[English] 日本語

Yorodumi

- PDB-9sd3: Crystal structure of Methanocaldococcus infernus Malate dehydrogenase -

+
Open data

-
Basic information

Entry

Database: PDB / ID: 9sd3

Title

Crystal structure of Methanocaldococcus infernus Malate dehydrogenase

Components

Malate dehydrogenase (NADP(+))

Keywords

OXIDOREDUCTASE / Malate dehydrogenase / NADP binding domain

Function / homology

Function and homology information

malate dehydrogenase (NADP+) / L-malate dehydrogenase (NADP+) activity / L-lactate dehydrogenase (NAD+) activity / lactate metabolic process / tricarboxylic acid cycle
Similarity search - Function

Biological species

Methanocaldococcus infernus (archaea)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.2 Å

Authors

Coquille, S. / Madern, D.

Funding support

France, 2items

Citation

Journal: J.Mol.Biol. / Year: 2025
Title: Unraveling the link between thermal adaptation and latent allostery in malate dehydrogenase from Methanococcales.
Authors: Pereira, C.S. / Coquille, S. / Brochier-Armanet, C. / Sterpone, F. / Madern, D.

History

Deposition	Aug 12, 2025	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Nov 26, 2025	Provider: repository / Type: Initial release
Revision 1.1	Dec 3, 2025	Group: Database references / Category: citation / citation_author Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name

-
Structure visualization

Structure viewer	Molecule: MolmilJmol/JSmol

-
Downloads & links

-
Download

PDBx/mmCIF format	9sd3.cif.gz	1.7 MB	Display	PDBx/mmCIF format
PDB format	pdb9sd3.ent.gz	1.2 MB	Display	PDB format
PDBx/mmJSON format	9sd3.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/sd/9sd3 ftp://data.pdbj.org/pub/pdb/validation_reports/sd/9sd3	HTTPS FTP

-
Related structure data

Related structure data	9s3kC 9s3yC 9sa7C 9sc9C 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
Related items in Molecule of the Month	#102 - Jun 2008 Lactate Dehydrogenase similarity (8) #154 - Oct 2012 Citric Acid Cycle similarity (6) #142 - Oct 2011 PDB Pioneers similarity (8) #34 - Oct 2002 Dihydrofolate Reductase similarity (1) #57 - Sep 2004 Catalase similarity (1)

-
Assembly

Deposited unit

A: Malate dehydrogenase (NADP(+))

B: Malate dehydrogenase (NADP(+))

C: Malate dehydrogenase (NADP(+))

D: Malate dehydrogenase (NADP(+))

E: Malate dehydrogenase (NADP(+))

F: Malate dehydrogenase (NADP(+))

G: Malate dehydrogenase (NADP(+))

H: Malate dehydrogenase (NADP(+))

hetero molecules

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

A: Malate dehydrogenase (NADP(+))

B: Malate dehydrogenase (NADP(+))

C: Malate dehydrogenase (NADP(+))

D: Malate dehydrogenase (NADP(+))

hetero molecules

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

E: Malate dehydrogenase (NADP(+))

F: Malate dehydrogenase (NADP(+))

G: Malate dehydrogenase (NADP(+))

H: Malate dehydrogenase (NADP(+))

hetero molecules

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

Unit cell

Length a, b, c (Å)	208.180, 103.680, 177.400
Angle α, β, γ (deg.)	90.000, 123.970, 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	B-610- HOH

-
Components

-
Protein , 1 types, 8 molecules ABCDEFGH

#1: Protein	Malate dehydrogenase (NADP(+)) Mass: 34514.984 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanocaldococcus infernus (archaea) / Gene: Metin_1004 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: D5VSV9, malate dehydrogenase (NADP+)

-
Non-polymers , 5 types, 866 molecules

#2: Chemical	ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE Mass: 745.421 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₂₁H₃₀N₇O₁₇P₃
#3: Chemical	... ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 36 / Source method: obtained synthetically / Formula: C₂H₃O₂
#4: Chemical	ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL Mass: 118.174 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₆H₁₄O₂ / Comment: precipitant*YM
#5: Chemical	ChemComp-K / POTASSIUM ION Mass: 39.098 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: K
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 809 / Source method: isolated from a natural source / Formula: H₂O

-
Details

Has ligand of interest	N
Has protein modification	N

-
Experimental details

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.88 Å³/Da / Density % sol: 57.38 %
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.2M ammonium acetate, 0.1M Hepes pH 7.5, 43-48% Methylpentanediol (MPD) Cryo-protectant: 10% Glycerol

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.873128 Å
Detector	Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: May 13, 2023
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.873128 Å / Relative weight: 1
Reflection	Resolution: 2.2→80 Å / Num. obs: 151936 / % possible obs: 95.6 % / Redundancy: 2.9 % / B_iso Wilson estimate: 41.58 Å² / CC_1/2: 0.998 / R_merge(I) obs: 0.075 / R_rim(I) all: 0.09 / Net I/σ(I): 9.55
Reflection shell	Resolution: 2.2→2.26 Å / R_merge(I) obs: 0.742 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 11375 / CC_1/2: 0.67 / R_rim(I) all: 0.896

