PDB-9s01: PYCR1 in complex with L-tartrate

ID or keywords:

Entry

Database: PDB / ID: 9s01

Title

PYCR1 in complex with L-tartrate

Components

Isoform 3 of Pyrroline-5-carboxylate reductase 1, mitochondrial

Keywords

OXIDOREDUCTASE / delta-1-pyrroline-5-carboxylate reductase / PYCR1 / cancer / crystallographic fragment screening (XFS) / molecular docking / proline metabolism

Function / homology

Function and homology information

pyrroline-5-carboxylate reductase / pyrroline-5-carboxylate reductase activity / L-proline biosynthetic process / Glutamate and glutamine metabolism / : / negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / regulation of mitochondrial membrane potential / cellular response to oxidative stress / mitochondrial matrix / mitochondrion / identical protein binding
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.65 Å

Authors

Ragin-Oh, W. / Czerwonka, D. / Ruszkowski, M.

Funding support

Poland, 1items

Citation

Journal: Bioorg.Chem. / Year: 2025
Title: Crystallographic fragment screening reveals new starting points for PYCR1 inhibitor design.
Authors: Ragin-Oh, W. / Czerwonka, D. / Tran, L.H. / Forlani, G. / Ruszkowski, M.

History

Deposition	Jul 16, 2025	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Oct 15, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	9s01.cif.gz	643.6 KB	Display	PDBx/mmCIF format
PDB format	pdb9s01.ent.gz	443.3 KB	Display	PDB format
PDBx/mmJSON format	9s01.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	9s01_validation.pdf.gz	1.8 MB	Display	wwPDB validaton report
Full document	9s01_full_validation.pdf.gz	1.8 MB	Display
Data in XML	9s01_validation.xml.gz	64.3 KB	Display
Data in CIF	9s01_validation.cif.gz	84.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/s0/9s01 ftp://data.pdbj.org/pub/pdb/validation_reports/s0/9s01	HTTPS FTP

-
Related structure data

Related structure data	9rzzC 9s02C 9s04C C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Experimental dataset #1	Data reference: 10.60884/PVIXQ6 / Data set type: diffraction image data

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#234 - Jun 2019 MDM2 and Cancer similarity (1) #228 - Dec 2018 Directed Evolution of Enzymes similarity (2) #111 - Mar 2009 Hydrogenase similarity (1) #127 - Jul 2010 Crystallins similarity (1)

Deposited unit

A: Isoform 3 of Pyrroline-5-carboxylate reductase 1, mitochondrial

B: Isoform 3 of Pyrroline-5-carboxylate reductase 1, mitochondrial

C: Isoform 3 of Pyrroline-5-carboxylate reductase 1, mitochondrial

D: Isoform 3 of Pyrroline-5-carboxylate reductase 1, mitochondrial

E: Isoform 3 of Pyrroline-5-carboxylate reductase 1, mitochondrial

hetero molecules

181 kDa, 5 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Isoform 3 of Pyrroline-5-carboxylate reductase 1, mitochondrial

B: Isoform 3 of Pyrroline-5-carboxylate reductase 1, mitochondrial

C: Isoform 3 of Pyrroline-5-carboxylate reductase 1, mitochondrial

D: Isoform 3 of Pyrroline-5-carboxylate reductase 1, mitochondrial

E: Isoform 3 of Pyrroline-5-carboxylate reductase 1, mitochondrial

hetero molecules

A: Isoform 3 of Pyrroline-5-carboxylate reductase 1, mitochondrial

B: Isoform 3 of Pyrroline-5-carboxylate reductase 1, mitochondrial

C: Isoform 3 of Pyrroline-5-carboxylate reductase 1, mitochondrial

D: Isoform 3 of Pyrroline-5-carboxylate reductase 1, mitochondrial

E: Isoform 3 of Pyrroline-5-carboxylate reductase 1, mitochondrial

hetero molecules

defined by author
Evidence: gel filtration
362 kDa, 10 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	164.196, 88.109, 116.245
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	18
Space group name H-M	P2₁2₁2
Space group name Hall	P22ab
Symmetry operation	#1: x,y,z #2: x+1/2,-y+1/2,-z #3: -x+1/2,y+1/2,-z #4: -x,-y,z

