[English] 日本語
Yorodumi
- PDB-9r2l: De novo designed N37 protein fold -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9r2l
TitleDe novo designed N37 protein fold
ComponentsN37
KeywordsDE NOVO PROTEIN / dark fold / de novo / unnatural
Function / homologyACETATE ION / ETHANOLAMINE / : / THIOCYANATE ION
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsPacesa, M. / Miao, Y. / Georgeon, S. / Schmidt, J. / Correia, B.E.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation Switzerland
Citation
Journal: To Be Published
Title: Reimagine accessibility of protein space with generative model
Authors: Miao, Y. / Pacesa, M. / Georgeon, S. / Schmidt, J. / Lu, T. / Huang, P. / Correia, B.E.
#1: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionApr 30, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 14, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: N37
B: N37
C: N37
D: N37
E: N37
F: N37
G: N37
H: N37
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,95828
Polymers137,8828
Non-polymers1,07520
Water9,242513
1
A: N37
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,4144
Polymers17,2351
Non-polymers1783
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: N37
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,5106
Polymers17,2351
Non-polymers2745
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: N37
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2932
Polymers17,2351
Non-polymers581
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: N37
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,3523
Polymers17,2351
Non-polymers1172
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: N37
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,3924
Polymers17,2351
Non-polymers1563
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: N37
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,3323
Polymers17,2351
Non-polymers972
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: N37
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,3323
Polymers17,2351
Non-polymers972
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: N37
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,3323
Polymers17,2351
Non-polymers972
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.760, 66.840, 81.120
Angle α, β, γ (deg.)78.814, 74.747, 62.558
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

-
Components

-
Protein , 1 types, 8 molecules ABCDEFGH

#1: Protein
N37


Mass: 17235.291 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)

-
Non-polymers , 5 types, 533 molecules

#2: Chemical ChemComp-ETA / ETHANOLAMINE


Type: L-peptide COOH carboxy terminus / Mass: 61.083 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H7NO
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical
ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: CNS
#5: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: K
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 513 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.11 Å3/Da / Density % sol: 41.58 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2 M Potassium thiocyanate 0.1 M Sodium acetate 5.5 25 % w/v PEG 2000 MME

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.87313 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Nov 14, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87313 Å / Relative weight: 1
ReflectionResolution: 2.199→77.98 Å / Num. obs: 56016 / % possible obs: 98 % / Redundancy: 4 % / Biso Wilson estimate: 32.53 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.137 / Net I/σ(I): 7.3
Reflection shellResolution: 2.199→2.237 Å / Redundancy: 4.1 % / Rmerge(I) obs: 1.042 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 2788 / CC1/2: 0.551 / % possible all: 97.2

-
Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
autoPROCdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→77.98 Å / SU ML: 0.3094 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 27.4944
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2318 2831 5.06 %
Rwork0.1991 53144 -
obs0.2009 55975 97.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.31 Å2
Refinement stepCycle: LAST / Resolution: 2.2→77.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8959 0 57 513 9529
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00199082
X-RAY DIFFRACTIONf_angle_d0.387312095
X-RAY DIFFRACTIONf_chiral_restr0.03751362
X-RAY DIFFRACTIONf_plane_restr0.00251516
X-RAY DIFFRACTIONf_dihedral_angle_d11.39723687
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.240.3431520.2912634X-RAY DIFFRACTION97.11
2.24-2.280.37551140.28622628X-RAY DIFFRACTION97.51
2.28-2.320.34261280.28082718X-RAY DIFFRACTION97.6
2.32-2.370.33181370.26372621X-RAY DIFFRACTION97.63
2.37-2.420.33031320.25432668X-RAY DIFFRACTION97.63
2.42-2.480.29871310.25592659X-RAY DIFFRACTION98
2.48-2.540.27061210.23832653X-RAY DIFFRACTION97.61
2.54-2.610.28261390.22392672X-RAY DIFFRACTION97.17
2.61-2.680.30411180.2312671X-RAY DIFFRACTION97.93
2.68-2.770.28021330.22522677X-RAY DIFFRACTION98.11
2.77-2.870.26581420.22732673X-RAY DIFFRACTION98.25
2.87-2.980.28921330.22632650X-RAY DIFFRACTION98.44
2.98-3.120.24511530.21482645X-RAY DIFFRACTION98.11
3.12-3.290.25291370.20152689X-RAY DIFFRACTION98.02
3.29-3.490.22061360.17572669X-RAY DIFFRACTION97.84
3.49-3.760.18341460.17732608X-RAY DIFFRACTION97.97
3.76-4.140.19381710.15972671X-RAY DIFFRACTION98.75
4.14-4.740.16861590.14742642X-RAY DIFFRACTION97.94
4.74-5.970.24641750.17622651X-RAY DIFFRACTION98.95
5.97-77.980.17031740.17942645X-RAY DIFFRACTION98.53
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)
10.0845021549725-0.168139120274-0.2009491811091.058634878850.09537234227790.5195703055920.05141978327560.462309779297-0.0240911483181-0.1531389600910.332669541028-0.2124346282460.03291481182140.6091233632628.64756560028E-50.295148988389-0.1011751715670.01746591015950.338555347543-0.06676247318570.273893898904-7.5467163534-5.808509696493.41499183325
21.69883074551-1.13700862380.02668751886381.213525927830.6997249905240.9039764790810.1443360048830.00355863516860.04335452775290.1752113874530.0674491236224-0.02604958650470.04050911033770.1656385238320.0002942420256890.358540637359-0.0627616732322-0.001409171175370.243183409468-0.02715335011810.332468608327-10.32108017130.3740681899326.04124982148
30.893690894021-0.711612943507-0.7230850726931.07682075275-0.3083334261561.035481198580.210090124303-0.01693058747070.157437161504-0.583284350116-0.00436885955056-0.247385124284-0.4867246626380.1590818108570.0001295325471090.4099374692110.0004920051642090.08558119155340.238984377667-0.009182376468940.3502837075111.025742739873.5212362779-13.3893082767
40.818157543747-0.161489738795-0.4149684044590.902849369049-1.187609059911.757756522120.235104366071-0.2193810923120.226346454571-0.01462049358520.164990877092-0.172679330055-0.2183084119940.2489720525420.002048706709050.18714640967-0.05605851607750.02808961105220.185165010448-0.01517876883090.251327503719-3.15022843465-0.220999160038-3.16822073666
50.4074009937380.068797268604-0.4351261563651.6875389152-0.4477075273030.5338508236320.0393850403126-0.2380150855220.08349453485110.0682564166941-0.1022594888850.8396043629770.1115655234940.442154575102-0.02253185776240.277160388263-0.00119219308721-0.002588334212930.391579799643-0.05087821969520.2428926906610.867959575438-8.73234518531.40495544337
60.182191684103-0.14618854595-0.2635218223681.67285676414-1.036159318261.784684699560.0859393687307-0.2457386509950.2958860416010.214969814545-0.111968660279-0.384894028983-0.3116756941071.083494867640.002648812215960.29453713338-0.1208863054140.002182936534320.479732943021-0.05560872120350.3637280266726.421113024650.2537579434560.148879925034
72.86096285116-0.805439217463-1.333076517721.59271133537-0.4114319468881.060767320890.01273620133550.132799632206-0.1489494470340.00716343453512-0.0578051934682-0.1272391307890.5386826407520.00566255044024-0.0002171887711260.225911835715-0.02215976877860.04306847230370.220913421150.01252571540350.260430596479-19.2663159062-32.88909277537.29802003134
81.24757685680.06582284451-0.5968163633760.1293397963580.45008942561.119695369940.219707496877-0.01555304661990.02895159946040.181514851806-0.02657953517970.215950523467-0.0456728033172-0.4054890173070.0001745821208350.362624230981-0.01484014588470.004622651637960.399175783109-0.03616451408480.292712293573-23.7828083519-28.42858069710.683598924778
90.274342088299-0.0812049176849-0.3292337019760.569751932529-0.3303053013711.87617770288-0.0904843776475-0.07794777602370.17724084602-0.0301313805310.24842400297-0.201733745429-0.3134446666980.1089793781134.65983949772E-50.316974637183-0.031743282418-0.0006809155543840.32352738868-0.07471044604260.354546230462-10.3644097247-25.3292993456-13.0693426672
100.913108649425-0.246915148342-0.2916834175910.296125743831-0.5854593663041.506954868860.2695564071340.1590291764150.19375696967-0.02528131686670.0419210025879-0.0829618128878-0.212450032644-0.1761513590089.4174635997E-50.2265496867120.01186236785820.02571072452890.232531599909-0.01119085187770.277155662985-14.8207731448-28.8438759829-2.58064214382
111.260952973990.1119977541621.017469073073.087897280271.167824595841.684113243450.543299604636-0.470594997395-0.1225848583670.546437064468-0.627148716651-0.2147416135260.686274509847-0.140420157137-0.04136745662330.390476920820.0696276281591-0.04486700522820.3164777788230.02164588296160.36889708715-10.8165204521-37.00663539242.46672103728
121.28486213104-0.172929186593-1.150365081110.8856411278951.150204296022.05872187337-0.016119330013-0.03412550355060.02294337657220.09219317328320.126976053169-0.219517990628-0.04116633359440.2358476944470.0001895478408270.2590034821060.0145881922781-0.0218561911340.367134594883-0.02702786560980.317500249235-5.76935597035-28.88917110711.10142633386
131.32395759040.491908513659-0.01322190273312.565664503681.62421957053.1749494584-0.0110424119385-0.1459762174210.4490873861580.6032815888680.09215351108220.6853619952530.68858535309-0.571728528088-0.1101183182710.3440043064420.0983037087411-0.08536288452460.3366720483710.07394761980030.365220890759-14.525428640611.7999947205-36.4299642921
142.60030103976-3.827363994971.473490031467.23160455139-1.281435719751.53145719466-0.00374483404778-0.612649648483-0.6234791237571.231146969720.7450964912021.84341624287-0.288276115723-0.915467353113-0.02182718749750.144782790129-0.06046319198030.1084173086780.312598880778-0.001978384695810.583704734834-15.84469969662.9958399205-28.5708083353
152.054762311020.04831278702210.596619977422.17778997939-1.673852332711.709945500160.196961906424-0.01481905966050.0430807117960.477013459408-0.1649899685730.1366014900880.195346571125-0.146874214756-0.003268626609860.293143245810.019698160954-0.0006656282974550.245686371944-0.01623761914220.314611458924-4.50211397933.9625330005-28.2461595725
163.227522247040.919413290722-1.580294090742.19142134309-1.847185707841.65327495540.1005387635740.2446577644220.187199206635-0.516095668049-0.192419789303-0.3002150598440.151082560817-0.254658434869-8.30765981816E-50.3366024691580.01601130868760.007415476441320.343528149644-0.02140401752330.335611892605-2.43616828238.04734353127-38.2459914825
170.3176017262710.431091159101-0.4719128324881.28003719383-0.7084357623980.593629856189-0.2442563740640.1370835200730.105990975167-0.42873294656-0.1519810003620.319456346252-0.846558773424-0.144272729289-0.001194224168920.262626833650.0994327315542-0.03568949447210.4764909988410.01943678505790.318682685886-27.2212834371-18.8915091756-36.6265839524
182.85343218307-0.7708449241520.0201950826181.54620138332-0.8785123682240.5773326095210.08718156238470.143414942753-0.229990297767-0.233587025597-0.075520301788-0.03164088146830.028072883374-0.893674023348-1.82047347943E-50.281875260950.00943077089901-0.008618846542810.411410655748-0.01529588548430.285395636433-31.1565643336-21.462572446-38.8805132817
190.6100497998790.271960033020.4786173971510.1290662632290.09689796798480.6797138526460.150765542173-0.22960358285-0.295371459451-0.2485467857960.1601632005040.03826647992570.345125922366-0.6584847675090.002623026375130.2748036378940.007620678543770.03150177255020.2834477569290.004430361998330.240864892084-30.9473138072-25.3937286599-29.8531314064
200.543867252625-1.051100543470.7497537117711.98057026846-1.350300444011.473135008040.1119592227020.134985318444-0.06061117692480.2129132389820.00717858807018-0.2299478740430.07068815757030.250397410856-0.0004201190492930.262289582424-0.009506925914490.007996140142020.287519103214-0.07612097750290.290176565983-12.7440841816-28.574784945-23.4503632123
211.009121086640.3020966975540.003972652600981.111410350210.988720673010.833016446690.186664519327-0.0377509869188-0.06423246572830.104575458291-0.112910720510.02758301532310.277756787941-0.2159905794830.0004607756593860.155856096009-0.0340367115037-0.02230331934820.2164081999930.01127645826690.22796014461-21.4482590565-24.8051575234-33.8797705648
220.248538135463-0.02870510389450.6141302278930.118648663201-0.03837896472871.53894849093-0.0247411391723-0.298227813120.0845161891837-0.4400996589730.123087462256-0.346230718484-0.276476851317-0.211367625002-0.0204218259310.457814634715-0.02061685906720.02304355167980.3113337691850.06323506553290.493711243994-18.1055131826-9.9739439353-31.2301467115
231.216208798340.3515972115330.8741794097680.4609145622970.5260802954940.72275009378-0.09691625935170.190360477667-0.467690973962-0.2201594582760.0788090977521-0.7114686511790.133622315578-0.07450163435950.0001408930740680.2710414986510.03459576173590.05580757132350.3588436044950.0008969763638430.347685736204-12.3410611555-25.1466182478-36.3280188748
240.964437561799-0.03692936321951.09604365777.025834307941.499525566091.63300970567-0.104920124680.2006788830010.48059434526-1.57613252679-0.00286350409851-1.32211151926-0.3523963582110.5320579484890.1813183782820.3523981958160.09854883659440.09592852922930.3393175787270.0371137091930.448549024424-18.869275045-23.7209631496-41.4083287271
250.5521047180670.016806496437-0.2842917892160.04924795145570.1939850201551.29447891555-0.187258630320.03415259955760.201657967151-0.116681973406-0.0418218468981-0.2912666218750.208452640561-0.794311737689-0.1749924061290.3930823668030.01275110969750.04904021933140.2560808965810.01438110442840.312034443506-22.67333944011.0180785552119.0027516721
261.707155521560.209603420875-1.41739265741.25536609012-0.4281924281471.17702282546-0.01801539696420.0910094317161-0.0670818306136-0.02310238695510.0626540783818-0.0730189852582-0.003441217249920.1751974166610.0001802361782290.3684265040260.03226390451840.04068101159390.207792391195-0.02451740755870.264193351235-16.45852694791.0331143802518.964831653
271.08214779744-0.654069693719-0.3287717742640.689280382587-0.6734332408362.08985524242-0.226902623037-0.214729356690.242197571846-0.09962047331730.178046680604-0.171117051993-0.3593496674430.15153884599-0.0002016373873470.406478722194-0.08213993613980.07045269364910.333837316264-0.03351068736340.351333103518-20.087462051512.55475379936.8693657749
281.3980102003-0.1472689524141.154203620181.740503644840.812567595691.349442866280.1242132067070.07471415689110.1435116230790.05143652252450.0752638778270.0584112324905-0.1296848735260.0384564090745-7.44595433721E-50.3016797745510.01932286040290.02186806347860.16643313072-0.02916239228870.277915620904-20.06265067877.0882656408226.6246867413
290.9534498016910.8174689921030.4061704892030.6488223849040.3960699209910.653472309937-0.127961965008-0.440028605855-0.0106435049995-0.577037009636-0.1317710192770.1304303830480.4607207719370.396838901926-0.006457620313280.3381587514380.02840514342250.0594520686470.418431731817-0.02773046175530.359542557241-28.876899684.4520201809221.8934125022
301.35544196803-0.4309453296090.3017037816311.1418395231-0.2599367588621.53516351606-0.00437109731369-0.1632747728770.8879445942750.2058593870980.0004427546183420.294444376506-0.432855751495-0.1920122334740.002831267476190.4449392833530.1271252513030.04222078390260.2837536440750.02469526998530.445300104411-25.659614206314.620381366823.3651840727
310.4139150479170.506916045720.1950058165620.5085201382930.2406982003360.206601167369-0.4026095701950.0241464033295-0.237930462047-0.4764275747110.2230504011410.1436919821280.598043480547-0.530684724918-1.34442023625E-50.38748070391-0.02038654131930.03613466602010.274749066085-0.0003360425100070.306958847048-35.4610250535-27.118805464817.9769160606
321.65910840297-0.458373617938-1.271364204430.3275714290150.5787622736031.10838948819-0.1079253329980.160765211759-0.1581495959820.01252376166670.0591741628043-0.04254463652080.3627121388750.1122544072980.001374891352380.296441323029-0.006621573205270.01173485691590.237204010785-0.006135362038150.240437586932-29.3601675148-27.190690312818.37227297
330.8224092805860.00490758722812-0.156544179241.100595864731.153717472121.113268732210.1458480663130.4408680361190.474340803548-0.07835621720320.103177445953-0.00416729416887-0.1495716673950.0804180932519-3.35813164566E-50.2331560866040.02279145956720.01795003249990.2777908720.0556819924530.235268714098-34.2730199173-15.696973451336.3129878179
340.1238187973880.23341510751-0.3980135945770.619571143433-0.4015929922391.171535620940.0240298086659-0.1216778200860.12912146392-0.0972275268560.0978402210495-0.03694279036750.1266468924220.009389599040550.0001042088373920.233458059866-0.007579969397170.02496872851720.281770665773-0.01114638634830.290524161173-33.3020394971-21.17845986726.0213270499
351.244417822670.474333771611-0.8633192766080.62155648438-0.4014244625493.20333397671-0.1081307692020.2233810536620.14487232586-0.1614381592260.06904285169420.299547882854-0.123227434749-0.3710304694853.08889004742E-50.221921123061-0.0289552398186-0.009207726960660.3470797528330.01715786006160.306394710288-40.8440888122-18.302180038622.8012596712
361.02610261766-0.163773855917-0.03244803029950.6435129285320.1076479403051.2066691525-0.7008249354330.5217815681620.393252763344-0.354423548760.670257022255-0.2161233463920.1012593977930.188735080274-8.17059248258E-50.27460207870.01168833357430.008317857254350.217985403974-0.02619749577430.28094275075-38.4528914215-16.802711976717.3227071824
370.577867385352-0.409162453539-0.4862690591861.760688522550.3920205913470.3559376426880.441497016002-0.535736725206-0.2402199946970.417258961175-0.0330063811647-0.3461805747070.567915426039-0.03959006867490.0007962310454050.537480884749-0.0973082766907-0.1124934366490.5181180640040.008316742149250.545130415935-26.6366960502-1.79438421196-17.0524833418
381.35098718267-0.2557480968530.1624338460340.629737778651-0.05477008127520.0127321430702-0.1892506689330.345265527028-0.351731042603-0.158361632660.128080668073-0.608858110272-0.2572504238360.4703680835180.03005788921290.5355152180280.0680094513698-0.1109579040530.402824892685-0.005801390973360.590881515727-29.956513466-8.08536622207-23.4737307348
391.08716858198-0.5468970110861.045316886051.134347607220.203546678991.507904273990.163850696172-0.263385949921-0.122419092805-0.255756616139-0.1718585454910.861139008014-0.0715259892769-0.2076444820710.004025971638130.466663844737-0.0282954759040.04498592247930.24457407337-0.01463183565090.374109496653-42.39664543662.86772968732-30.6649332631
401.68522956487-0.3912434190770.07506588349911.383488818791.479680134481.663359102550.0571511614196-0.170315714683-0.196695011-0.446350747503-0.0760349551742-0.3770903174010.6233875469320.18877400265-0.0001127010463640.282917899619-0.0955600835203-0.04569413272010.34645070608-0.005550508473090.321001600965-35.2327451016-1.06909584764-22.2707441698
411.40976586257-0.887634363857-0.9908472445083.063598978330.7398956971210.8712746089110.120919744495-1.060863825610.697812800269-0.3745981703820.025952910342-0.5354825955010.158616483780.0316766569187-0.04794212142710.412781594806-0.0155059057975-0.0460061879890.689005595581-0.1226587878020.372990839199-30.04958151785.84854730942-15.7290168762
421.00980172993-0.0963163954725-0.1065723616091.22927213343-0.9290703331940.6606669122960.153669049511-1.14654279910.1711651361690.682606361863-0.4448318718460.2083840660210.13816118974-0.609993203205-0.04088235272250.502738136896-0.09267993207170.1045189729080.644849193934-0.06069463389080.434338872194-40.25187183724.98209622965-15.8641888525
432.31481922147-0.4184052657961.141089910942.00353734240.2100795879430.624544846539-0.0748200553243-0.2750407196070.03941165818310.2364418582580.16579802884-0.2261623872630.511565273760.4401719501960.04236566959630.2990477582130.0744438156491-0.05170337513280.4036363858210.04511814957520.274824297874-40.4028555341-31.6384878497-14.9924772948
441.904464211690.1978129891310.7760219085010.8341076123770.5901961159651.767400416590.07902182833-0.0188771405725-0.106407691694-0.1789640344410.13158717320.04141382031170.160043703712-0.1408471692510.0001067575195450.259648143615-0.002807794254530.05121591570170.2691195195790.02297003400550.284073888152-50.7975625495-30.3814763189-28.1104831363
451.79601233056-0.129603189333-0.1129744425470.887284496078-0.3216967084850.74934827718-0.0329454553953-0.0739939651831-0.0777921556035-0.06582737262460.1276833169470.0009983098762650.1935645806240.1191468921260.001279261119840.1785265692520.0308593184634-0.03217453551150.265235914501-0.005680927387240.239225396265-48.5640817861-29.627797807-20.3026944215
460.9068102970230.5003378807710.6869881863221.22266304187-0.8156850476362.45046716755-0.122365484743-0.3378013970990.3908079198630.394613881156-0.007828112714940.371373207587-0.419757086626-0.430231263704-0.005914729987040.3753389105750.113528872576-0.03296372637260.305399227801-0.02705419299860.300222673035-50.6588333041-23.0917986667-17.7638296732
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 22 )AA1 - 221 - 22
22chain 'A' and (resid 23 through 43 )AA23 - 4323 - 43
33chain 'A' and (resid 44 through 65 )AA44 - 6544 - 65
44chain 'A' and (resid 66 through 90 )AA66 - 9066 - 90
55chain 'A' and (resid 91 through 108 )AA91 - 10891 - 108
66chain 'A' and (resid 109 through 136 )AA109 - 135109 - 135
77chain 'B' and (resid 1 through 27 )BE1 - 271 - 27
88chain 'B' and (resid 28 through 43 )BE28 - 4328 - 43
99chain 'B' and (resid 44 through 65 )BE44 - 6544 - 65
1010chain 'B' and (resid 66 through 90 )BE66 - 9066 - 90
1111chain 'B' and (resid 91 through 108 )BE91 - 10891 - 108
1212chain 'B' and (resid 109 through 138 )BE109 - 138109 - 138
1313chain 'C' and (resid 2 through 29 )CJ2 - 291 - 22
1414chain 'C' and (resid 30 through 46 )CJ30 - 4623 - 39
1515chain 'C' and (resid 47 through 90 )CJ47 - 9040 - 83
1616chain 'C' and (resid 91 through 138 )CJ91 - 13884 - 131
1717chain 'D' and (resid 1 through 11 )DM1 - 111 - 11
1818chain 'D' and (resid 12 through 27 )DM12 - 2712 - 27
1919chain 'D' and (resid 28 through 43 )DM28 - 4328 - 43
2020chain 'D' and (resid 44 through 65 )DM44 - 6544 - 65
2121chain 'D' and (resid 66 through 99 )DM66 - 9966 - 99
2222chain 'D' and (resid 100 through 108 )DM100 - 108100 - 108
2323chain 'D' and (resid 109 through 126 )DM109 - 126109 - 126
2424chain 'D' and (resid 127 through 138 )DM127 - 138127 - 138
2525chain 'E' and (resid 1 through 11 )EO1 - 111 - 11
2626chain 'E' and (resid 12 through 43 )EO12 - 4312 - 43
2727chain 'E' and (resid 44 through 65 )EO44 - 6544 - 65
2828chain 'E' and (resid 66 through 90 )EO66 - 9066 - 90
2929chain 'E' and (resid 91 through 108 )EO91 - 10891 - 108
3030chain 'E' and (resid 109 through 135 )EO109 - 135109 - 135
3131chain 'F' and (resid 1 through 11 )FR1 - 111 - 11
3232chain 'F' and (resid 12 through 43 )FR12 - 4312 - 43
3333chain 'F' and (resid 44 through 65 )FR44 - 6544 - 65
3434chain 'F' and (resid 66 through 90 )FR66 - 9066 - 90
3535chain 'F' and (resid 91 through 126 )FR91 - 12691 - 126
3636chain 'F' and (resid 127 through 138 )FR127 - 138127 - 138
3737chain 'G' and (resid 2 through 28 )GT2 - 281 - 22
3838chain 'G' and (resid 29 through 43 )GT29 - 4323 - 37
3939chain 'G' and (resid 44 through 65 )GT44 - 6538 - 59
4040chain 'G' and (resid 66 through 90 )GT66 - 9060 - 84
4141chain 'G' and (resid 91 through 108 )GT91 - 10885 - 102
4242chain 'G' and (resid 109 through 137 )GT109 - 137103 - 131
4343chain 'H' and (resid 1 through 27 )HV1 - 271 - 27
4444chain 'H' and (resid 28 through 65 )HV28 - 6528 - 65
4545chain 'H' and (resid 66 through 99 )HV66 - 9966 - 99
4646chain 'H' and (resid 100 through 140 )HV100 - 140100 - 140

+
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