[English] 日本語
Yorodumi
- PDB-6vk8: Crystal Structure of Methylosinus trichosporium OB3b Soluble Meth... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6vk8
TitleCrystal Structure of Methylosinus trichosporium OB3b Soluble Methane Monooxygenase Hydroxylase and Regulatory Component Complex with small organic carboxylate at active center
Components
  • (Methane monooxygenase ...) x 2
  • (Methane monooxygenase) x 2
KeywordsOXIDOREDUCTASE / Methane Monooxygenase Hydroxylase
Function / homology
Function and homology information


methane monooxygenase [NAD(P)H] activity / methane metabolic process / methane monooxygenase (soluble) / : / : / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen / : / monooxygenase activity / one-carbon metabolic process / metal ion binding
Similarity search - Function
Monooxygenase component MmoB/DmpM / Monooxygenase component MmoB/DmpM superfamily / MmoB/DmpM family / Methane monooxygenase, gamma chain / Methane monooxygenase, gamma chain, domain 1 / Methane monooxygenase, gamma chain, domain 2 / Methane monooxygenase, gamma chain superfamily / Methane monooxygenase, hydrolase gamma chain / Methane/phenol monooxygenase, hydroxylase component / Propane/methane/phenol/toluene hydroxylase ...Monooxygenase component MmoB/DmpM / Monooxygenase component MmoB/DmpM superfamily / MmoB/DmpM family / Methane monooxygenase, gamma chain / Methane monooxygenase, gamma chain, domain 1 / Methane monooxygenase, gamma chain, domain 2 / Methane monooxygenase, gamma chain superfamily / Methane monooxygenase, hydrolase gamma chain / Methane/phenol monooxygenase, hydroxylase component / Propane/methane/phenol/toluene hydroxylase / Methane/Phenol/Alkene Hydroxylase / Ribonucleotide reductase-like / Ferritin-like superfamily
Similarity search - Domain/homology
BENZOIC ACID / : / SUCCINIC ACID / Methane monooxygenase / Methane monooxygenase regulatory protein B / Methane monooxygenase component A alpha chain / Methane monooxygenase / Methane monooxygenase component A alpha chain / Methane monooxygenase regulatory protein B
Similarity search - Component
Biological speciesMethylosinus trichosporium OB3b (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.03 Å
AuthorsJones, J.C. / Banerjee, R. / Shi, K. / Aihara, H. / Lipscomb, J.D.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM118030, GM08347 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM118000, GM118047 United States
CitationJournal: Biochemistry / Year: 2020
Title: Structural Studies of theMethylosinus trichosporiumOB3b Soluble Methane Monooxygenase Hydroxylase and Regulatory Component Complex Reveal a Transient Substrate Tunnel.
Authors: Jones, J.C. / Banerjee, R. / Shi, K. / Aihara, H. / Lipscomb, J.D.
History
DepositionJan 18, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 26, 2020Group: Database references / Category: citation / citation_author / Item: _citation.title / _citation_author.identifier_ORCID
Revision 1.2Sep 2, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Methane monooxygenase component A alpha chain
B: Methane monooxygenase
C: Methane monooxygenase
D: Methane monooxygenase regulatory protein B
E: Methane monooxygenase component A alpha chain
F: Methane monooxygenase
G: Methane monooxygenase
H: Methane monooxygenase regulatory protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)281,28938
Polymers279,3368
Non-polymers1,95330
Water24,8971382
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area60300 Å2
ΔGint-186 kcal/mol
Surface area65640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.866, 105.349, 297.720
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22
13
23
14
24

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ASPASPGLYGLY(chain 'A' and (resid 12 through 315 or resid 317 through 526 or resid 801 through 802))AA12 - 31412 - 314
121TRPTRPPHEPHE(chain 'A' and (resid 12 through 315 or resid 317 through 526 or resid 801 through 802))AA317 - 526317 - 526
211ASPASPGLYGLY(chain 'E' and (resid 12 through 315 or resid 317 through 526 or resid 801 through 802))EE12 - 31412 - 314
221TRPTRPPHEPHE(chain 'E' and (resid 12 through 315 or resid 317 through 526 or resid 801 through 802))EE317 - 526317 - 526
112PROPROLEULEU(chain 'B' and (resid 4 through 320 or resid 322 through 395))BB4 - 3204 - 320
122ALAALAASNASN(chain 'B' and (resid 4 through 320 or resid 322 through 395))BB322 - 395322 - 395
212PROPROLEULEU(chain 'F' and (resid 4 through 320 or resid 322 through 395))FF4 - 3204 - 320
222ALAALAASNASN(chain 'F' and (resid 4 through 320 or resid 322 through 395))FF322 - 395322 - 395
113ALAALAGLNGLNchain 'C'CC2 - 1682 - 168
213ALAALAGLNGLNchain 'G'GG2 - 1682 - 168
114SERSERARGARGchain 'D'DD2 - 1332 - 133
214SERSERARGARG(chain 'H' and resid 2 through 133)HH2 - 1332 - 133