-
Processing

Software

Name	Version	Classification
PHENIX	1.21.2_5419+SVN	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.2→66.91 Å / SU ML: 0.3087 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.4555
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2175	7596	5 %
R_work	0.1836	144289	-
obs	0.1853	151885	95.77 %

Solvent computation

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

Displacement parameters

B_iso mean: 52.23 Å²

Refinement step

Cycle: LAST / Resolution: 2.2→66.91 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	19394	0	576	809	20779

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0031	20251
X-RAY DIFFRACTION	f_angle_d	0.5678	27307
X-RAY DIFFRACTION	f_chiral_restr	0.0441	3207
X-RAY DIFFRACTION	f_plane_restr	0.0039	3423
X-RAY DIFFRACTION	f_dihedral_angle_d	13.7923	7786

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.2-2.23	0.372	254	0.3756	4830	X-RAY DIFFRACTION	97.64
2.23-2.25	0.4067	258	0.3588	4906	X-RAY DIFFRACTION	97.27
2.25-2.28	0.3229	254	0.3098	4825	X-RAY DIFFRACTION	97.49
2.28-2.31	0.3579	259	0.3166	4916	X-RAY DIFFRACTION	97.73
2.31-2.34	0.3291	256	0.2914	4858	X-RAY DIFFRACTION	97.76
2.34-2.37	0.3326	259	0.2815	4905	X-RAY DIFFRACTION	97.54
2.37-2.4	0.3248	256	0.2836	4868	X-RAY DIFFRACTION	97.08
2.4-2.44	0.2913	253	0.2508	4805	X-RAY DIFFRACTION	96.93
2.44-2.48	0.2844	259	0.2418	4927	X-RAY DIFFRACTION	97.32
2.48-2.52	0.2799	256	0.2416	4857	X-RAY DIFFRACTION	97.58
2.52-2.56	0.2909	257	0.2315	4878	X-RAY DIFFRACTION	97.57
2.56-2.61	0.2708	254	0.225	4824	X-RAY DIFFRACTION	96.87
2.61-2.66	0.2469	257	0.2206	4875	X-RAY DIFFRACTION	96.81
2.66-2.71	0.27	254	0.2251	4840	X-RAY DIFFRACTION	96.77
2.71-2.77	0.2713	256	0.2315	4850	X-RAY DIFFRACTION	96.74
2.77-2.84	0.2805	256	0.2246	4865	X-RAY DIFFRACTION	96.77
2.84-2.91	0.2424	254	0.2027	4831	X-RAY DIFFRACTION	96.31
2.91-2.99	0.2655	252	0.1986	4793	X-RAY DIFFRACTION	96.11
2.99-3.07	0.2286	253	0.1867	4804	X-RAY DIFFRACTION	95.34
3.07-3.17	0.2253	252	0.1768	4785	X-RAY DIFFRACTION	95.63
3.17-3.29	0.2132	252	0.174	4780	X-RAY DIFFRACTION	95.25
3.29-3.42	0.2151	251	0.1664	4783	X-RAY DIFFRACTION	95
3.42-3.57	0.1904	250	0.1608	4738	X-RAY DIFFRACTION	94.61
3.57-3.76	0.1822	251	0.1485	4777	X-RAY DIFFRACTION	94.44
3.76-4	0.1725	249	0.1448	4732	X-RAY DIFFRACTION	93.84
4-4.31	0.1688	245	0.131	4653	X-RAY DIFFRACTION	92.8
4.31-4.74	0.1483	245	0.1255	4643	X-RAY DIFFRACTION	91.83
4.74-5.42	0.166	247	0.147	4703	X-RAY DIFFRACTION	92.99
5.42-6.83	0.2155	250	0.1925	4756	X-RAY DIFFRACTION	93.08
6.83-66.91	0.1765	247	0.1599	4682	X-RAY DIFFRACTION	90.39

