[English] 日本語
Yorodumi
- PDB-7mtu: Crystal Structure of the Catalytic Domain of the Inosine Monophos... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7mtu
TitleCrystal Structure of the Catalytic Domain of the Inosine Monophosphate Dehydrogenase from Bacillus anthracis in the complex with IMP and the inhibitor P221
ComponentsInosine-5'-monophosphate dehydrogenase
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / IMPDH / TIM barrel / delta CBS / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / OXIDOREDUCTASE / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex
Function / homology
Function and homology information


IMP dehydrogenase activity / IMP dehydrogenase / GMP biosynthetic process / nucleotide binding / metal ion binding
Similarity search - Function
Inosine-5'-monophosphate dehydrogenase / IMP dehydrogenase / GMP reductase, conserved site / IMP dehydrogenase / GMP reductase signature. / IMP dehydrogenase/GMP reductase / IMP dehydrogenase / GMP reductase domain / CBS domain superfamily / Domain in cystathionine beta-synthase and other proteins. / CBS domain / CBS domain / CBS domain profile. / Aldolase-type TIM barrel
Similarity search - Domain/homology
INOSINIC ACID / : / Chem-ZO7 / Inosine-5'-monophosphate dehydrogenase
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.34 Å
AuthorsKim, Y. / Maltseva, N. / Makowska-Grzyska, M. / Gu, M. / Gollapalli, D. / Hedstrom, L. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: To Be Published
Title: Crystal Structure of the Catalytic Domain of the Inosine Monophosphate Dehydrogenase from Bacillus anthracis in the complex with IMP and the inhibitor P221
Authors: Kim, Y. / Maltseva, N. / Makowska-Grzyska, M. / Gu, M. / Gollapalli, D. / Hedstrom, L. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionMay 13, 2021Deposition site: RCSB / Processing site: RCSB
SupersessionJun 9, 2021ID: 5UUW
Revision 1.0Jun 9, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_high

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Inosine-5'-monophosphate dehydrogenase
B: Inosine-5'-monophosphate dehydrogenase
C: Inosine-5'-monophosphate dehydrogenase
D: Inosine-5'-monophosphate dehydrogenase
E: Inosine-5'-monophosphate dehydrogenase
F: Inosine-5'-monophosphate dehydrogenase
G: Inosine-5'-monophosphate dehydrogenase
H: Inosine-5'-monophosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)333,23640
Polymers325,6778
Non-polymers7,56032
Water9,674537
1
A: Inosine-5'-monophosphate dehydrogenase
B: Inosine-5'-monophosphate dehydrogenase
C: Inosine-5'-monophosphate dehydrogenase
D: Inosine-5'-monophosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,66020
Polymers162,8384
Non-polymers3,82116
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25800 Å2
ΔGint-117 kcal/mol
Surface area46810 Å2
MethodPISA
2
E: Inosine-5'-monophosphate dehydrogenase
F: Inosine-5'-monophosphate dehydrogenase
G: Inosine-5'-monophosphate dehydrogenase
H: Inosine-5'-monophosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,57720
Polymers162,8384
Non-polymers3,73816
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25640 Å2
ΔGint-117 kcal/mol
Surface area46770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.270, 89.334, 104.334
Angle α, β, γ (deg.)98.891, 90.402, 96.011
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
Inosine-5'-monophosphate dehydrogenase / IMP dehydrogenase / IMPD / IMPDH


Mass: 40709.574 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium)
Gene: guaB, BA_0008, A9486_01210, ABW01_29210, BVG01_30935, COL95_27530
Plasmid: pMCSG7 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): gold / References: UniProt: A0A6H3A7R4, IMP dehydrogenase

-
Non-polymers , 6 types, 569 molecules

#2: Chemical
ChemComp-IMP / INOSINIC ACID / Inosinic acid


Mass: 348.206 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H13N4O8P