NCS ensembles :
ID
1
2
3
4

-
Components

-
Methane monooxygenase ... , 2 types, 4 molecules AEDH

#1: Protein Methane monooxygenase component A alpha chain


Mass: 60031.293 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Methylosinus trichosporium OB3b (bacteria)
References: UniProt: A0A2D2D5X0, UniProt: P27353*PLUS
#4: Protein Methane monooxygenase regulatory protein B


Mass: 14896.885 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Methylosinus trichosporium OB3b (bacteria)
References: UniProt: A0A2D2D0T8, UniProt: P27356*PLUS

-
Protein , 2 types, 4 molecules BFCG

#2: Protein Methane monooxygenase


Mass: 45295.340 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Methylosinus trichosporium OB3b (bacteria)
References: UniProt: A0A2D2D5X7
#3: Protein Methane monooxygenase


Mass: 19444.400 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Methylosinus trichosporium OB3b (bacteria)
References: UniProt: A0A2D2D0T0

-
Non-polymers , 5 types, 1412 molecules

#5: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-SIN / SUCCINIC ACID


Mass: 118.088 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O4
#7: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C2H6O2
#8: Chemical ChemComp-BEZ / BENZOIC ACID


Mass: 122.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H6O2
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1382 / 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: 2.86 Å3/Da / Density % sol: 56.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: Tacsimate, PEG3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 7, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.03→101.87 Å / Num. obs: 203307 / % possible obs: 98.5 % / Redundancy: 4.1 % / Biso Wilson estimate: 34.52 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.137 / Net I/σ(I): 7.9
Reflection shellResolution: 2.03→2.1 Å / Num. unique obs: 19824 / CC1/2: 0.387 / Rpim(I) all: 1.105