Components on special symmetry positions

ID	Model	Components
1	1	B-609- HOH
2	1	E-407- HOH

#1: Protein	Isoform 3 of Pyrroline-5-carboxylate reductase 1, mitochondrial / P5C reductase 1 / P5CR 1 Mass: 36075.453 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PYCR1 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: P32322, pyrroline-5-carboxylate reductase
#2: Chemical	ChemComp-TLA / L(+)-TARTARIC ACID Mass: 150.087 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₄H₆O₆ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 674 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	N

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.33 Å³/Da / Density % sol: 47.23 %
Crystal grow	Temperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: Based on Morpheus 2.34 condition (Molecular Dimensions), containing 0.02 M sodium formate, 0.02 M ammonium acetate, 0.02 M sodium citrate tribasic, 0.02 M potassium sodium tartrate, 0.02 M ...Details: Based on Morpheus 2.34 condition (Molecular Dimensions), containing 0.02 M sodium formate, 0.02 M ammonium acetate, 0.02 M sodium citrate tribasic, 0.02 M potassium sodium tartrate, 0.02 M sodium oxamate, 0.1 M Tris (base), BICINE pH 8.5, 20% ethylene glycol, 10% PEG 8000, and supplemented with 10% ethylene glycol for cryoprotection.

Crystal

Density Matthews: 2.33 Å³/Da / Density % sol: 47.23 %

Crystal grow

Temperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Based on Morpheus 2.34 condition (Molecular Dimensions), containing 0.02 M sodium formate, 0.02 M ammonium acetate, 0.02 M sodium citrate tribasic, 0.02 M potassium sodium tartrate, 0.02 M ...

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.9763 Å
Detector	Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Nov 12, 2023
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9763 Å / Relative weight: 1
Reflection	Resolution: 1.65→37.21 Å / Num. obs: 201497 / % possible obs: 99.9 % / Redundancy: 13.6 % / B_iso Wilson estimate: 30.43 Å² / CC_1/2: 1 / R_merge(I) obs: 0.06 / R_rim(I) all: 0.06 / Net I/σ(I): 22.86
Reflection shell	Resolution: 1.65→1.75 Å / Redundancy: 13.8 % / R_merge(I) obs: 2 / Mean I/σ(I) obs: 1.45 / Num. unique obs: 32213 / R_rim(I) all: 2.1 / % possible all: 99.7

-
Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.65→37.21 Å / SU ML: 0.1977 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.6253
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2038	1999	0.99 %
R_work	0.1825	199321	-
obs	0.1827	201320	99.87 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 51.89 Å²

Refinement step

Cycle: LAST / Resolution: 1.65→37.21 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10091	0	46	674	10811

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0038	10404
X-RAY DIFFRACTION	f_angle_d	0.6723	14093
X-RAY DIFFRACTION	f_chiral_restr	0.0433	1687
X-RAY DIFFRACTION	f_plane_restr	0.0062	1828
X-RAY DIFFRACTION	f_dihedral_angle_d	12.0241	3796

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 (%)
1.65-1.69	0.4039	141	0.3555	14016	X-RAY DIFFRACTION	99.14
1.69-1.74	0.3291	140	0.3191	14068	X-RAY DIFFRACTION	99.82
1.74-1.79	0.2871	142	0.2732	14122	X-RAY DIFFRACTION	99.92
1.79-1.85	0.267	141	0.2509	14152	X-RAY DIFFRACTION	99.98
1.85-1.91	0.2837	142	0.2384	14137	X-RAY DIFFRACTION	99.94
1.91-1.99	0.2483	142	0.2163	14136	X-RAY DIFFRACTION	99.83
1.99-2.08	0.2289	142	0.1852	14144	X-RAY DIFFRACTION	99.87
2.08-2.19	0.2122	143	0.1741	14217	X-RAY DIFFRACTION	99.99
2.19-2.33	0.1824	142	0.1701	14207	X-RAY DIFFRACTION	99.97
2.33-2.51	0.1723	143	0.1765	14220	X-RAY DIFFRACTION	99.98
2.51-2.76	0.2165	143	0.1762	14279	X-RAY DIFFRACTION	99.95
2.76-3.16	0.205	144	0.1819	14353	X-RAY DIFFRACTION	99.99
3.16-3.98	0.1749	145	0.1665	14425	X-RAY DIFFRACTION	100
3.98-37.21	0.1954	149	0.1692	14845	X-RAY DIFFRACTION	99.83

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	5.10541107548	4.01691439188	2.37415978108	7.99706147246	-0.139411145572	7.4494590931	-0.245400469259	0.336526649872	0.209216301333	-1.73656545243	0.332134765394	0.452401337558	-0.386781245219	-0.234857856564	0.0667890893661	0.843754716025	0.0630691580017	-0.0813344038067	0.393999970556	0.0321203497932	0.528385417868	14.8077000623	26.9833118423	46.5259340032
2	2.37209285634	2.65809397784	2.84093721219	6.73509717919	-0.06653682307	7.41493997884	-0.678937443243	0.540455612073	0.637587703801	-1.85235995977	0.43333034805	2.01894719714	-0.0869727310598	-0.824586753921	0.0221153382165	1.16508546678	0.0274441782956	-0.318938596699	0.551339760674	0.0509485564563	0.979078383105	9.0298257601	26.5139890545	41.4028507083
3	6.2581235753	-0.999500717539	3.79452203372	7.40790543512	-3.31743842074	6.7400923648	-0.0908044880536	0.153248944027	-0.323770078447	-1.08350739448	0.349057123292	1.26107895287	-0.0846809516587	-0.664718086217	-0.28868523034	0.671703661225	0.0114616068527	-0.0917323150665	0.347211153314	-0.0238529921385	0.568778669707	11.8487434654	13.3549871375	50.4427679839
4	1.79019157433	-1.12927650346	0.596502842857	8.17767159581	-0.263877566919	0.756463453347	0.0798561714516	0.120156998275	-0.218587596203	-0.242889164363	-0.0420354901661	-0.435313195876	0.096601566304	0.163438829002	-0.0479609578985	0.406269300097	0.0165672184379	0.105921146774	0.323487303485	-0.032135012381	0.384726911644	22.8140398736	21.5156025905	55.7068762624
5	0.910162462171	-1.04544028579	-0.219859307487	2.6766037845	0.151746526173	0.750472649047	0.0226683375862	0.0594063484212	-0.0399783686797	-0.269402531497	-0.00510719559385	-0.0527975362609	0.0764702927497	0.0132036194522	0.00554863662776	0.263182890848	-0.0148726703342	0.0248441019971	0.271445857333	-0.0099718440693	0.221039834335	12.854269019	44.2222796782	63.1492513279
6	0.426668836558	-0.413355877274	0.598044323187	3.06491130628	0.548080927317	2.06339956916	0.00128818126363	0.0670841794842	-0.0380843789445	-0.239592279311	0.0463204624644	-0.478034751211	0.136850377124	0.35006455034	-0.117261578036	0.276592055151	0.0207703939214	0.0363226863914	0.32528655693	-0.0135626149326	0.357577787892	21.934859267	51.2164950036	75.3704458759
7	5.43965263095	1.44602710139	0.770681380725	8.72907723018	4.45562585458	3.81281659794	0.0706532621192	0.193924908096	-0.726729407938	0.217399133073	-0.109903593526	0.346301732374	0.552287326401	-0.102288433127	0.0201744563534	0.299595507459	0.00112144739591	-0.00844659910621	0.291549387389	0.0191113426689	0.32886117099	9.33983078716	27.0677038166	72.5687276413
8	7.41232791032	2.65175297243	2.21988084731	7.51293187961	4.33491587384	5.22767196062	-0.328345604158	1.27631816633	-0.175968448354	-1.11509910065	0.192180812711	-1.08393763168	-0.582646172878	1.00116672885	0.327581662736	0.531220591722	-0.0276205264739	0.161702805204	0.461499511249	0.0489463034015	0.750406069024	33.6141305046	67.099602158	54.055469551
9	7.14949207403	2.19337350133	2.65777283242	6.59080926617	3.7227401351	5.28352857707	-0.227898991538	0.497054705699	-0.154752396448	-0.284021469832	0.25298726745	-0.860205628575	0.160598598329	0.466831068893	-0.0566415545267	0.295527803751	0.0422684383999	0.0904436857621	0.381956348497	0.125493266301	0.677749232438	35.9734965247	60.843935534	59.3123447657
10	8.42778577485	-2.37785866079	-2.21935847197	3.66241925392	2.9457990188	2.66337547422	0.690414116902	-1.65365134526	0.137982742378	2.76763198505	0.123793079172	-1.79730193649	0.797666907722	-0.0786241612914	-0.786321079629	1.12677867421	-0.117915086778	-0.136357387427	0.755258853228	0.0231784594737	0.709550279203	40.9102174882	60.4834143359	70.7783474502
11	6.64830048127	-2.07468140339	4.79790730858	3.07833264662	1.7783554448	7.7653826622	-0.00975493460911	-0.666105165078	0.0456382878164	0.226469666502	0.270503366748	-0.935818605324	0.0864493523416	-0.131966831241	-0.175393524512	0.367127624211	-0.0569020191693	-0.0101806267471	0.410548763245	0.096919060998	0.731990892502	33.9917905095	74.1246426359	66.9169770481
12	2.72274955901	-1.03330527106	0.822362978574	2.28650059583	0.16329161386	1.87760292277	-0.0396251088565	-0.135212989223	0.491095195389	0.101892929275	0.213692056677	-0.110747542596	-0.542206207671	0.113764776147	-0.0106810252542	0.435800213767	-0.0075319298471	0.0754492706282	0.369982760974	0.0900991596778	0.661201766873	24.7910553213	77.6318325615	62.434012015
13	1.26426210527	-0.470589462914	0.29041891002	2.01042541296	-0.100354182902	0.815645403025	-0.0126621313195	0.180786059761	0.317285991379	-0.348444744094	0.00999164932752	-0.0123232919563	-0.0546783563477	0.0122665368692	-0.0322541942206	0.352215787526	-0.0153581991313	0.0980555326465	0.323667427841	0.0661865495605	0.483292034682	23.013408001	68.0808120033	58.5364222467
14	4.3787959068	1.09968036064	-0.547898376781	7.24805814451	-2.30076940134	6.88917333107	-0.0487768130635	0.519014662449	0.260900852455	-0.739064528032	0.0485709922339	-0.101619031927	-0.311730239279	0.0537982788549	0.0156863805182	0.424808137111	-0.0167965619469	0.0914607028767	0.325289597701	0.0652502429256	0.353614551471	21.992043006	64.9939082715	51.6888972959
15	1.4444407836	-0.943524620586	0.203150105414	6.85232473437	-3.05769688012	1.91844644085	0.0455495530257	0.112633534944	0.187663332163	0.00295106321625	-0.0372347528332	0.0566762326067	-0.115434249849	0.0183480993149	-0.00373481924388	0.261208308464	-0.00613145187064	0.0309486969533	0.300372895028	-0.0266137610165	0.276002385239	16.5888419208	50.4412899454	69.4883150775
16	1.92464984947	-1.91328435416	1.24658692922	6.15062647376	-4.48724222949	4.49005083874	0.0195652269504	0.223954062629	0.0818218877587	-0.340578128263	-0.183639509174	-0.370483603479	0.0353816511495	0.185658484205	0.212484060002	0.299992933409	-0.0122536341796	0.0798213853746	0.274014277202	-0.0313014249413	0.30525344633	20.4228488167	37.0276990005	63.6558592775
17	4.74133693408	1.127988583	-0.346908475939	7.77854674007	-0.836503274028	0.463412184743	-0.0907673562058	0.453988367704	0.0813295949093	-0.585888897867	0.0851816846679	-0.100557286886	0.158825094461	-0.159177583055	0.0166151655511	0.211007107331	0.00817047983087	0.00247083316563	0.265134788727	0.00557486237253	0.221703733297	3.71291817015	36.6909565353	62.9542625782
18	5.83679769537	0.826606032528	-0.0947634328183	7.66826644221	1.00109479718	6.35111928087	0.0272139914769	-0.170241657647	0.87654122953	0.217119068689	-0.135656382851	-0.0490109124649	-0.757791582741	0.170650533409	0.0727546098233	0.264479226996	0.0317224331113	-0.00642730779654	0.287445726556	0.00286772915645	0.292539740261	10.4559903951	61.0464872091	73.6584601232
19	6.38110583223	1.93204434149	-2.55284282756	7.99778596852	2.95855085755	6.71767721408	-0.0291588418429	0.620648733204	0.630624156492	-1.55423315571	0.0346669605985	-0.847181148465	-0.291152010122	0.06232886538	0.0448924436181	0.633033833023	0.0583378204448	0.204524388426	0.420470526219	0.108882445739	0.809585918295	45.0200409273	26.8570731131	84.6562721447
20	1.61739342457	0.231599143667	-0.0835564595169	8.01634663197	-0.191864628117	1.91665645257	-0.0700276489546	0.132203642764	0.0526908703769	-0.576869410429	0.0769476827063	-0.531619362277	0.322467003836	0.173484143761	0.00310643475308	0.323965140429	0.0366669311151	-0.021550757779	0.298598508841	0.0147208406328	0.4421928779	37.5041506002	17.2001381183	92.6088302669
21	0.870593485955	-0.772693337359	0.142070720756	3.844838531	-1.79782669948	1.16281411783	-0.0400447604851	-0.0340522843484	-0.0180450506705	-0.063251388626	-0.00748148294129	-0.340169569868	0.049015999647	0.0736271327086	0.0975914089228	0.184187118315	0.00711520249488	-0.0207287717343	0.258524071217	-0.0210911680668	0.302082258604	26.7366182303	44.1784805965	92.2406873343
22	1.28753341663	-0.390434027594	-0.0670201142009	5.35045976048	1.87218248746	2.43091068711	-0.0110018026973	-0.0607320954909	-0.103021766251	0.139662508185	0.0755684860877	-0.221525360318	0.202047086511	0.0667236782987	-0.0850708687162	0.182000253045	-0.00202191939214	-0.00356405067345	0.282091473885	0.039677578624	0.27055498345	17.0843297521	39.784433923	98.3205004524
23	4.61070173401	-2.68090198082	1.40634544873	8.10892452887	3.45680015972	8.56340424638	-0.107576236198	0.00654214883562	-0.317067393081	0.83825132013	0.200249629274	-0.302608821611	-0.025536526558	0.273434129046	-0.0826312410316	0.469307911358	-0.0867142158544	-0.163269850697	0.320895536202	0.0874550323104	0.399846407588	36.6176797018	62.2811580668	110.745855871
24	7.60258248344	-3.29187481322	3.90613803431	5.94613299293	1.13017950807	6.63497513257	-0.120679579033	-0.829020641978	-0.434393638196	1.08960763541	-0.0541877551205	0.529350145531	0.134603022094	-0.635624866241	0.196944945565	0.565921871136	-0.120142397442	-0.0468294153537	0.409891312833	0.0393773134668	0.529913392275	34.0632558952	62.1954041509	118.140176129
25	1.10391126469	-1.16920671798	0.735217194605	7.10983122444	-4.8673416371	7.93368665695	0.0663163001045	-0.322245349736	0.01116147002	0.437465387122	0.32572382806	0.43919925856	-0.372135191316	-0.5981353057	-0.334230172859	0.429891812394	-0.0362715772048	-0.0619204339644	0.349607962406	0.0211800086176	0.45892475832	30.9573796515	74.7473088968	109.173057375
26	1.6195259986	0.488348892576	-0.353230368855	8.60040768134	-0.840164529086	1.71287303763	0.00407846968879	0.0599733538079	0.0577601689361	0.0695142065092	0.0883315193474	-0.172672267853	-0.27142305909	0.137735549821	-0.0936741188403	0.346004477023	-0.0305216396849	-0.0971389915753	0.304055229819	0.0123846691745	0.403123585437	34.5031364612	68.2277999773	99.9172123472
27	6.74122213662	1.97029165503	3.18576764688	6.32230971184	2.24174615081	7.18423678296	-0.140418952037	0.196379123219	0.012690169731	-0.324389835906	0.238849209091	-0.6973704722	-0.502318353623	0.493459762044	-0.0386131237681	0.274400070821	-0.0555626118084	0.0106832553594	0.345457178115	-0.00927363305018	0.500900001692	40.4008589031	64.9379752225	96.5317267926
28	2.26234127976	3.91104855552	-0.664225674613	8.75460887362	-2.12112283828	1.10235035811	-0.00572445185329	-0.0358144251743	0.201785328839	0.0535220191872	-0.0337771090185	0.0366704896851	-0.103237250655	0.0596612493588	0.0241763188873	0.263441751065	0.0307191471162	-0.0294711377656	0.29596532278	-0.0152805378613	0.31517212605	21.7191184781	50.411279627	97.3483982252
29	5.35864970532	4.7587897938	-3.54217709729	6.91001948134	-4.55704596275	3.78174700108	-0.0309599651035	-0.0385456553261	-0.0725582625714	0.193986585415	-0.129763445941	-0.49765628766	-0.0911981525832	0.167869483565	0.195396509474	0.23024274177	0.0336862701808	-0.0777578977776	0.257376442315	-0.0372760609574	0.358265935073	28.1032790633	36.8762173642	99.4649574397
30	0.19864174328	1.00463865568	0.413781476509	5.81911523743	0.492295348798	4.63108387452	0.00208030093958	0.200968241446	-0.147325060794	-0.0832114892196	-0.0313253603584	-0.683072636937	-0.0285979587867	0.368487591077	0.0157068996868	0.220221556419	-0.000965319715463	-0.0147169582696	0.277694650185	0.0238143265349	0.342913043808	23.8937921105	36.7758245384	82.9429949232
31	4.95323181892	1.16763256701	0.515741101076	6.82436784846	3.71704510659	8.08740923405	0.091434616624	-0.239279489095	0.815872722196	-0.0462238839586	-0.197367954596	0.272119095687	-0.874816920401	-0.216108030193	0.152514406383	0.235855768136	0.0152030643936	0.000221601164462	0.284052341885	0.018309301126	0.331780306891	15.87418657	60.9916255547	92.9692370384
32	4.82214769471	-1.65802692789	4.31850857729	2.93554634089	0.904153773656	8.43218261638	0.00260822345919	-0.037334586207	0.403068861732	0.527063641955	-0.157936811958	-1.69534820803	-0.245600342677	0.636489307494	0.0280349785178	0.612485585976	-0.0604658785955	-0.164478462793	0.409689169087	0.0843765369444	0.845476233009	16.0104338046	26.7391360256	128.934385206
33	1.73521764981	-0.166514391948	0.17500069364	5.27690679294	-0.42966915223	1.43957171308	0.0201017164522	-0.20819418471	-0.362507268288	0.45648538319	0.0198798330986	-0.433464155325	0.234233345771	0.0854621826198	-0.0553523708057	0.48994530312	-0.00858373177002	-0.0598070739935	0.328602424507	0.0543481377438	0.409555965235	5.2246008499	17.9692701001	123.793528007
34	1.26207712609	0.300461817611	0.0789304901983	1.63011080453	0.193831877319	0.573738655937	-0.0146353367994	-0.0643291443347	-0.111208448513	0.2463316377	0.0340691575637	-0.0135306232738	0.05500562259	-0.0332148591005	-0.00898615291698	0.278467391881	0.00832966294113	0.00688876743558	0.258489886932	0.0110063866167	0.21613087315	-0.97584221551	44.1146875065	110.285889046

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 22 )	A	A	1 - 22	1 - 22
2	2	chain 'A' and (resid 23 through 48 )	A	A	23 - 48	23 - 48
3	3	chain 'A' and (resid 49 through 110 )	A	A	49 - 110	49 - 110
4	4	chain 'A' and (resid 111 through 163 )	A	A	111 - 163	111 - 163
5	5	chain 'A' and (resid 164 through 218 )	A	A	164 - 218	164 - 218
6	6	chain 'A' and (resid 219 through 249 )	A	A	219 - 249	219 - 249
7	7	chain 'A' and (resid 250 through 273 )	A	A	250 - 273	250 - 273
8	8	chain 'B' and (resid -4 through 9 )	B	D	-4 - 9	1 - 14
9	9	chain 'B' and (resid 10 through 33 )	B	D	10 - 33	15 - 38
10	10	chain 'B' and (resid 34 through 48 )	B	D	34 - 48	39 - 53
11	11	chain 'B' and (resid 49 through 85 )	B	D	49 - 85	54 - 90
12	12	chain 'B' and (resid 86 through 110 )	B	D	86 - 110	91 - 115
13	13	chain 'B' and (resid 111 through 142 )	B	D	111 - 142	116 - 147
14	14	chain 'B' and (resid 143 through 163 )	B	D	143 - 163	148 - 168
15	15	chain 'B' and (resid 164 through 194 )	B	D	164 - 194	169 - 199
16	16	chain 'B' and (resid 195 through 219 )	B	D	195 - 219	200 - 224
17	17	chain 'B' and (resid 220 through 249 )	B	D	220 - 249	225 - 254
18	18	chain 'B' and (resid 250 through 273 )	B	D	250 - 273	255 - 278
19	19	chain 'C' and (resid 1 through 48 )	C	G	1 - 48	1 - 48
20	20	chain 'C' and (resid 49 through 163 )	C	G	49 - 163	49 - 163
21	21	chain 'C' and (resid 164 through 219 )	C	G	164 - 219	164 - 219
22	22	chain 'C' and (resid 220 through 273 )	C	G	220 - 273	220 - 273
23	23	chain 'D' and (resid -1 through 21 )	D	J	-1 - 21	1 - 23
24	24	chain 'D' and (resid 22 through 47 )	D	J	22 - 47	24 - 49
25	25	chain 'D' and (resid 48 through 110 )	D	J	48 - 110	50 - 112
26	26	chain 'D' and (resid 111 through 142 )	D	J	111 - 142	113 - 144
27	27	chain 'D' and (resid 143 through 163 )	D	J	143 - 163	145 - 165
28	28	chain 'D' and (resid 164 through 194 )	D	J	164 - 194	166 - 196
29	29	chain 'D' and (resid 195 through 219 )	D	J	195 - 219	197 - 221
30	30	chain 'D' and (resid 220 through 249 )	D	J	220 - 249	222 - 251
31	31	chain 'D' and (resid 250 through 273 )	D	J	250 - 273	252 - 275
32	32	chain 'E' and (resid 1 through 48 )	E	L	1 - 48	1 - 48
33	33	chain 'E' and (resid 49 through 176 )	E	L	49 - 176	49 - 176
34	34	chain 'E' and (resid 177 through 273 )	E	L	177 - 273	177 - 273

-
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