.0477922344002	0.484993201581	0.0191403160674	0.0301209810504	-0.0306794663422	0.035125400993	-0.0271472189616	0.100178855075	0.000414182403211	0.044423467173	0.00863041798726	0.0989312149292	0.00142943331817	0.0239132433964	0.0947835965868	-0.00416794661403	0.108831327195	3.69698160974	13.3620052631	45.5898851988
9	0.928406264487	0.524885182143	0.921235876154	1.2571879432	0.357796722602	0.920976785238	0.0510105546305	-0.0470431831194	-0.165427235299	0.132190938297	-0.0195011861917	0.0348300833832	0.0874665616242	0.00450909593404	-0.0449068485964	0.125321665869	0.0104648562995	0.0451748559091	0.109958059526	0.0120273565728	0.136676831916	3.512650532	6.36525547986	50.6436917403
10	1.93270200521	0.561076740931	-1.02296670163	1.33022332453	-0.242517714687	1.48838682353	-0.0349402074308	0.0912952087921	0.102692844987	-0.0139838555114	0.0902289891378	-0.0447784104171	0.0521238261723	0.049571873931	-0.0492122025294	0.0690223965035	0.00225356956583	-0.0163604604425	0.0637676225068	0.003165280879	0.073809421499	16.1628122351	33.5844002584	41.2807512623
11	-0.0110353354305	0.226605531651	-0.26786404043	6.10654333001	-5.57197996485	5.49997828079	0.039334291048	-0.0623174055371	-0.0232134703931	0.0041293841607	-0.300836841204	-0.095935781864	-0.103226138669	0.0661579995146	0.288622500725	0.138146965588	-0.0228203144768	-0.00830175755961	0.149512388951	0.00620971292491	0.148778324561	19.9022674295	-7.2030835159	-7.44724013082
12	0.753716720174	0.0273497587938	-0.562720255994	0.79767299153	-0.00422181311203	1.00343165812	0.00857026870178	-0.0779472683439	-0.0315388429659	0.0132642781664	-0.062268350362	0.153713729198	0.0140033045623	0.0581187625138	0.0603738729054	0.0927648509201	-0.00137701923804	-0.0270454713608	0.0913757800147	-0.00675606382064	0.122261807527	-0.590898402883	-1.7261458071	0.198366614515
13	0.777386954974	-0.414843215948	-0.837441323058	1.31250316311	0.331881397122	0.90387139279	0.0376862949106	0.0388791779826	0.107593327724	-0.0982269320625	-0.0440871043381	0.0605330531671	-0.0711488978563	-0.0057806924991	-0.00163288606668	0.120405978184	-0.00967567253269	-0.0489124663579	0.103125493718	0.00748152331965	0.121648285146	1.46312897655	4.52296505049	-5.79909756319
14	1.97059338459	-0.518959360561	1.27177930901	1.04360590359	-0.439748969304	1.84108255552	-0.0143406156003	-0.0187228159311	-0.0767361426323	0.00299596863716	0.0424631974148	0.0520242531836	-0.0114362804086	0.0979436808104	-0.0278992662553	0.0877297886174	-0.000284190255445	0.0242148584424	0.0671419599589	0.00311401498851	0.0730169064468	14.4114457336	-22.7318172437	3.39775010533
15	1.79879194363	-2.75830764885	1.14064356916	5.72855612377	-1.70353868413	0.713062501393	0.111667340395	0.0368239663838	0.110859423031	-0.546462522051	-0.0132297827365	-0.449980727678	0.0212946094349	0.241517665802	-0.075226147162	0.232372934205	-0.034934363692	0.055342021091	0.235934974512	-0.0511119209173	0.154069756036	26.4507222963	17.4675083021	-12.1137862325
16	1.24092741057	1.2029908578	1.60686906336	3.34967437435	1.76225776595	2.98737470676	0.199547607383	0.117526299008	-0.438042192229	0.235609190031	0.19462744074	-0.528881563354	0.577886565774	0.264578401496	-0.418003446933	0.208950328101	0.0451324901129	-0.0440029513168	0.259303653333	-0.0240518273999	0.279122191971	27.0129030245	4.85310858734	3.00397174326
17	1.69201509674	-0.903201544165	-0.0237969873681	2.12772980031	-0.253616956881	0.8935458526	-0.010147968012	-0.00281847679679	-0.0241127602747	0.017235835684	0.00793868719756	0.112794196823	0.00307535909248	0.0118054813927	0.00272347586886	0.082945293176	-0.017263718687	-0.00756310833998	0.0863578993336	-0.0198589466964	0.0621779353859	6.18663832482	24.6618211857	9.15378553162
18	2.35730807697	0.095745098079	-1.93420147607	2.34463382566	-0.508272361452	2.90901475647	0.0592318785592	0.0648233944334	0.30708427096	0.0235575049954	0.0390402345095	-0.0259021628187	-0.217033177917	-0.00678612252435	-0.0812903748038	0.093862755073	-0.0195078793596	-0.0163387844351	0.101204042021	-0.0118766527709	0.119181440434	9.46254797496	36.4606051381	7.17893237494
19	2.02390317079	0.605172081057	-1.06651015656	1.40528742348	-0.418459709042	1.91273228149	-0.0576544458109	0.025698892407	-0.0586906459738	-0.000181863012431	0.0626430387837	-0.0879653396427	0.0923647716465	0.145062295072	0.00919585955795	0.0858751424646	0.00345898359352	-0.016599860369	0.0929314350701	-0.012857256239	0.0696805310752	15.9674624216	21.9105282018	8.39851569099
20	3.37107036948	-0.0453365646326	-2.11054261636	0.149203898502	0.0161144263612	1.31846677189	-0.102866701231	-0.0846722781429	-0.116649434171	-0.0358526911495	0.0105706965506	0.0239546595343	0.199267076668	0.0556790124702	0.119750693814	0.178793752882	-0.00383088806315	-0.0386806657463	0.148151067223	-0.00388979008727	0.125104792189	19.9174287468	12.1975711686	5.14910045569