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-ZO7 / N-{2-chloro-5-[({2-[3-(prop-1-en-2-yl)phenyl]propan-2-yl}carbamoyl)amino]phenyl}-beta-D-arabinopyranosylamine


Mass: 475.965 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C24H30ClN3O5 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: K
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 537 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.34 Å3/Da / Density % sol: 47.46 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: 10 % (W/V) PEG-3000, SODIUM/POTASSIUM PHOSPHATE PH 6.2

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 17, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.34→50 Å / Num. obs: 118528 / % possible obs: 95.6 % / Redundancy: 2.3 % / Biso Wilson estimate: 32.72 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 6.95
Reflection shellResolution: 2.34→2.39 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.757 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 5009 / % possible all: 80.9

-
Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDBID 4MJM
Resolution: 2.34→41.68 Å / SU ML: 0.3243 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 31.9298
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2745 4635 4.92 %
Rwork0.2312 89643 -
obs0.2333 94278 75.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.25 Å2
Refinement stepCycle: LAST / Resolution: 2.34→41.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20488 0 497 537 21522
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.001621332
X-RAY DIFFRACTIONf_angle_d0.503728892
X-RAY DIFFRACTIONf_chiral_restr0.04143374
X-RAY DIFFRACTIONf_plane_restr0.00323687
X-RAY DIFFRACTIONf_dihedral_angle_d13.48387803
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.34-2.370.2757420.2904658X-RAY DIFFRACTION16.95
2.37-2.40.4255350.2935921X-RAY DIFFRACTION23.4
2.4-2.430.3956590.28361123X-RAY DIFFRACTION28.2
2.43-2.460.3407620.28091233X-RAY DIFFRACTION31.2
2.46-2.490.2975750.29261408X-RAY DIFFRACTION35.82
2.49-2.520.3343730.29831550X-RAY DIFFRACTION39.11
2.52-2.560.3104910.28821802X-RAY DIFFRACTION45.92
2.56-2.60.34181140.28161985X-RAY DIFFRACTION50.71
2.6-2.640.3061200.28642293X-RAY DIFFRACTION58.48
2.64-2.680.3121420.28812597X-RAY DIFFRACTION65.56
2.68-2.730.35571310.29152933X-RAY DIFFRACTION74.68
2.73-2.780.34331570.28463271X-RAY DIFFRACTION82.32
2.78-2.830.30541810.28453532X-RAY DIFFRACTION90.34
2.83-2.890.32931860.27333783X-RAY DIFFRACTION94.61
2.89-2.950.32042110.27233735X-RAY DIFFRACTION96.31
2.95-3.020.31182230.26683796X-RAY DIFFRACTION96.98
3.02-3.090.34181930.26713864X-RAY DIFFRACTION97.24
3.1-3.180.30222060.26613824X-RAY DIFFRACTION97.39
3.18-3.270.31121650.25613859X-RAY DIFFRACTION97.76
3.27-3.380.31841990.25283830X-RAY DIFFRACTION97.58
3.38-3.50.28891930.23793862X-RAY DIFFRACTION97.31
3.5-3.640.26812160.23043791X-RAY DIFFRACTION96.95
3.64-3.80.27991980.21383836X-RAY DIFFRACTION97.39
3.8-40.23791920.20013832X-RAY DIFFRACTION96.61
4-4.250.21811950.18643766X-RAY DIFFRACTION96.33
4.25-4.580.20952040.18383784X-RAY DIFFRACTION95.8
4.58-5.040.22091890.18173746X-RAY DIFFRACTION95.58
5.04-5.770.26552040.20513771X-RAY DIFFRACTION95.6
5.77-7.260.25261900.21823730X-RAY DIFFRACTION95.15
7.27-41.680.23681890.20993528X-RAY DIFFRACTION89.48
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)
11.08799634535-0.6151004076990.1026310892151.3431557592-0.08213506567740.844389709123-0.1315049126230.181940300639-0.0689164391966-0.213471360541-0.0229286319103-0.048850951874-0.212489063234-0.0348954019697-0.008875605589060.166391559591-0.0376605020760.01573676163730.2242296573810.02724475370770.150340330732-6.18691407313-2.89355535888-15.5365685836
20.609204483559-0.391992238856-0.05509299168870.8864756644140.1003837134170.735116278343-0.145173704910.0273147797529-0.121328942904-0.0692018906681-0.004164865051090.4810806486510.101888191353-0.455013044640.01140040812240.173559712319-0.0926045547683-0.1226245726770.459031431264-0.03519250278680.307433997578-35.3725954909-14.8408771212-10.7685583975
31.095985896030.1987234696530.1025938638490.618672364999-0.1798357840730.07917933762440.1004165156630.187256535654-0.379238731669-0.248761071135-0.1397444518770.01964784100350.338591097485-0.2482072217690.1076692623450.247062519224-0.0899125172083-0.03612822756340.307429227382-0.04305209660320.265386766759-23.7492803994-21.6044096933-20.5182699045
40.50099854845-0.1868666538690.007890207699980.419096663187-0.2106688627130.190925988709-0.109379683324-0.055010564514-0.0514304155636-0.0594826359214-0.08676519499270.05877545548830.0369336719957-0.1990532664860.07832135643080.18526232395-0.0324376646798-0.05629557853920.208330531-0.002121820070540.129777557742-17.9516239249-8.85776233827-12.5748511142
52.01567438367-0.958018780012-0.6480377039231.817551132380.1354882388520.962683852841-0.253822462715-0.23571254944-0.1128460779440.371601414335-0.119353242465-0.06038245428880.234851420993-0.3069902207030.2211234010940.245445093414-0.00323452764538-0.01528725691660.377465366891-0.02464110046850.247240827427-25.5149520971-14.91932425467.37368091661
60.972673224880.552630320048-0.4000830424981.17825635922-0.4964441508051.055257692180.124629739906-0.00748154985142-0.0240728914218-0.0636178941355-0.1930686409830.213178991994-0.249051660784-0.2265384010050.141070661360.186667607241-0.0189302493312-0.07080761380480.281217470667-0.002940645973370.189581287458-28.77286895415.26919663545-6.77230740204
71.08519593596-0.08616306621170.1965009525380.8026948215550.397484132741.343448079760.0833461825262-0.0240353474115-0.286054829807-0.1219553116560.0706533272510.177590893856-0.113495823481-0.0496431705696-0.07783931735910.295344130309-0.0122928503608-0.106813238660.1319313311075.72695140527E-50.14339236352-16.43447311227.17117767194-6.07928844146
80.637529252624-0.00704956557859-0.1352439322980.489867145814-0.07735655159720.435554152847-0.06222842877840.03449893132460.172573451544-0.231329151552-0.0383603841942-0.0655489170027-0.169923355378-0.01932480880090.05784119254130.356242425144-0.05907676757840.01018141530760.1764516672860.1090577742320.273622707903-2.8431348760823.2210094936-5.35776223653
90.2552293797910.00656298003661-0.0808678727660.418889557162-0.008355079038560.0859203229284-0.03192973230120.05456510042540.208450483339-0.157051900762-0.01648994008540.358328656313-0.482037529885-0.215743437770.005656143280530.6081101367480.206703152974-0.05177407425420.1735770661690.07288027785840.335350546502-20.513582346533.9980478893-4.50715076803
100.741837677129-0.00728877730425-0.06918126479850.8338790719410.398140135460.1996394587780.02823222537440.0847031875250.132873895521-0.0157607850344-0.0600564489259-0.0470008629031-0.385571143864-0.03656520353250.01663930371080.3010615388-0.0263039107058-0.005364487008770.1056017094130.0193300800980.150218315371-9.9279256180921.5815024949-0.193256121163
110.1701903666740.213686098871-0.05369812820311.009870159680.1903288973151.359754246440.0375035460713-0.2337669497090.1311633312840.0533761541088-0.1659699946940.108683226552-0.0842936122464-0.1121497065730.1135605979820.3160189333470.01675551971820.002454141216330.06479066440610.0311029012910.218649680987-11.582364421322.40093416058.09626604962
120.436885716393-0.009971416088160.1683723979290.8493493375530.02776784568130.5249915083970.08711403420760.00655191033718-0.02114359698-0.02556852775-0.216923508391-0.240066980085-0.2558913690030.106855348352-0.0162634170410.236531950541-0.02614943281030.01975033875510.2338156198270.08766962270470.3102728684655.8315419164817.39037052554.11711190332
130.48970190051-0.109621237548-0.05704009839730.375998029459-0.265668753280.7001349996970.1264084545060.03783973091910.00392846957649-0.106814683743-0.0785553016649-0.1570905985150.06851359940410.084742082356-0.06249460324420.2247643834790.05287052174460.09240548454240.1418795488250.016091223780.3093867362647.54380359659-21.8332310929-5.6264180263
140.6455040338090.2810038664080.01277941874410.1847778229390.06227034925490.582470900263-0.0385356485166-0.162691004923-0.2230209284280.281479728910.161761740955-0.22689625350.3104528006160.2182851988450.08575691898490.3557068687250.174979768718-0.0002756741054930.156132665031-0.0119323017110.50775210462914.2669364097-37.69959310411.3582791309
150.02364348518470.05357018342130.005780323254680.3444297213490.02785695174140.196853830635-0.0456179854121-0.006910786042450.009285609479180.09402871095740.0548131433288-0.1268058236130.1793100982350.2466056445440.007408375259690.2631761623550.1949835311040.06549421165790.33035682479-0.06401471318980.59368001313823.6829868294-33.29416725785.92557162376
160.055726904964-0.0604753128126-0.06846414424920.106945471170.008227382617470.178468024492-0.06692113643710.0156623302942-0.193560209308-0.08018766570890.10950917112-0.2257203558030.1362699546160.2464230847430.18358398596-0.0007209645392730.1112937597820.2325165564940.248581206365-0.001039487909890.50576309789917.0185059302-23.1414801077-2.86214545125
170.6886552199420.35770631273-0.3284010901051.084292003970.1139530050061.321574127950.117949938678-0.200700280467-0.03923208741210.334034844898-0.100347280651-0.2296697137880.0872780289494-0.06651732811410.02256453012110.236653987720.07519399908570.03502739622270.267300533390.05402143405140.2323761498736.06779599929-22.89861017916.0335834039
180.885113414998-0.3385720432810.9203066118290.938417778076-0.4192246081571.12559840858-0.0254990819296-0.0443257413047-0.122960501751-0.0493792632120.252360456010.1058648754470.143370153977-0.0366594319374-0.08704906137880.1887785863280.02617080581450.01212474490530.120527060659-0.0176611925920.307021739491-5.77101756416-29.12799663-1.49422240623
190.9938214650890.162261370847-0.2255859071841.13042685507-0.1058775205581.1110778421-0.1083154558520.0653075067664-0.002527125155780.0502107604189-0.0759946897764-0.2406783246420.0623977476933-0.2329366033430.1877451822360.254627048973-0.00207317656337-0.05349459237710.208105482643-0.01237377059070.141657507961-6.15076613187-17.3341116381-3.93780044799
200.967291653239-0.380077472797-0.08857616775791.10751083704-0.0957838996840.8923999513820.0391476028870.188369776652-0.0344934197148-0.17620644452-0.136341178379-0.34398133631-0.00506957935590.00952060668089-0.2254952710860.1028077426830.03424169117870.1439266520250.2294204857370.02285999216940.30344015011615.03199259484.17540349519-5.90056367697
210.373600424870.1067577172460.07182759289171.173618690820.3295717354660.327228270650.0045873477276-0.0113996030095-0.143553232519-0.002910247306030.0318013817977-0.2792811513380.04650063475780.1708277073370.00568202085670.13639517339-0.0549631202289-0.007134929971070.500220036889-0.02598566405570.55616545619831.43335211135.1761716682313.6037902988
220.226330932122-0.258112029271-0.02946440962390.563065582421-0.0831598564380.355305392671-0.0362193454437-0.3955714497240.2090101901190.200552379388-0.00294227606478-0.321015549748-0.261991495030.1880995490340.003531198606570.425940586238-0.19368376758-0.2320351179520.508515296272-0.06556962171860.69116334646531.118199553815.58354547724.2692255354
230.7762643372390.09741038162410.2329554132260.1071514502230.1631963602010.4783484518580.0531445850933-0.1520230215940.2518634990510.0706300040630.0516643517981-0.184619165258-0.1486777392770.1968272860940.06950476576990.576591755647-0.318531931543-0.1761500882290.519477131898-0.03311708578840.69111787262232.793641094524.522350875917.4699715554
240.722389229731-0.08534144425720.5617345474140.0102148553228-0.06783644689790.434158957307-0.00948856658707-0.1078230060160.08889343147420.214012342797-0.158502634471-0.356017303205-0.1973545848110.228004330854-0.009535715893140.405306089982-0.233563833035-0.1212765536360.4625707068920.07833282700930.64726791071629.64099974825.27905469697.4423163967
250.188352968279-0.2597327038270.1078235571820.384408855385-7.10256591117E-50.645123028645-0.0277490455159-0.0704772621261-0.0421221848442-0.1155055003010.0678001735513-0.367965650372-0.3088579944110.385565827044-0.008156090021920.176679525832-0.1668650689890.06634276103910.3379041412060.02700703731880.432847882422.964949486712.96323860993.01020322502
260.535090501657-0.03550672005440.261250064310.8825602607430.01493965226680.56491588041-0.0822323516159-0.196409618854-0.07635675596940.1727758635950.0850185249185-0.085373591228-0.2479757821770.2371936582960.002509387483730.282364216902-0.0409561574543-0.03900268783960.2866166392330.04974176439840.38635150997317.03210389617.1278789468420.446581629
270.756218460813-0.339159850584-0.1359828558090.580283979358-0.1905966226341.10479090084-0.108889772383-0.01871349045750.1172508555130.203214799680.0621697539421-0.198276388319-0.2014867123310.0195413829405-0.008231094403790.1253933095020.07120677584190.0837945796270.275427728274-0.06674054408430.44119480401616.3749803026-7.065025127225.79243376947
280.66291524966-0.135108373111-0.38014173380.834091745255-0.0005654240786160.487915951451-0.126184173920.1751623407460.164506459947-0.2334141870650.03852639171840.240293381704-0.0929138618929-0.4659604548670.1680005953840.3179571367340.0167299780208-0.166966798740.659743746266-0.08295782494730.351006906549-55.64801784569.11996293288-56.5028493696
291.09624672392-0.7723756215480.2366800687721.20033363612-0.1735904252390.313471573252-0.0218525212076-0.0116658623736-0.06176840397980.0188895202245-0.23762984160.4206274570850.031121244642-0.484837549924-0.2261600021730.202769662991-0.1165054829580.05981922957580.852096163837-0.2153691985350.520128925795-71.0030447546-0.705452880961-37.9126078515
300.120999720025-0.139044975627-0.2183568732920.2850924517690.4364271007270.671615727914-0.114283004202-0.185567090052-0.3009495170560.212929668441-0.06679715006410.3475076041110.278280288612-0.1806391022630.02866623548580.583970394343-0.3866596745680.1274690348841.12520606301-0.1916639696210.794636682076-71.1862760894-13.6480718676-33.5089765856
310.0022736952535-0.00805356195130.004024073627950.025834994842-0.01459167839620.008123243828350.0697061485184-0.0429973003487-0.1968603082270.0550614246542-0.04660557605520.2852616325160.104742159888-0.1501100493130.08696588323030.663427829444-0.461400338908-0.00133842917060.947112182414-0.1448578562870.954665112291-72.9165011257-17.6434646878-41.9631372993
320.7537892156410.419818227654-0.3056380421140.243981619199-0.1747624942270.126260585036-0.1797585473520.0546685279844-0.0756586448697-0.0173557552694-0.1739774035670.3041358120680.0473068479481-0.2770907008540.07086799266530.531514139138-0.3739405526290.093475042110.99751140196-0.2808263442060.582275526863-69.6433830959-15.5208142954-51.7799587125
330.790009753881-0.0881445931628-0.2215615173820.216088657049-0.1582083041880.606524956388-0.00866846460048-0.00731426028776-0.0347224932845-0.147028572981-0.002241086167480.3234304343660.224733421969-0.2971022226890.1222254492280.459463565731-0.301705647197-0.0787839201960.908266829261-0.2241048974120.48863266771-69.5009773966-9.1097856252-55.3000580137
340.5389437797260.1516510697880.2808988921441.292081038670.1060681868080.43255693064-0.1108541209050.1637635911250.0535642363379-0.2160351807390.01023693123330.5417901368910.147365738763-0.6286817370120.1493275295520.2175186334-0.109684974161-0.1177382881320.758460253302-0.1536025089710.31186482392-60.63583506840.105073478296-50.7120199901
351.24676955728-0.5209932713530.03274014425880.308920427286-0.05637645133060.9909654948290.00800174858823-0.2710438638490.1861004446210.262707397003-0.1577067884970.06393197671240.430872825985-0.08644633608990.05623408491830.387547600252-0.2398826659290.0133777030730.521558932567-0.007874640815110.393984105866-53.7407291158-7.28574427316-29.82168637
360.686077107462-0.129118454879-0.1999670139690.09705081608340.3565859169711.42526601222-0.107059704553-0.2627961797880.0619816069870.1691215520830.07319776889070.1163657118770.212522301526-0.369589177665-0.04313039853320.149039831092-0.08326696096440.03474105127110.623232684997-0.1175543817740.362742485686-59.18628937693.47752313974-35.2836998692
370.6713400681650.0753011077804-0.1518572969920.6638196855790.1307517544330.749407992112-0.085729901734-0.117451300212-0.116405489396-0.00268859722905-0.02862492706640.167300500685-0.0177977952723-0.5327384682590.03776443498570.2490642579680.04729801263210.03488370614990.517770858998-0.01093309838650.280505777346-55.325897428315.517702619-43.492373677
380.7689102907360.01345981757640.1869512573960.6976205070140.0389205043510.8764022906120.018274567092-0.1728492409770.259874330105-0.00562011054813-0.104553913660.273266900491-0.427542406199-0.4608540642440.03245787899540.5102404827240.226822861458-0.02082634209150.354959720999-0.04994063620450.367530532164-48.597006937337.9005569891-40.5375839527
390.09537210504160.07906297362620.006555027628890.312707198508-0.04439235125680.01020530351010.06452942402530.01446367568830.1406304701250.09674524456170.01710288816350.13086844482-0.16075645746-0.1566073170630.1504940105340.5355394883680.3781542009090.09912338150410.696465115222-0.1085219503870.536308740221-62.170857604940.8755385466-35.6411447331
400.567272896370.3038896182810.1717396112140.6340213370590.1189497183830.358459732177-0.0138835230831-0.06884284014630.147699993628-0.0341054320537-0.08096042762380.164084377991-0.377200219838-0.5205575026080.01006953986840.3111555373890.194282994092-0.09084749938340.382141190931-0.0211021275990.260683423572-47.881811789731.7504551615-42.5621001517
411.133256639790.4384498332491.248425081881.43725165387-0.08758786099881.67480874716-0.162058444345-0.294369264107-0.07080740973490.05776056283010.0816368520724-0.0201549370691-0.03583672451250.0106991120860.05019212513530.331704567948-0.001705819211310.02019568466480.2222155707530.008906797933830.0897326989862-25.244685345322.2346207214-39.7061355685
420.216547126589-0.2265943027780.04962941402130.3330400642750.04414199095450.1113938085630.0523515786870.299317649678-0.0656933011959-0.203289730551-0.02543951690720.1200655876450.0730767950893-0.318880822505-0.05018211648330.470793790297-0.0250145066594-0.0704191494570.4016025667970.01965620135180.102199370225-34.45519512697.47702411988-68.2871292903
430.635253977430.162824915289-0.1389432304750.999419283808-0.1911996357350.716909971782-0.1248901625550.171221659785-0.395752666622-0.134761498364-0.0984194922972-0.2062487119790.632069660872-0.0592184326331-0.007992279556680.587944080724-0.0575300832497-0.03460287401180.266004337595-0.08961798014520.327272803426-26.0608918248-24.6184554026-60.3988252311
440.2066519960340.004595626191970.07210917233471.76887988975-0.115847897710.03243270271730.09527903411470.42139101911-0.152865435368-0.324955746354-0.0985236535252-0.1979963902490.2711562525630.1930122999190.08398629032870.5819566648880.07149430705840.1254442451960.353347637143-0.07884499618610.283323813661-17.9925143986-16.1866624085-72.3222146633
450.3087762854460.1721473958320.09135527647280.4308346922820.1166595018840.362676419593-0.02851235688020.18448745997-0.134865908529-0.290841525213-0.09479245413970.07188253696250.272842566238-0.1030772813840.07982667037790.484751103348-0.0640078202297-0.03051564868470.291933621027-0.09538955889860.119048803485-30.2276994299-10.1300526468-65.6237649674
460.835995739781-0.179200309199-0.7616893166660.2561525088810.08969639025131.563206817780.11830467526-0.2988513420530.01158132018150.149714612592-0.0151987583226-0.232110847363-0.1025226534280.2759137904540.01887098959660.529073519682-0.0403584897203-0.04509313308340.3135808075760.07571189125150.140700523388-23.4626638343-16.1079453193-40.4570889042
470.4817358581930.05280043125640.2139076830012.11830150798-0.6599087896491.36239856072-0.0162430355121-0.301502004434-0.3106609670490.0161957227442-0.321545569271-0.4298536929220.3668650150490.1452409310570.2054586014740.2415090366110.008579635339770.007206177462690.355546064765-0.01588756145950.219508919131-18.0798769351-9.97199120702-49.0625920171
480.944032243056-0.0720932437825-0.229139765150.4478516053770.2720564179060.201683563247-0.105102201545-0.00181377396653-0.09934074011920.0117879691720.02007414961270.03245229622270.279319325295-0.221569935778-0.00828649388590.598135579047-0.221796493551-0.03615279500920.37063027315-0.06933278856240.285665480545-43.3308965611-19.3236459608-52.7559307723
490.364450443034-0.0312380606191-0.2432711858070.953502815355-0.08129473732140.49777913971-0.1062095343360.2270568589110.1515725418990.008043245960240.003842222773640.1029762551180.311175078338-0.153319714140.06825124676460.38280706018-0.176022631694-0.05092407816330.489260454336-0.104636001620.293007382724-45.4580728497-7.54899958659-52.2857607048
500.786334866838-0.1651234012030.1545939915310.5207813085370.03068075816620.44434321782-0.08508403031310.1877228103370.0505648214872-0.225220961129-0.05502788245560.120738008554-0.105063280091-0.2290794154050.05887934788730.4663633524690.0381951324157-0.07722364695330.319401106875-0.005663997078870.061242711541-32.769667805617.4271341132-65.14702236
510.715876763799-0.2267358646940.01441798837070.7266092411070.1662017761390.723350391215-0.1456550025340.03051304574040.149350223548-0.194676586970.174604434012-0.340216748021-0.1210793103710.6325926238610.05401221457890.380296365669-0.1001495175580.09966412666640.306173745519-0.03514226000360.264311309637-5.6616508479920.6154293312-58.3532854567
520.3756472974550.3875103763940.4859631433580.8962999366470.1182102957040.922625257993-0.0866938364090.06277290335610.0765566415115-0.02810732714330.0948020818891-0.471331811136-0.2178735493160.341164938036-0.02780959175260.486703062235-0.3455114216340.0008027876416250.5641812482230.03591337471990.534786812201-0.42906090917932.5460282177-54.3314112624
531.401119961430.2881863294530.04760530352970.1627476393160.08663530011620.05847423077420.1192214748240.1746412081710.211488916876-0.0235390359896-0.0498669164723-0.00974515196327-0.3998010513980.207623506669-0.003229435064540.641537174872-0.2845630577950.04184088953920.360525018580.01178457025170.23825612325-8.4551827465336.965157251-58.8615000427
540.5027953721250.1600287831-0.2509503817750.1545553689830.08490290483740.436681583155-0.04966934115450.07714954641860.141914559572-0.216076255456-0.0400586297921-0.156605854204-0.5259752745050.1715220252510.0858018757620.455904938662-0.0474190291759-0.01101494235360.1961296413480.05340604300250.136761171629-19.273926142826.9852389366-62.443728012
550.322910029936-0.280123361332-0.175177575150.686600245721-0.5948639794331.60819840953-0.0944517493485-0.343339480718-0.0989911225280.3637473284080.0767006575859-0.01670122569680.1769586465780.2927382840660.06679541429070.1971165513330.01795818749210.01124390598510.325238266298-0.01533688675870.270332002798-9.912936357716.5866938953-38.0632269826
560.570248608186-0.0654090439297-0.04417216905540.16458292205-0.2856827197470.5793088243290.00177096837711-0.1605017237170.052648286902-0.0253773436224-0.0837010886533-0.180623088437-0.1599478027950.2999758242270.04301327691690.222426236573-0.01222941320830.03082543686060.2551020859450.009984917944270.219655310796-13.903802537717.7284458668-48.9423933554
571.07774178606-0.01059125187840.02127507731961.17700865876-0.3720197229711.16248918437-0.0443901258803-0.08030776862260.0360236190402-0.0969603608338-0.0366537197876-0.1368853223280.0179610366097-0.152684796610.1296575299270.2932832898850.05344436187280.05453613286440.205484332327-0.03116573905620.189632165305-23.00789568514.71656894378-59.1355119897
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid -2 through 26 )AA-2 - 261 - 29
22chain 'A' and (resid 27 through 242 )AA27 - 24230 - 118
33chain 'A' and (resid 243 through 292 )AA243 - 292119 - 168
44chain 'A' and (resid 293 through 368 )AA293 - 368169 - 244
55chain 'A' and (resid 369 through 427 )AA369 - 427245 - 290
66chain 'A' and (resid 428 through 445 )AA428 - 445291 - 308
77chain 'A' and (resid 446 through 486 )AA446 - 486309 - 349
88chain 'B' and (resid -1 through 56 )BG-1 - 561 - 58
99chain 'B' and (resid 57 through 291 )BG57 - 29159 - 166
1010chain 'B' and (resid 292 through 389 )BG292 - 389167 - 264
1111chain 'B' and (resid 390 through 445 )BG390 - 445265 - 308
1212chain 'B' and (resid 446 through 487 )BG446 - 487309 - 350
1313chain 'C' and (resid -3 through 56 )CK-3 - 561 - 60
1414chain 'C' and (resid 57 through 232 )CK57 - 23261 - 109
1515chain 'C' and (resid 233 through 257 )CK233 - 257110 - 134
1616chain 'C' and (resid 258 through 355 )CK258 - 355135 - 232
1717chain 'C' and (resid 356 through 427 )CK356 - 427233 - 292
1818chain 'C' and (resid 428 through 446 )CK428 - 446293 - 311
1919chain 'C' and (resid 447 through 486 )CK447 - 486312 - 351
2020chain 'D' and (resid -1 through 26 )DQ-1 - 261 - 28
2121chain 'D' and (resid 27 through 56 )DQ27 - 5629 - 58
2222chain 'D' and (resid 57 through 91 )DQ57 - 9159 - 93
2323chain 'D' and (resid 92 through 242 )DQ92 - 24294 - 117
2424chain 'D' and (resid 243 through 270 )DQ243 - 270118 - 145
2525chain 'D' and (resid 271 through 355 )DQ271 - 355146 - 230
2626chain 'D' and (resid 356 through 445 )DQ356 - 445231 - 308
2727chain 'D' and (resid 446 through 486 )DQ446 - 486309 - 349
2828chain 'E' and (resid -1 through 28 )EU-1 - 281 - 30
2929chain 'E' and (resid 29 through 65 )EU29 - 6531 - 67
3030chain 'E' and (resid 66 through 91 )EU66 - 9168 - 93
3131chain 'E' and (resid 92 through 242 )EU92 - 24294 - 117
3232chain 'E' and (resid 243 through 270 )EU243 - 270118 - 145
3333chain 'E' and (resid 271 through 292 )EU271 - 292146 - 167
3434chain 'E' and (resid 293 through 363 )EU293 - 363168 - 238
3535chain 'E' and (resid 364 through 398 )EU364 - 398239 - 273
3636chain 'E' and (resid 399 through 446 )EU399 - 446274 - 307
3737chain 'E' and (resid 447 through 486 )EU447 - 486308 - 347
3838chain 'F' and (resid -1 through 232 )FY-1 - 2321 - 107
3939chain 'F' and (resid 233 through 257 )FY233 - 257108 - 132
4040chain 'F' and (resid 258 through 471 )FY258 - 471133 - 333
4141chain 'F' and (resid 472 through 486 )FY472 - 486334 - 348
4242chain 'G' and (resid -3 through 19 )GG-3 - 191 - 23
4343chain 'G' and (resid 20 through 242 )GG20 - 24224 - 119
4444chain 'G' and (resid 243 through 270 )GG243 - 270120 - 147
4545chain 'G' and (resid 271 through 368 )GG271 - 368148 - 245
4646chain 'G' and (resid 369 through 389 )GG369 - 389246 - 266
4747chain 'G' and (resid 390 through 427 )GG390 - 427267 - 291
4848chain 'G' and (resid 428 through 446 )GG428 - 446292 - 310
4949chain 'G' and (resid 447 through 487 )GG447 - 487311 - 351
5050chain 'H' and (resid -2 through 26 )HH-2 - 261 - 29
5151chain 'H' and (resid 27 through 77 )HH27 - 7730 - 80
5252chain 'H' and (resid 78 through 232 )HH78 - 23281 - 108
5353chain 'H' and (resid 233 through 257 )HH233 - 257109 - 133
5454chain 'H' and (resid 258 through 368 )HH258 - 368134 - 244
5555chain 'H' and (resid 369 through 389 )HH369 - 389245 - 265
5656chain 'H' and (resid 390 through 445 )HH390 - 445266 - 308
5757chain 'H' and (resid 446 through 486 )HH446 - 486309 - 349

+
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