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	0.605163834542	0.243797897796	0.0594540828675	0.00737699475342	0.383596900044	0.604293129507	-0.024878433533	-0.30539716714	0.000782022193198	-0.00884472237616	0.0159449963655	-0.00761384149551	-0.00995237394461	0.00244478055985	-7.87961707736E-6	0.378849913529	0.0605114365083	0.00424463618161	0.455827372906	0.000849739916202	0.355961211604	-15.3509614515	-8.04663076208	51.903347127
2	0.822854054573	-0.0596468594579	-0.369340067802	0.0544534018772	0.0389628941402	0.237258727785	-0.33058172955	-0.475656297358	-0.0467596964473	-0.238415606587	0.380947376666	0.263982508026	-0.142293501952	0.546487733979	0.0513215111126	0.441195027383	-0.047766509746	-0.0495321938397	0.442454016824	-0.0501858661198	0.370053238973	0.20506121694	1.24690842502	50.3839793613
3	1.25473021184	-0.028355063201	-0.0868526106631	0.350092289311	-0.081708032547	1.01686609748	0.0506706391053	-0.0437426496005	0.0711949255081	-0.0910083674138	-0.0174705879607	-0.0217793363906	-0.0716570032438	0.0967559512618	8.62039017027E-6	0.414707983957	0.0304053430919	0.00511045237433	0.263604773055	-0.00699680066467	0.337184402655	-11.2883499855	1.97380501259	31.3820833552
4	0.265061048791	0.0574032286292	-0.0256324132367	0.383988251163	0.00197411709089	0.0670185354637	0.0896958825428	-0.0357299930647	0.731118198234	-0.00523958104896	-0.0610281260242	-0.269162438054	-0.132259050811	0.392621027967	-5.8405539495E-5	0.592910804193	-0.0554862293193	0.0464379227248	0.44555251808	0.00901673652206	0.607865222717	2.77740537175	10.3841390323	32.6645280961
5	0.268624818705	0.0922294596798	-0.181112899231	0.0813889207727	0.0996345997069	0.250356493179	0.0837974901323	-0.069082794257	0.121619562201	-0.0729616344158	-0.0164614500519	-0.0037368540466	-0.149026381927	-0.0670577837027	1.09512665796E-5	0.477613254775	0.11426222204	0.00490892953599	0.443392114833	-0.0595762423525	0.394298333999	-32.9645474175	5.22772040579	42.3581387158
6	0.222820610536	0.31652657516	-0.312837944515	0.277566690385	-0.324861783859	0.233527713095	0.200794640426	0.345683529345	-0.0940421563015	-0.418013437214	-0.198984807689	0.1086037981	-0.252914843755	-0.43243931308	-2.31889048376E-5	0.453197406635	0.211841831009	-0.0440571371904	0.511214255549	-0.0661510193425	0.370438834999	-39.4723887888	8.5786283228	38.9337649952
7	-0.065793883519	0.0156533584258	0.0212747025542	0.0224942944104	0.0925903224614	0.0385952109525	0.334182849292	0.205809001571	-0.00450187482586	-0.0159287213133	0.100728332573	-0.311971296897	0.299198087334	0.0812117036813	0.00023474798074	0.367503773407	0.0513812508305	0.0093714258789	0.473853831823	-0.126327629275	0.447733985235	-38.5923436475	4.61280099181	61.1601456874
8	0.218539538002	0.327587993333	-0.160750987809	0.447160058579	-0.487296648898	0.536984650078	0.123180619556	0.0551906725993	0.211147237138	0.238738933911	-0.595603437929	0.246009859872	-0.575419637658	0.121659424125	-0.0604818222088	0.460085038223	0.107464769919	0.0224305638457	0.547257928057	-0.189394186978	0.444122215089	-47.7098647409	8.66610248029	57.3604156806
9	0.209390512663	0.14468572829	-0.329719556941	0.638447977768	-0.0561777643348	0.749678328073	-0.0323854324929	-0.332817796864	-0.0153618729893	0.0114586412138	-0.171524097097	0.0235289587547	0.0860960566345	-0.16234889753	-0.000362629637161	0.380007105	0.0379609107783	0.0277607442184	0.621613222362	-0.0236390655563	0.376532187035	-41.5591603824	-14.4550436644	56.0062715226
10	-0.00619417136098	-0.0342140498014	-0.0257593523646	0.242838787637	0.215874443977	0.115028108772	-0.0487889505555	-0.466389272612	-0.0224352833053	0.438860909293	0.202122388876	0.303732156617	-0.131087810496	-0.439090796649	-4.38407425243E-5	0.513835119014	0.0303710901114	0.00376742364021	0.752469654634	-0.000985968358603	0.411880361288	-30.8192163617	-12.1843359963	65.7505059974
11	0.330207286615	0.0708701271603	-0.560638702327	0.785871461051	0.160535710855	0.278529721357	0.0111619807635	-0.131251567194	0.039322523395	-0.0248243979191	-0.152949881157	0.105208335912	-0.00415864605843	-0.34596515058	-5.76496854116E-6	0.338030281759	0.0604950646126	0.010724335668	0.638449428067	-0.060693478906	0.408256084721	-47.6245622611	-11.7866222521	50.7031449795