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 'B' and (resid 259 through 361 )	B	D	259 - 361	289 - 399
2	2	chain 'C' and (resid 3 through 24 )	C	I	3 - 24	1 - 26
3	3	chain 'C' and (resid 25 through 61 )	C	I	25 - 61	27 - 65
4	4	chain 'C' and (resid 62 through 153 )	C	I	62 - 153	66 - 168
5	5	chain 'C' and (resid 154 through 221 )	C	I	154 - 221	169 - 252
6	6	chain 'C' and (resid 222 through 258 )	C	I	222 - 258	253 - 285
7	7	chain 'C' and (resid 259 through 361 )	C	I	259 - 361	286 - 394
8	8	chain 'D' and (resid 3 through 183 )	D	N	3 - 183	1 - 217
9	9	chain 'D' and (resid 184 through 258 )	D	N	184 - 258	218 - 307
10	10	chain 'D' and (resid 259 through 361 )	D	N	259 - 361	308 - 418
11	11	chain 'A' and (resid 4 through 24 )	A	A	4 - 24	1 - 25
12	12	chain 'A' and (resid 25 through 183 )	A	A	25 - 183	26 - 210
13	13	chain 'A' and (resid 184 through 258 )	A	A	184 - 258	211 - 298
14	14	chain 'A' and (resid 259 through 361 )	A	A	259 - 361	299 - 411
15	15	chain 'B' and (resid 3 through 24 )	B	D	3 - 24	1 - 24
16	16	chain 'B' and (resid 25 through 61 )	B	D	25 - 61	25 - 69
17	17	chain 'B' and (resid 62 through 121 )	B	D	62 - 121	70 - 137
18	18	chain 'B' and (resid 122 through 172 )	B	D	122 - 172	138 - 195
19	19	chain 'B' and (resid 173 through 221 )	B	D	173 - 221	196 - 253
20	20	chain 'B' and (resid 222 through 258 )	B	D	222 - 258	254 - 288

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Protein , 1 types, 4 molecules ABCD

-
Non-polymers , 5 types, 1949 molecules

-
Details

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Protein , 1 types, 4 molecules ABCD

-Non-polymers , 5 types, 1949 molecules

-Details

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Protein , 1 types, 4 molecules ABCD

-
Non-polymers , 5 types, 1949 molecules

-
Details

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi