[English] 日本語
Yorodumi
- PDB-8cp4: [4Fe-4S] cluster containing LarE in complex with AMP -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8cp4
Title[4Fe-4S] cluster containing LarE in complex with AMP
ComponentsNAD_synthase domain-containing protein
KeywordsTRANSFERASE / LAR / SULFUR TRANSFERASE / LARE / AMP / 4FE-4S / THIOLATION / [FE-S] CLUSTER / IRON-SULFUR CLUSTER / PP-LOOP / ATP PYROPHOSPHATASE / LACTATE / LACTATE RACEMIZATION
Function / homologyPyridinium-3,5-bisthiocarboxylic acid mononucleotide synthase LarE / sulfurtransferase activity / NAD/GMP synthase / NAD synthase / Rossmann-like alpha/beta/alpha sandwich fold / ADENOSINE MONOPHOSPHATE / IRON/SULFUR CLUSTER / NAD/GMP synthase domain-containing protein
Function and homology information
Biological speciesMethanococcus maripaludis (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.19 Å
AuthorsZecchin, P. / Pecqueur, L. / Golinelli-Pimpaneau, B.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research AgencyANR-11-LABX-0011 France
CitationJournal: Protein Sci. / Year: 2024
Title: Structure-based insights into the mechanism of [4Fe-4S]-dependent sulfur insertase LarE.
Authors: Zecchin, P. / Pecqueur, L. / Oltmanns, J. / Velours, C. / Schunemann, V. / Fontecave, M. / Golinelli-Pimpaneau, B.
History
DepositionMar 1, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 31, 2024Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Database references / Refinement description / Category: citation / struct_ncs_dom_lim
Item: _citation.journal_volume / _citation.year ..._citation.journal_volume / _citation.year / _struct_ncs_dom_lim.beg_auth_asym_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_auth_seq_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_asym_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_auth_seq_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: NAD_synthase domain-containing protein
B: NAD_synthase domain-containing protein
C: NAD_synthase domain-containing protein
D: NAD_synthase domain-containing protein
E: NAD_synthase domain-containing protein
F: NAD_synthase domain-containing protein
G: NAD_synthase domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)221,33226
Polymers218,1337
Non-polymers3,19919
Water724
1
A: NAD_synthase domain-containing protein
hetero molecules

A: NAD_synthase domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,86310
Polymers62,3242
Non-polymers1,5408
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation1
2
B: NAD_synthase domain-containing protein
D: NAD_synthase domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,1698
Polymers62,3242
Non-polymers8456
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: NAD_synthase domain-containing protein
E: NAD_synthase domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,1337
Polymers62,3242
Non-polymers8105
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
F: NAD_synthase domain-containing protein
G: NAD_synthase domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,0986
Polymers62,3242
Non-polymers7744
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)186.170, 212.690, 196.740
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 16 through 19 or (resid 20...
d_2ens_1(chain "B" and (resid 16 through 140 or (resid 141...
d_3ens_1(chain "C" and (resid 16 through 19 or (resid 20...
d_4ens_1(chain "D" and (resid 16 through 19 or (resid 20...
d_5ens_1(chain "E" and (resid 16 through 19 or (resid 20...
d_6ens_1(chain "F" and (resid 16 through 19 or (resid 20...
d_7ens_1(chain "G" and (resid 16 through 19 or (resid 20...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11GLYGLYGLYGLYAA7 - 25918 - 270
d_12SF4SF4SF4SF4AH301
d_21GLYGLYGLYGLYBB7 - 25918 - 270
d_22SF4SF4SF4SF4BL301
d_31GLYGLYGLYGLYCC7 - 25918 - 270
d_32SF4SF4SF4SF4CP301
d_41GLYGLYGLYGLYDD7 - 25918 - 270
d_42SF4SF4SF4SF4DS301
d_51GLYGLYGLYGLYEE7 - 25918 - 270
d_52SF4SF4SF4SF4EU301
d_61GLYGLYGLYGLYFF7 - 25918 - 270
d_62SF4SF4SF4SF4FW301
d_71GLYGLYGLYGLYGG7 - 25918 - 270
d_72SF4SF4SF4SF4GY301