12	0.0507969443166	-0.0971796106847	0.183082338498	0.1355805549	0.0810808102277	0.240899447876	-0.00703765920876	-0.695795755369	-0.0152671872266	0.236272918384	-0.0719116782676	0.260361377697	0.0195466077712	-0.265199392701	0.00314087982807	0.503203516416	0.0228259028263	0.143447824981	0.740296539543	-0.0643831063824	0.513929389886	-52.6252793917	-9.32269160231	67.4328979719
13	-0.00487783390901	-0.0331851668794	-0.0314616429835	0.0136124508485	-0.0511187870625	0.165291834014	0.0960523097159	-0.133674167866	-0.0375071662137	-0.144854950538	-0.020792765891	-0.0851701572877	0.170054051591	-0.232106671303	8.18167412039E-5	0.42367184494	0.0250287312291	0.00708824069951	0.249072701866	-0.00101502878314	0.435855242676	-24.4665349053	-32.0314705684	24.5228498995
14	0.247466545557	0.215405485638	0.0251873230079	0.280010236531	0.0960267693121	0.150820832847	-0.0402000252127	0.0605624827203	-0.0800493228426	-0.133117708596	-0.0129074614208	-0.0374883806481	0.017730494744	0.02294290151	-4.81925857653E-6	0.418565828441	0.0732040436874	0.0173884491343	0.37178551628	-0.00522106121807	0.387070039233	-21.0851954066	-28.6776731779	18.9717806986
15	0.357385198488	-0.487626705912	0.0909085262207	0.553677093032	-0.0481654453589	0.698068670868	0.0867606787321	-0.0426067371462	-0.101631027665	-0.0131985144063	-0.0629532068861	-0.038365218575	0.0373653701833	-0.0272615119703	9.88721351081E-6	0.412409929488	0.0542941806249	-0.00713253408483	0.363302424123	0.00880297203392	0.42242362363	-21.1563572443	-37.8091175751	22.9328393498
16	0.244841679015	-0.011988987953	0.343450648262	0.127722459786	-0.357968655353	1.39782226278	-0.177330282892	0.0213666148028	-0.280218002392	0.0290312688809	-0.0460766364748	0.0795852191948	0.536017971978	0.511970647458	-0.0347034548436	0.503824674553	0.0512204872451	0.0600871487207	0.28857301715	0.00112459100018	0.672094628838	-22.2056868982	-50.510054158	26.7731082625
17	0.0921520286196	-0.128588645221	-0.0742636288793	0.155661956202	0.113013941026	0.124895969478	-0.0131062848521	0.169151384324	0.040257718477	0.337560146865	0.102623844832	0.109496023469	0.197362099816	0.0424211191043	-5.48877151507E-5	0.47763492739	0.0105935932485	0.0306035239307	0.330867150274	0.0588018484584	0.569272920886	-22.9575994301	-45.7659006185	33.8821488357
18	0.0146131080211	0.0144674100986	0.0694064054526	0.31684543377	0.0284940928676	0.386414828678	-0.146635304888	-0.216694552628	-0.285230392418	0.208106579129	0.0377742394026	0.190062820881	0.117370978237	-0.0214099921103	3.16475045074E-5	0.441121327817	0.00955198472375	0.0405095042876	0.485775613818	0.0493190350541	0.474614938433	-34.9140879688	-36.8883425274	38.3892312248
19	0.072472722622	-0.109671528325	0.183253182201	0.0844338207131	-0.0963353391249	0.263057244461	0.146533737852	-0.109242804954	-0.108648581731	-0.0730505278564	-0.249780934112	0.196612846946	-0.146213476138	-0.25986942608	4.83214820019E-6	0.41948946116	-0.0448655126421	0.0768849940189	0.488282953108	0.0240225106791	0.52956288152	-45.874569652	-33.4645254189	44.901130777
20	0.852479770647	-0.664697019869	-0.796562612341	0.693394031315	-0.248127719953	0.748525947992	-0.144465407957	-0.235677089521	-0.243494982873	0.170145692127	-0.00286558034336	0.18799073825	0.0134945938652	-0.0655627197949	-0.000157348263817	0.403846071377	0.00155140763939	0.0435980613244	0.376066910493	0.0784360106617	0.480757913096	-33.2469686557	-38.3826513795	39.6848495619
21	0.155868940495	0.0740316417837	-0.00393096451598	0.320231601756	-0.0322121623185	0.0427402742485	0.406260582211	-0.100184851252	-0.343236007781	0.281907754586	-0.132270493934	0.126432792466	0.14545636158	-0.279779629632	-3.47691136131E-5	0.702220738526	-0.0815880598659	0.111834821399	0.464266229032	0.105940588816	0.808945991197	-34.7173769808	-54.2110493752	41.9320867203
22	0.751624336843	0.171469989995	0.270582574643	1.24104746238	-0.162528941596	0.296334424948	0.0679886938309	-0.198745332942	-0.0150237572835	-0.03078730414	-0.106281831026	0.220161130106	0.0640156179261	-0.324475014283	1.08775435118E-5	0.369373561539	0.0664758131257	-0.0415203889094	0.505285316432	-0.0797606910564	0.47791096513	-46.2233770656	-23.1577634005	21.6081617522
23	0.0687354654273	0.215279751651	-0.192369559167	0.225395019368	-0.250376555885	0.220635550188	-0.130439486731	0.250157782656	-0.25272452247	-0.0826407845558	0.078165815707	0.265773948544	0.271907282975	0.340991601322	-1.05304856145E-5	0.47477624982	0.108496725389	-0.119964338651	0.660929929928	-0.118991045908	0.545849004858	-44.8679255284	-19.211066025	2.16208515858
24	0.625028693329	0.229286682178	-0.435308988785	0.464823947228	0.044632891377	0.709482452939	0.0368906643184	0.0817846858172	0.0281468343722	-0.162694652781	-0.0970618645673	0.0737780861338	-0.147921587404	-0.0928788365657	7.31273581694E-6	0.441997296676	0.072401841022	-0.0476132043047	0.381943966682	-0.00663307284197	0.363890655456	-28.3207809961	-10.6937075001	10.6172214706
25	0.429769121352	-0.282203904109	-0.0503730777462	0.395503223146	-0.129121591067	0.270874807057	0.0955801021003	0.39013368333	0.225651563783	-0.224695487722	-0.116410611604	0.154329211036	-0.558772199664	-0.234032040012	-1.53146980497E-5	0.652446047805	0.086541744493	-0.0731758602948	0.539858140969	0.063008658752	0.465138286572	-33.9884532441	-1.6734139229	1.42787102992
26	0.82819052728	0.329235140289	0.045713781497	0.250264317442	-0.0914614383663	0.266305759842	-0.0639571135395	-0.247343455665	-0.0793925401123	0.130675800396	-0.022737494468	-0.123642735569	0.0655782161221	0.112675344941	8.11121815746E-6	0.383379833368	0.0792213011032	-0.0555083363215	0.577381721648	0.0620134862082	0.38587684924	34.785125443	-33.6986389231	64.0581004076
27	-0.00309291768979	0.0214719249336	-0.0378608616579	0.0634191693617	-0.106194773448	0.070756492355	0.0122689910283	-0.360444522209	-0.260478863431	0.124781520623	-0.326504632699	-0.291724342039	-0.085823175292	0.338434205166	-0.0168799374614	0.465499520084	-0.0471430642147	-0.141927463119	0.824591541969	0.0272380289101	0.497679934077	47.0269916616	-21.1518958245	69.1272792569
28	0.483084048399	-0.157086034344	-0.110702161535	0.687991063761	-0.656384742186	0.601561920174	0.00915641430689	0.0161467432657	0.0931170407482	0.0455988609985	-0.0619957267628	-0.185516935406	-0.0987964166026	0.289154438963	-1.4861477514E-5	0.39098316309	-0.00293639372632	-0.0687244241161	0.523981972623	0.00843581359739	0.475855398783	33.4803567511	-12.5387056322	51.2669348193
29	0.77660197356	-0.113113331463	0.23404894793	0.9997848211	-0.20153423313	0.388427277282	-0.173821712118	8.12632154607E-5	0.0345176513234	0.0414301907605	-0.0506568973734	-0.307295238528	0.0114189258841	0.30982674227	-3.94542728305E-5	0.357409530007	-0.0153575020995	-0.068517324146	0.558973489199	0.0539662936602	0.492379957588	38.4479224756	-17.580240963	51.2050641732
30	0.196129215967	0.00113050821704	-0.278957141506	0.146348261301	0.0781515471478	0.421810742247	-0.00914791873262	-0.387573402091	0.527615303719	-0.16083207276	-0.323356393576	-0.228653418501	-0.0722447437048	0.73306432131	-0.0106526458228	0.623237721697	-0.159300611652	-0.268929347488	0.688253192396	0.0807590514851	0.967424159264	46.2638047017	-4.30712845197	58.0381047099
31	0.315153562818	-0.0566038697379	-0.199638380712	0.954116879737	0.446669919842	0.228931655418	-0.0382720225003	-0.0483038692641	0.0194977283869	0.05062531375	0.0867929029074	0.0366108251931	-0.00991151771878	-0.136306414692	2.49271295633E-5	0.417045212892	0.0781951549856	-0.00727992290279	0.545904779171	0.0465113722288	0.369598794511	11.6416395019	-22.4062261026	58.4453320107
32	0.0162055147891	0.0179985187022	0.00531583528372	-0.016460262385	0.0340939879339	0.0658614441385	-0.0462163634958	-0.228633704405	-0.340424383808	0.179704014526	0.0608199233058	-0.0550457321746	0.225409271356	0.0274940269287	3.95787596322E-5	0.484012471216	0.083865582291	0.00585666041499	0.695635719453	0.16830493361	0.370933236822	8.56363535841	-33.5338451393	74.6251846644
33	0.861673327159	0.5558383039	0.783914961611	0.396976346625	0.290780024027	0.930557093228	-0.189660512205	-0.450331692006	0.0444836528964	0.750035108534	0.0636685718911	0.22140098777	-0.600863166849	-0.206022229959	-0.29866993244	0.53798738913	0.142030143103	0.0974902565846	0.867103779045	0.18362270339	0.375227817879	-0.963913249846	-32.1427514078	72.0850007138
34	0.00670833298413	0.0509616495408	-0.0221832258454	0.399152385743	0.0174476764111	-0.0150687203546	-0.0340352963133	-0.33618930367	-0.211675327109	0.0943919434087	0.0622678584535	0.178706951387	0.13305361287	-0.226971112484	2.21030612419E-5	0.436544777946	0.0855093400673	0.0428386321095	0.575223897505	0.166105726451	0.449083325908	6.28678623408	-41.7955861383	62.5139068771
35	0.0852382756837	0.15555108362	0.0415901130251	0.993759058419	-0.531709791599	0.313160708804	-0.0547718093306	-0.40620929033	-0.232252068016	-0.0282105220409	0.140465177643	0.00569480936565	0.0877940186359	0.114572959367	-3.04922728826E-6	0.452783017378	0.0840451633718	0.00518639915321	0.604427988269	0.189949161972	0.49104472529	19.774568234	-54.0877594201	62.7990212123
36	0.622766370301	-0.41473699849	-0.568368785894	0.969760291956	0.128824506405	0.666949906799	-0.207013590743	-0.185625294782	-0.214421389093	0.0252906839085	0.114458896276	0.114021137794	0.132831266739	-0.127211949415	-0.00254253060896	0.371527164164	0.0305499783868	0.0521979445444	0.485152989313	0.156642295442	0.416344880322	3.47622255739	-47.5454441823	61.4159570981
37	0.00564276870858	-0.0422932780785	-0.0373314548624	0.0873481579608	0.0514519783149	0.0471873052081	0.151204301404	0.0944852770713	-0.0779213034938	-0.284838337143	0.126162983992	0.239845648645	0.0210699284027	0.489709547325	6.21213451221E-6	0.420756666686	0.0694248059455	-0.00526562778711	0.429632889461	-0.0447979779966	0.426007785706	32.8138408015	-43.0524220293	27.2770481904
38	0.219957986601	-0.206359602727	0.0758740828257	0.156461635552	-0.0674128822446	0.0970613462388	-0.00203443161528	0.227623664144	0.0848316559104	-0.0082561617398	-0.0711657168221	-0.216696854156	-0.0332870505478	0.260093549824	6.49416312716E-6	0.407806311834	0.0584458964109	0.0407880903869	0.469695034717	0.0172715947378	0.404826975222	34.9524513684	-36.6576397622	24.4069891618
39	0.213308799873	0.0827221875658	0.18335950199	0.208707978843	-0.00532888188259	0.218677182781	0.104478839952	-0.0159049877472	0.149439748708	-0.0544684067226	0.0894433797592	-0.176021820713	-0.135742058933	0.237833971909	4.70691916976E-5	0.360991375725	0.0626214910243	0.0232951490161	0.593180819466	0.00532490610857	0.493499241487	42.0340676635	-39.3946959924	27.0557428735
40	0.0429070333489	-0.0308436697333	-0.0801498043257	0.0920212426213	-0.0864317207435	0.34886020356	0.104341540759	0.240898529249	-0.150921935314	-0.500890220045	-0.0867385592377	0.304560642613	-0.424066356293	-0.213256485058	0.0213978239985	0.490304211814	0.150575629753	-0.157743741272	0.709628925871	-0.138785371733	0.587539216398	30.8536741695	-56.758461006	18.3590445684
41	-0.0335154005625	-0.00628974024354	0.0988223749311	0.125179029806	-0.127211036852	0.158091582103	0.39004063521	-0.443099062263	-0.397983791518	-0.14095927342	-0.303391634017	-0.174158585751	0.360178818581	-0.172886871638	-3.51665731661E-6	0.551729108651	0.143428684971	-0.0343787110155	0.533665261264	-0.0853155118258	0.537162044014	40.509179462	-58.8093708018	20.8087433216
42	0.1117458606	-0.13699090436	-0.167933549697	0.186597196448	0.00275612079734	0.0324147729803	0.208473743758	0.0804685355258	-0.0989033051462	0.0709836434138	0.00892260846702	-0.0371180263472	0.154990967794	0.129960545465	1.49457504303E-5	0.441332653412	0.147217760775	-0.0736602276102	0.459753730899	-0.123605997043	0.476922259182	38.5813943905	-58.6272356028	28.9521903671
43	0.258616430698	0.188320781994	0.11886837939	0.780306262233	-0.514443097439	0.416562277176	0.0664001272211	-0.0266674427292	-0.258006636359	0.111896282669	0.0772113925651	0.221425778572	0.18114791631	0.0419209907785	5.38118892783E-6	0.47262907061	0.0198430594505	-0.0273642346225	0.376201292053	0.0191423071131	0.562258290817	17.9302002074	-58.7306037882	39.3535500673
44	0.0739204457973	-0.0516304319367	-0.109157961538	0.0629827700614	0.0526544822476	0.109806192492	0.233045412432	0.352958186037	-0.569675638819	-0.310021617878	-0.00720082796321	0.265602011054	0.261196778113	0.153038667379	0.0015225224905	0.436563603678	0.0650843890987	-0.0862762697402	0.362819623758	-0.0480494936176	0.61699979475	13.2650977243	-59.1742267715	25.8157683058
45	0.0618681682084	-0.0178404093018	-0.019203969004	0.0159818565463	-0.152885577449	0.369847832342	0.0486369722045	-0.017061698293	-0.0750496651759	0.0265361962884	0.00359128757973	0.152088393592	0.0484946099899	0.0905012344109	1.32924358369E-5	0.377105130188	0.0686159649098	-0.0525876223971	0.421631666713	-0.00579481952948	0.456058193734	29.538866702	-51.9256090144	37.1941529322
46	0.200889583834	-0.182780283296	-0.00247359784636	0.231270177385	0.16857311683	0.248528407021	-0.0376001724165	-0.305676014966	-0.0119433271134	0.170298469644	0.247197709632	0.015669710393	0.297717271731	0.428692747608	0.00631106480713	0.552254527156	0.130827561829	-0.0397456011407	0.445734911544	0.0501092598764	0.473923312396	32.6265171023	-64.4194421106	42.5482245285
47	0.138791801249	0.111473586306	0.0656054942374	0.382865814102	0.286301824188	0.15516228301	0.0788038309392	0.326043231157	-0.657686633795	-0.400531360796	-0.209133616442	0.113397197624	-0.0252051173588	-0.019546246754	-3.77118201169E-5	0.6526079265	0.0979648952844	-0.0585223809162	0.514361978074	-0.0766409446975	0.864350772655	29.7173824416	-72.9718724277	31.2677502113
48	0.441788066155	-0.614929777555	0.11622037058	1.45547877827	0.390155323259	0.425997718712	0.121715125959	-0.0494029729312	-0.110278915163	-0.0973368218278	-0.0583980067597	0.104758187799	-0.000399307894382	-0.18942550536	6.79135325277E-6	0.362554989182	0.0481008782229	-0.013575369035	0.368681052078	0.0131431536164	0.384520948732	9.30094632339	-40.1275406178	26.4612063892
49	0.122591935593	0.239466225868	0.077311450674	0.0513854880617	0.114593196218	0.033049936249	-0.00548913770931	0.116666442061	0.16407213609	-0.0199667225769	0.132964036596	0.0515606014178	0.14257679081	-0.0253539489825	2.58958049929E-5	0.408485598222	0.0999072772205	0.0685473302236	0.454380502968	0.0595676072612	0.346048492441	14.7686756244	-28.9729041132	10.6645289196
50	0.0490437864171	-0.0393028784347	0.094295025323	0.45919136459	0.030583059451	0.141756483197	-0.155075876125	0.210420097938	0.16656592479	-0.117718241393	0.130848182696	0.102755748462	0.138484272227	0.199281756806	-4.66681404404E-6	0.44854602376	0.0815649737258	0.0163998517072	0.437294832811	0.0100718079356	0.29623460929	5.41055013161	-25.828913109	11.5720136034
51	0.500842756197	0.232117631264	0.670201498754	0.876033497109	-0.0401216491445	0.299934378164	0.000150056939688	0.1657251831	-0.0305244066482	-0.0730213895802	-0.0418515767405	-0.0673390864267	-0.10504768647	0.0589828247963	-2.53887222462E-6	0.368914639634	0.0274349661865	0.0451964759038	0.42809153748	0.0358019780796	0.347784585512	20.0480381652	-18.8324583967	24.4758237633
52	0.424269450582	0.180952552172	0.30780855503	0.326188130683	-0.0408508280343	0.58848760531	0.163078788717	0.471617648532	-0.299322243353	-0.15093384213	-0.279544705665	-0.591117538933	0.184750659167	0.643665019743	-0.005171997428	0.503705178631	-0.0679285977641	0.060428223476	0.538709839852	0.264047966212	0.702552974903	38.4931966405	-12.851537074	24.512922617
53	0.30345845792	-0.431321382792	0.391354541769	0.476917723798	0.0216903794727	0.539041405391	0.0432917014238	0.0895758796941	0.0632188173852	-0.00616067503601	-0.0414023838352	-0.0248949489743	-0.00878053210877	0.170723493862	4.97221037413E-7	0.367293017362	0.0222481032391	0.0240285534738	0.405191738157	0.0202387310238	0.382751254816	19.5419386272	-24.6225792535	25.667285665
54	-0.0337966842048	0.0975106996417	0.118581465219	0.206545528472	0.0319276854993	0.222376039104	-0.118786370863	-0.172255812706	0.124784025034	0.0457767009068	0.0269328138451	0.169505344946	-0.0634180371123	0.00945112354024	-1.05897230622E-6	0.421917211155	0.0168338438636	0.0191822265779	0.343637463696	0.036393031097	0.393153950337	13.3056433827	-9.70801831354	27.4102242446
55	0.144428662928	0.258624722331	-0.17073923323	0.169163720963	-0.00227298833249	0.166425975499	0.171050104632	0.4466929916	0.532016655479	-0.253498836164	-0.238090542214	0.194189099545	-0.224169560948	0.0181408050441	-2.53473800555E-5	0.511554288699	0.0144561404139	0.00803821726625	0.544306268007	0.117980238204	0.475451557131	15.5612849301	-8.79379914943	12.7720297338