NCS oper:
IDCodeMatrixVector
1given(0.975662095644, -0.203125240357, -0.0826051563341), (0.202341973317, 0.688799113522, 0.696141872785), (-0.0845056267765, -0.695913728806, 0.713135948541)9.63232580667, 57.7478990509, 33.5560060856
2given(0.910913683542, -0.214403796041, -0.352515635651), (0.309822853397, -0.208794988347, 0.927585280367), (-0.272481303301, -0.954167524643, -0.123767016072)-1.71666782253, 124.985760341, 6.5191783474
3given(-0.955828849485, -0.272128779967, 0.111072668131), (-0.258159904184, 0.596613202956, -0.759872456357), (0.140515744184, -0.754982525078, -0.640512851131)21.6081048138, -12.1419428814, -32.2126215986
4given(-0.894959005678, -0.261596982655, 0.361407521812), (-0.290128963249, -0.274140798609, -0.916881675693), (0.338930026466, -0.925426302416, 0.169447915172)35.2238253151, 35.7303060055, 20.0880712921
5given(0.866208333721, -0.107259913981, -0.488035278893), (0.128919987683, -0.895650564266, 0.425663838617), (-0.482765739637, -0.431631066517, -0.76199203608)-17.0275040337, 144.7665127, -59.1827729578
6given(-0.859206107908, -0.0878281049192, 0.50403480844), (-0.126942497922, -0.917755246013, -0.376312251512), (0.495631381527, -0.387313222602, 0.777391793913)31.4742455318, 105.582209048, 15.7067999632

-
Components

#1: Protein
NAD_synthase domain-containing protein / LarE / ATP-dependent sacrificial sulfur transferase LarE / NAD_synthase domain-containing protein


Mass: 31161.916 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanococcus maripaludis (archaea) / Gene: MMP1239,larE / Plasmid: PET15B / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6LXV7
#2: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C10H14N5O7P / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP*YM
#4: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 4.73 Å3/Da / Density % sol: 74.01 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 4.1 M NaCl, 0.1 M HEPES pH 7.5, 10 % Glycerol
Temp details: Crystallization under Anaerobic conditions (Jacomex Glove Box)

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.978565 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 10, 2020 / Details: U20
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978565 Å / Relative weight: 1
ReflectionResolution: 3.19→47.87 Å / Num. obs: 64718 / % possible obs: 99.6 % / Redundancy: 7.8 % / Biso Wilson estimate: 128.14 Å2 / CC1/2: 0.996 / Rrim(I) all: 0.163 / Net I/σ(I): 7.6
Reflection shell
Resolution (Å)Mean I/σ(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID% possible all
9.42-47.8725.2626690.9950.077198
6.72-9.4220.5245120.9970.0871100
5.51-6.7213.1157620.990.1411100
4.78-5.5111.4267530.9880.1591100
4.28-4.789.5776210.9860.1941100
3.91-4.286.1683850.970.31100
3.62-3.913.3690980.8950.5541100
3.39-3.621.6997520.7041.071100
3.19-3.390.77101660.3542.1198.2

-
Processing

Software
NameVersionClassification
MxCuBEDec, 2020data collection
XDSDec, 2020data reduction
XDSDec, 2020data scaling
PHENIXJan 31, 2020phasing
PHENIXJan 31, 2020model building
PHENIX1.20.1-4487refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.19→47.87 Å / SU ML: 0.5096 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.821
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2525 3230 5 %
Rwork0.2164 61363 -
obs0.2182 64593 99.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 140.55 Å2
Refinement stepCycle: LAST / Resolution: 3.19→47.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14441 0 90 4 14535
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013514747
X-RAY DIFFRACTIONf_angle_d1.463319866
X-RAY DIFFRACTIONf_chiral_restr0.10272280
X-RAY DIFFRACTIONf_plane_restr0.01112508
X-RAY DIFFRACTIONf_dihedral_angle_d5.7321919
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS1.19776922246
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS1.24088096227
ens_1d_4AX-RAY DIFFRACTIONTorsion NCS1.0072309169
ens_1d_5AX-RAY DIFFRACTIONTorsion NCS1.16396048401
ens_1d_6AX-RAY DIFFRACTIONTorsion NCS1.06361828998
ens_1d_7AX-RAY DIFFRACTIONTorsion NCS1.0785459414
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.19-3.240.41331280.42822392X-RAY DIFFRACTION90.88
3.24-3.290.43981410.41052671X-RAY DIFFRACTION99.75
3.29-3.350.38011390.36352649X-RAY DIFFRACTION99.96
3.35-3.40.34421390.33542628X-RAY DIFFRACTION99.93
3.4-3.460.34531400.31942667X-RAY DIFFRACTION99.96
3.46-3.530.33011390.31842650X-RAY DIFFRACTION100
3.53-3.60.37121400.32432656X-RAY DIFFRACTION99.96
3.6-3.680.3721410.32772665X-RAY DIFFRACTION100
3.68-3.770.38381390.30092641X-RAY DIFFRACTION99.96
3.77-3.860.3331410.282681X-RAY DIFFRACTION100
3.86-3.970.26711400.24132673X-RAY DIFFRACTION100
3.97-4.080.24941390.22822634X-RAY DIFFRACTION99.93
4.08-4.210.23811410.22272683X-RAY DIFFRACTION100
4.21-4.360.28931410.21782675X-RAY DIFFRACTION100
4.36-4.540.26831410.22062677X-RAY DIFFRACTION99.86
4.54-4.750.21731410.18522677X-RAY DIFFRACTION100
4.75-50.2321410.1912670X-RAY DIFFRACTION100
5-5.310.25491410.2012687X-RAY DIFFRACTION100
5.31-5.720.23821410.19342685X-RAY DIFFRACTION100
5.72-6.290.24681430.20932717X-RAY DIFFRACTION100
6.29-7.20.24891440.2142723X-RAY DIFFRACTION100
7.2-9.060.18871440.16482742X-RAY DIFFRACTION99.97
9.06-47.870.1961460.1682820X-RAY DIFFRACTION98.93
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
12.7246071908-0.1561362329781.226413181183.627633980140.4357878049982.463831353690.401264985445-0.229961147968-0.6250967387980.2627569520010.248864050321-0.4999261825050.5123408233870.801167548184-0.0001846841127791.30788735460.291950335714-0.2438696502741.44973775349-0.349665272391.3783029475739.225.318-44.409
20.833271859424-0.0179654211632-0.1310797992570.1332220223210.03174825044610.0226167764806-0.513196153172-0.5058716638220.6931132972470.4228942067610.862302185991.78233304603-1.07610582036-1.21680078927-0.01954617309881.510949107170.05301328769980.01105896721851.303619700170.008911136813071.8921851889217.17140.484-43.56
34.985809793660.321069315856-1.408781900141.026190672861.351409600061.698414089930.4679711860431.02601583347-0.0474606958788-0.1542142200420.128696461235-0.06762177944670.04756612618210.533369283515-0.01165160062131.370841725990.347839991986-0.2241109683621.64470706475-0.2529933856591.3614131820933.6428.978-51.163
44.94475417765-0.2237692358850.258087857380.9746430719570.5609898463333.490925424040.527165971059-0.742685823885-1.036942985940.6174627421160.396738095604-0.3123448349651.305794341950.2792334084750.007646728929891.76518597230.0854029751775-0.4456098116460.9364789515360.04472598206891.254461583037.3218.666-42.961
52.86237849241-1.008191582592.567889063124.09699495833-0.486727706122.254191211740.1025932350890.654286395732-0.2503871860590.5674421710230.2101785119-1.367132130450.1319383227450.3892088293230.0009009273411651.16934473253-0.0252371514667-0.09536752512021.28039587441-0.2527396197441.6392514654646.06152.317-18.703
60.435591010988-0.0563704760969-0.05036025258280.359899766186-0.3322446657250.20046887551-0.2645058478271.630984287140.697108072417-0.9689590293880.03598152224710.543301783454-0.619287676441-1.002612162390.001236206570641.37722290889-0.05322612231090.07614188695511.811780765140.2482323999131.5435210068222.0958.369-27.328
71.816550751751.027126029561.976690196612.19475367686-0.149158377081.99831087690.1557888827880.888316339877-0.273672661613-0.1867409586960.179580134713-0.7453748122370.2183258620470.5242672206180.01906441024021.23232455320.03100410908420.0762634716241.46167996657-0.2589305507461.4692904260240.5848.949-26.104
84.326655900631.291932819070.04971386234043.282992197920.1965606271314.39940446240.220909466474-1.17283590486-0.183907416211.037111351770.0761611920605-0.4768953398050.438798428144-0.1153514505-0.01882295129281.42789800206-0.193331653673-0.09733864788511.211237986630.04685009036950.93736545632216.92842.347-10.57
92.48877005880.6411437518471.0269890962.479924231631.751601884782.30840203726-0.404546485289-0.02814975280811.119432359950.393898310276-0.0437116288263-0.20874394459-0.6971496499950.7957148870860.002154191236861.41499778952-0.263614023365-0.4415434606121.278296204050.4219300201131.5388115567644.24390.514-21.961
100.3706437929740.2296937975940.4929156452840.2880183861660.2623348361340.541299220347-1.230012759461.92175286141.0170763696-1.35735499913-0.7448030681930.04458842544330.893250340996-1.751045226860.006365085790891.39138892698-0.315334170721-0.3670079565371.91393271787-0.05450544333861.9572229742620.86381.375-31.47
114.973820651461.45896518389-1.379575063333.521041293980.4356222815221.34050075102-0.6546801735530.3649277391930.264202925474-0.0474287763570.2228927577410.2064713259490.1329709555580.267624897855-0.01575165904271.28482749238-0.137861342593-0.2595900689991.239468198840.2650613833941.3434177656340.76281.533-24.131
123.068090942120.928135581787-1.879810582492.5878852272-0.7874894068911.35760638049-0.416555774673-0.934176400341.560144902210.66378684876-0.345356316931-0.200025554224-0.609864308381-0.1454543227310.00193371079451.536712695060.0557039720948-0.3677794263991.19165613543-0.2921911843241.5496464049516.64183.775-8.301
131.434781920061.43181923794-1.571635189913.77307789944-1.115085578474.03321936387-0.3954909257140.268664425252-0.1255359525030.03574202170220.4325894662550.1670263356410.507515524355-0.474904683512-0.0149433179961.27278825071-0.336790526304-0.02003319158951.735480099130.3949338211761.19058898038-25.02530.084-20.164
141.82409825667-0.195725938516-1.237760361251.95943053742-0.5500904648251.56321660991-0.284622246877-0.4537005854110.1610872704250.140090969390.4427875665250.300257705236-0.189043734489-0.419226777042-0.03526404702961.34581605565-0.3202688353890.02683950497591.867721291540.2995040619771.31873213872-24.1534.783-12.253
155.31702691967-1.315011154470.7133761563252.368765199620.537527689191.986457047830.365708610877-0.420204973969-0.7856118155590.52606569033-0.0869201217634-0.1850434869011.27542089709-0.5844101263280.005832439822621.50645757948-0.32241294019-0.1087190177371.066299583340.1933097253341.06791391144.20529.631-17.774
160.0456933539863-0.2016116474120.2772029458420.5778498757080.0822558852030.68931213553-0.80160533237-2.11259987804-0.1718208847761.132021861970.9542682239641.25207472611-0.7309913703750.5097978186480.0024569917171.740346725090.3010738374250.4632890560933.63954095260.006067556203981.66101416386-30.85263.0773.32
170.423356079151-0.6267222083750.0008374886304862.045934965791.793256473691.43048090256-0.02890250972180.531279561382-0.6841521297011.61565412558-0.2540831845040.0336596629187-0.286246734059-2.3557944905-0.00297448735471.679483921740.02272741627840.3146548552182.344165006590.1271703901211.26306123176-17.49154.8931.862
180.6916855311440.0970528148205-0.1349811628620.0187859477477-0.006416195301780.815629395661-0.788469317599-0.338467892130.883469794473-1.918695430960.791722468928-0.03978763539770.596392593303-0.5951884137990.008558044881521.35765845693-0.2679405420720.05161213748461.72728218914-0.2311586012031.51572253707-6.7859.693-18.953
190.7697901007660.3220717496520.9267513854380.0957857050426-0.02281077829251.12485464805-0.673193400141-1.110749848160.309071424148-1.069517808440.3765037110761.201847534020.500546434679-0.663542303851-0.007727074595321.4207689171-0.1859811320990.101985166721.929195783340.1788920903331.155761851-19.6657.125-13.478
202.57438045116-0.8230995579741.891077807270.735899391866-0.4537047067152.61430396378-0.867369443218-2.740665818321.193880214160.6068728067030.3390265203061.31641130498-0.386170242014-1.38734443667-0.0006222303586111.346323812370.3667972879970.104593190662.40257833415-0.4567136307911.7593860662-24.15268.328-6.448
21-0.02327980268190.0221438894543-0.01943049689280.716126488235-0.2193486966220.1029020221-0.0713416142810.8561990754140.2787639646291.23958067792-0.9155619681051.09224682903-1.28680039585-2.04741540897-0.1079669024932.098855101260.2992120616490.4034413235682.27289992906-0.4578998809881.62120198897-17.12467.5279.462
223.029495316340.8471832135041.895792308843.85617768357-0.7151799933212.13877993862-0.178707773769-1.213105877290.05978801515451.15704099178-0.160905132909-0.07344678952690.116730311544-0.0983759270853-0.03126584320831.442181856970.0129484057245-0.003641705310711.54260054545-0.1300357842831.061988542087.84767.618-1.92
231.996522021712.084098733331.715755783573.445885829990.4052627744253.18130379198-0.03664178439820.385153233870.921933765597-0.58419466759-0.1084305925220.624034544733-0.6378660409150.688879395010.0004486300836451.67055163654-0.570495305367-0.7190412011861.671118201570.8213778487182.0608413327135.714108.261-55.535
240.100672163997-0.122121729961-0.01699255869840.8147958406380.5295571099210.298793902017-2.38916289111.441680643180.595151633364-0.811933749506-0.2333345129120.7954182217310.0924072446223-1.189040168390.01669193809151.62558234035-0.491288342513-0.3375551241681.74711530280.2615667908912.0427923752514.87391.991-51.88
252.154291706691.67820240663-0.04689110689961.100126374780.3548994945620.149596153402-0.6419902602970.758832445324-0.1027975845970.435496225918-0.4483509166-0.259749266866-0.3727684319840.392675970386-0.01658902035481.70797999561-0.439860104903-0.685107745081.552829572470.8417314017972.0100768249832.31796.365-53.723
260.09120695759970.295231792710.1715141942391.082208489891.036593086651.34618654598-1.39459693740.6483558200320.7070475758730.72123538463-1.576950283931.014271964570.193878314140.106769620098-0.2641582208511.57462052367-0.192196730184-1.146541521.645381313041.060992994181.9395981329336.40896.778-45.555
270.2786621214060.305430958367-0.4527853655820.308033058255-0.3631950087420.400334576577-0.7213736315091.992166754821.52836045907-0.2051809962330.3676663048940.126589446353-0.5215989931080.7936291917880.02798849343071.74414120133-0.539997052458-0.5964176185741.838072229730.5288083615082.1313279292535.192114.929-44.408
280.975648569336-0.872180655141-1.421693964111.231917700021.100689118431.8180648718-0.5899373223240.3955458622120.77624081614-0.0911064962037-0.641673390669-0.743551464352-1.58854455947-0.06359337948280.03600337139212.02937803791-0.231866779505-1.181599690951.024891165940.2300584751792.1662325356610.198108.029-42.045
290.5912575158570.0242418563442-1.125164110180.0795595517403-0.6899887802582.9660650371-0.445476365169-0.03760512017061.195020052280.2868745893430.002972548232571.11690207906-1.458731750450.678463096834-0.05599461889452.01378764186-0.0135921627317-1.055844874080.796351432325-0.06930998857242.633600405436.014113.783-33.427
300.5331418705780.276379883706-0.4657752238460.201837813239-0.2756279931150.430064643545-0.791442230344-0.5340380716050.1247735519220.4846918622620.745646367066-0.192865259789-0.15842104528-0.1530065620760.0003181654349141.792761225570.710495055636-0.3940833305642.32798843042-1.0182620462.08140121847-36.395.844-11.704
310.281942187171-0.2128228271240.1897006518310.115970443556-0.04550157380881.41534894055-0.773864960663-0.505953907034-0.7673685473971.016136200250.204473822830.536260497903-1.903796259470.0124429182118-0.0365806457122.19436472641.13441319201-0.4844029200661.79850358952-0.5197327892541.93931932094-30.22397.311-8.709
320.945856275714-0.3495012111660.434257149851.39662770915-1.568127379551.383865518280.374602166432-0.3780166496890.6059199203141.62377971976-0.06103660177980.407207847053-1.566551704260.111922736131-0.000695161967382.058132368680.398989225078-0.2166563243812.07031641043-0.7865980362382.00665828766-18.76191.33-6.882
331.376744171530.8461341958470.6593246274280.9358659750250.2312008761050.27728226041-0.4758556657570.38570557789-0.5641184932340.159295625928-0.1216267772640.499664984214-0.389532624798-1.00613013316-0.002956094092121.490836669670.261367404181-0.1461167242471.5858037253-0.7112437966532.32473288307-16.63882.457-21.63
341.517285031380.136802805933-1.150997303170.7771004531290.162515460241.09095437647-0.378207590206-0.7706169705040.213424904890.2889652022350.1669206061140.546614031665-0.696620421514-0.07519770075330.004734077534931.89863510130.592844712659-0.4939075534582.08157774546-0.8016745159051.8860416279-29.46997.153-20.132
350.2368637189870.079332783931-0.420563082130.5618515581030.004103511741310.269883015283-0.71574908761-0.490515030767-0.1359459662590.860328311165-0.07299642730180.567293945876-0.780753887358-0.532438878477-0.004311846421891.709259905950.399214819789-0.4332858422341.89502489606-0.5116483044682.01784292886-11.22698.004-17.918
360.226978530849-0.01110848684670.136789682610.539711166031-0.08889396346450.251099768621-0.870776698861-0.8876107000170.8683667921140.000439373967941-0.2684727813881.26672065366-0.733075068609-0.62780012970.00829965155751.786015613680.226639661436-0.9023623640661.25099194921-0.5516936530332.2085360433-0.33101.478-17.503
371.44127003330.372030365487-0.850566094940.946379582872-1.685360234512.21759378318-0.662448190679-0.8377771079480.845373102055-0.03966818558310.04275565541090.536004622013-1.208821271320.819863822903-0.003657460441741.875922230440.0819208277064-0.9860492532191.0933357281-0.4417884635892.212120846764.79107.324-22.957
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 5:80 )A5 - 80
2X-RAY DIFFRACTION2( CHAIN A AND RESID 81:94 )A81 - 94
3X-RAY DIFFRACTION3( CHAIN A AND RESID 95:175 )A95 - 175
4X-RAY DIFFRACTION4( CHAIN A AND RESID 176:259 )A176 - 259
5X-RAY DIFFRACTION5( CHAIN B AND RESID 6:80 )B6 - 80
6X-RAY DIFFRACTION6( CHAIN B AND RESID 81:94 )B81 - 94
7X-RAY DIFFRACTION7( CHAIN B AND RESID 95:175 )B95 - 175
8X-RAY DIFFRACTION8( CHAIN B AND RESID 176:259 )B176 - 259
9X-RAY DIFFRACTION9( CHAIN C AND RESID 4:80 )C4 - 80
10X-RAY DIFFRACTION10( CHAIN C AND RESID 81:94 )C81 - 94
11X-RAY DIFFRACTION11( CHAIN C AND RESID 95:174 )C95 - 174
12X-RAY DIFFRACTION12( CHAIN C AND RESID 175:259 )C175 - 259
13X-RAY DIFFRACTION13( CHAIN D AND RESID -1:114 )D-1 - 114
14X-RAY DIFFRACTION14( CHAIN D AND RESID 115:174 )D115 - 174
15X-RAY DIFFRACTION15( CHAIN D AND RESID 175:259 )D175 - 259
16X-RAY DIFFRACTION16( CHAIN E AND RESID 7:31 )E7 - 31
17X-RAY DIFFRACTION17( CHAIN E AND RESID 32:80 )E32 - 80
18X-RAY DIFFRACTION18( CHAIN E AND RESID 81:94 )E81 - 94
19X-RAY DIFFRACTION19( CHAIN E AND RESID 95:114 )E95 - 114
20X-RAY DIFFRACTION20( CHAIN E AND RESID 115:153 )E115 - 153
21X-RAY DIFFRACTION21( CHAIN E AND RESID 154:174 )E154 - 174
22X-RAY DIFFRACTION22( CHAIN E AND RESID 175:259 )E175 - 259
23X-RAY DIFFRACTION23( CHAIN F AND RESID 7:80 )F7 - 80
24X-RAY DIFFRACTION24( CHAIN F AND RESID 81:94 )F81 - 94
25X-RAY DIFFRACTION25( CHAIN F AND RESID 95:129 )F95 - 129
26X-RAY DIFFRACTION26( CHAIN F AND RESID 130:153 )F130 - 153
27X-RAY DIFFRACTION27( CHAIN F AND RESID 154:174 )F154 - 174
28X-RAY DIFFRACTION28( CHAIN F AND RESID 175:221 )F175 - 221
29X-RAY DIFFRACTION29( CHAIN F AND RESID 222:259 )F222 - 259
30X-RAY DIFFRACTION30( CHAIN G AND RESID 7:31 )G7 - 31
31X-RAY DIFFRACTION31( CHAIN G AND RESID 32:44 )G32 - 44
32X-RAY DIFFRACTION32( CHAIN G AND RESID 45:80 )G45 - 80
33X-RAY DIFFRACTION33( CHAIN G AND RESID 81:114 )G81 - 114
34X-RAY DIFFRACTION34( CHAIN G AND RESID 115:164 )G115 - 164
35X-RAY DIFFRACTION35( CHAIN G AND RESID 165:185 )G165 - 185
36X-RAY DIFFRACTION36( CHAIN G AND RESID 186:214 )G186 - 214
37X-RAY DIFFRACTION37( CHAIN G AND RESID 215:259 )G215 - 259

+
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

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

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

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
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

Read more