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 91 )	A	A	1 - 91	1 - 91
2	2	chain 'A' and (resid 92 through 113 )	A	A	92 - 113	92 - 113
3	3	chain 'A' and (resid 114 through 288 )	A	A	114 - 288	114 - 288
4	4	chain 'A' and (resid 289 through 312 )	A	A	289 - 312	289 - 312
5	5	chain 'B' and (resid 1 through 55 )	B	B	1 - 55	1 - 55
6	6	chain 'B' and (resid 56 through 76 )	B	B	56 - 76	56 - 76
7	7	chain 'B' and (resid 77 through 91 )	B	B	77 - 91	77 - 91
8	8	chain 'B' and (resid 92 through 113 )	B	B	92 - 113	92 - 113
9	9	chain 'B' and (resid 114 through 206 )	B	B	114 - 206	114 - 206
10	10	chain 'B' and (resid 207 through 225 )	B	B	207 - 225	207 - 225
11	11	chain 'B' and (resid 226 through 288 )	B	B	226 - 288	226 - 288
12	12	chain 'B' and (resid 289 through 312 )	B	B	289 - 312	289 - 312
13	13	chain 'C' and (resid 1 through 21 )	C	C	1 - 21	1 - 21
14	14	chain 'C' and (resid 22 through 55 )	C	C	22 - 55	22 - 55
15	15	chain 'C' and (resid 56 through 91 )	C	C	56 - 91	56 - 91
16	16	chain 'C' and (resid 92 through 113 )	C	C	92 - 113	92 - 113
17	17	chain 'C' and (resid 114 through 136 )	C	C	114 - 136	114 - 136
18	18	chain 'C' and (resid 137 through 163 )	C	C	137 - 163	137 - 163
19	19	chain 'C' and (resid 164 through 206 )	C	C	164 - 206	164 - 206
20	20	chain 'C' and (resid 207 through 288 )	C	C	207 - 288	207 - 288
21	21	chain 'C' and (resid 289 through 312 )	C	C	289 - 312	289 - 312
22	22	chain 'D' and (resid 1 through 76 )	D	D	1 - 76	1 - 76
23	23	chain 'D' and (resid 77 through 113 )	D	D	77 - 113	77 - 113
24	24	chain 'D' and (resid 114 through 258 )	D	D	114 - 258	114 - 258
25	25	chain 'D' and (resid 259 through 312 )	D	D	259 - 312	259 - 312
26	26	chain 'E' and (resid 1 through 91 )	E	E	1 - 91	1 - 91
27	27	chain 'E' and (resid 92 through 113 )	E	E	92 - 113	92 - 113
28	28	chain 'E' and (resid 114 through 215 )	E	E	114 - 215	114 - 215
29	29	chain 'E' and (resid 216 through 288 )	E	E	216 - 288	216 - 288
30	30	chain 'E' and (resid 289 through 312 )	E	E	289 - 312	289 - 312
31	31	chain 'F' and (resid 1 through 76 )	F	F	1 - 76	1 - 76
32	32	chain 'F' and (resid 77 through 91 )	F	F	77 - 91	77 - 91
33	33	chain 'F' and (resid 92 through 113 )	F	F	92 - 113	92 - 113
34	34	chain 'F' and (resid 114 through 163 )	F	F	114 - 163	114 - 163
35	35	chain 'F' and (resid 164 through 225 )	F	F	164 - 225	164 - 225
36	36	chain 'F' and (resid 226 through 312 )	F	F	226 - 312	226 - 312
37	37	chain 'G' and (resid 1 through 21 )	G	G	1 - 21	1 - 21
38	38	chain 'G' and (resid 22 through 55 )	G	G	22 - 55	22 - 55
39	39	chain 'G' and (resid 56 through 76 )	G	G	56 - 76	56 - 76
40	40	chain 'G' and (resid 77 through 91 )	G	G	77 - 91	77 - 91
41	41	chain 'G' and (resid 92 through 113 )	G	G	92 - 113	92 - 113
42	42	chain 'G' and (resid 114 through 136 )	G	G	114 - 136	114 - 136
43	43	chain 'G' and (resid 137 through 206 )	G	G	137 - 206	137 - 206
44	44	chain 'G' and (resid 207 through 225 )	G	G	207 - 225	207 - 225
45	45	chain 'G' and (resid 226 through 258 )	G	G	226 - 258	226 - 258
46	46	chain 'G' and (resid 259 through 288 )	G	G	259 - 288	259 - 288
47	47	chain 'G' and (resid 289 through 312 )	G	G	289 - 312	289 - 312
48	48	chain 'H' and (resid 1 through 76 )	H	H	1 - 76	1 - 76
49	49	chain 'H' and (resid 77 through 91 )	H	H	77 - 91	77 - 91
50	50	chain 'H' and (resid 92 through 113 )	H	H	92 - 113	92 - 113
51	51	chain 'H' and (resid 114 through 195 )	H	H	114 - 195	114 - 195
52	52	chain 'H' and (resid 196 through 215 )	H	H	196 - 215	196 - 215
53	53	chain 'H' and (resid 216 through 258 )	H	H	216 - 258	216 - 258
54	54	chain 'H' and (resid 259 through 288 )	H	H	259 - 288	259 - 288
55	55	chain 'H' and (resid 289 through 312 )	H	H	289 - 312	289 - 312

+
About Yorodumi

-
News

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

New format data for meta-information of EMDB entries

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

Related info.:EMDB header

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

-
Aug 12, 2020. Covid-19 info

Covid-19 info

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

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

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

+
Mar 5, 2020. Novel coronavirus structure data

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

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

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

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

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Protein , 1 types, 8 molecules ABCDEFGH

-
Non-polymers , 5 types, 866 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, 8 molecules ABCDEFGH

-Non-polymers , 5 types, 866 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, 8 molecules ABCDEFGH

-
Non-polymers , 5 types, 866 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