-
Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
PHENIXphasing
PHENIXdata scaling
PHENIXdata processing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.03→85.99 Å / SU ML: 0.2706 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 22.4855
RfactorNum. reflection% reflection
Rfree0.2075 10347 5.11 %
Rwork0.1667 --
obs0.1688 202365 97.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 36.59 Å2
Refinement stepCycle: LAST / Resolution: 2.03→85.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19484 0 117 1382 20983
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006920120
X-RAY DIFFRACTIONf_angle_d0.836327269
X-RAY DIFFRACTIONf_chiral_restr0.04922859
X-RAY DIFFRACTIONf_plane_restr0.00553517
X-RAY DIFFRACTIONf_dihedral_angle_d16.49987217
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.03-2.050.37043390.33136035X-RAY DIFFRACTION93.6
2.05-2.080.3523040.32416215X-RAY DIFFRACTION95.17
2.08-2.10.31333760.29366247X-RAY DIFFRACTION97.3
2.1-2.130.34573250.29996348X-RAY DIFFRACTION97.99
2.13-2.160.32263640.27946373X-RAY DIFFRACTION98.35
2.16-2.190.32543260.27316403X-RAY DIFFRACTION98.43
2.19-2.220.31553360.26016358X-RAY DIFFRACTION98.48
2.22-2.250.31143670.2626359X-RAY DIFFRACTION97.83
2.25-2.290.29643390.24086342X-RAY DIFFRACTION98.03
2.29-2.320.27523400.23516335X-RAY DIFFRACTION97.18
2.32-2.360.25973470.22056139X-RAY DIFFRACTION94.85
2.36-2.410.24523460.2066368X-RAY DIFFRACTION98.37
2.41-2.450.24883520.19286400X-RAY DIFFRACTION98.93
2.45-2.50.26533530.1956411X-RAY DIFFRACTION98.87
2.5-2.560.24663530.17696463X-RAY DIFFRACTION99
2.56-2.620.23583100.17836502X-RAY DIFFRACTION98.95
2.62-2.680.24363630.16766390X-RAY DIFFRACTION98.83
2.68-2.760.20433580.1616448X-RAY DIFFRACTION99.07
2.76-2.840.20013540.15576477X-RAY DIFFRACTION98.96
2.84-2.930.19323500.16246384X-RAY DIFFRACTION98.11
2.93-3.030.22033410.16326262X-RAY DIFFRACTION96.03
3.03-3.150.21053700.1656300X-RAY DIFFRACTION96.91
3.15-3.30.21283820.16366533X-RAY DIFFRACTION99.53
3.3-3.470.19863230.15816499X-RAY DIFFRACTION99.01
3.47-3.690.20563040.15026560X-RAY DIFFRACTION98.95
3.69-3.970.16273010.13566518X-RAY DIFFRACTION98.24
3.97-4.370.15473500.12046517X-RAY DIFFRACTION98.09
4.37-5.010.14663320.11496454X-RAY DIFFRACTION96.75
5.01-6.310.16563500.12876645X-RAY DIFFRACTION98.9
6.31-85.990.14923920.14326733X-RAY DIFFRACTION96.78
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)
11.86608035862-0.270524195362-1.174753536810.7800644212590.189296941731.83272298892-0.0862901565338-0.269729585734-0.3441907967-0.05595243333180.0003798011202010.011720768460.25918554830.1967137050420.08105630608230.2914493861830.0265417303083-0.04450400085840.2288438482660.0550325672670.297209705795-0.423060483051-5.6776407128737.2631343069
20.6689564499970.146933919861-0.4114106602440.06131220369120.005547795062040.936019525339-0.0224259740421-0.00671653235359-0.09703578004060.1470913675380.009610804341250.02577714563420.175835820989-0.00125770644098-0.003890775067640.243663877180.0306316485421-0.02757548119840.23288357479-0.002816965278040.22234638348910.949179405515.543571042231.2563817259
30.3149631207970.335019889322-0.02797856580410.354641219330.002616895019610.5287775785270.01695417975220.00681320478757-0.0766547133144-0.005993260468850.00744523723315-0.05979782977040.08209058308980.0540294990886-0.02207608186330.2327328992950.03170813579610.001424623552490.247320152004-0.01769981019080.21888255580917.576961187618.90286412721.2296722439
40.971306263499-0.797147463316-0.1974151751562.67051175352-0.4392395639760.916745702352-0.08239783561560.00241850890805-0.243184813132-0.07841121978170.02196430845440.11741128280.3436729006740.1298915297990.04895084432940.3201906679680.00150451237076-0.007440640382740.368076316521-0.04131215719030.29891976408919.32679824029.9667249746731.3132180413
50.603436973333-0.01516250488010.1707888694513.19752826756-0.2555439470810.4549887184220.1511099004680.0484913144988-0.256217315638-0.0576071488753-0.3137068567930.2509923833870.1591593485240.2564250164020.1458456644630.2739747318140.05961728387380.03581360816150.293253442927-0.00683200787420.31691494271131.912316800512.100395222920.3276838869
60.4126935595220.282306020963-0.4073321202710.6300113879080.01306279443460.9685098989920.0468886121688-0.0681353028388-0.1381065866170.0518305708091-0.0860141276148-0.1243284306110.1668309992570.2189634807160.06380254966540.2487574018130.0444001419420.001667383231460.2923115355050.007946053469950.271788360536.239748711618.217628144626.4996975389
70.8346511338290.05304704687410.1058533794910.591233343565-0.1889136116311.23896767579-0.01634073513770.02542838358780.03593441384250.01884123512320.00434535480563-0.049267984874-0.1539376938760.1535139225436.02160649555E-50.2430859473770.01545155760940.02071679144610.255682673151-0.02022561588880.2393212507936.398384352838.478436540314.3434412252
80.4199446518250.080687316936-0.1363169479360.5297706163820.175656776810.119880815388-0.009684116707330.106812267086-0.06259321262690.004280641192960.0130396719502-0.02009422752950.0368026378618-0.00858488982351-0.006169898936040.2469457917910.01600760173120.02835497775570.258085582308-0.02190287974110.24525344560234.152759123918.5409046732.71796484545
91.48888792297-0.431991752399-0.765218642050.877944781856-0.1830060280030.9332900363730.05732698397790.2487240780780.00662424400630.0185365189142-0.0403526761975-0.0637874670576-0.235149375014-0.00857297583994-0.01005632146860.238689774814-0.018344059110.009538147182360.278358095625-0.0003120411364950.22316643836524.763316096737.36654921892.45759693723
100.9574993780110.41436988678-0.3212066336071.339822325170.5067677469510.9254280780620.146608519297-0.0443424038464-0.00340950243460.084865155833-0.0186330391226-0.02809925137510.01032907372370.135132251644-0.07989671861570.2411882334710.01454650678277.91815463381E-50.21960231989-0.01817762353980.22850975522321.998554127241.110909694729.7597420437
110.2700801822820.0289581726964-0.1311381308670.306034335183-0.08432318881710.459788318322-0.01600937333460.0337740170163-0.079598570529-0.03263847061960.02424517496820.008641032521010.122356243209-0.0369938106198-0.008541880531550.2338686749040.00399508215761-0.01769517144540.202420820564-0.01317445022880.2246132931-3.223996794134.337322957622.1167635414
120.8287648391620.587351753768-1.018073732020.750674364842-0.8292488327531.345777194410.003300527889760.195609269362-0.1127855329410.01352750398420.07967841809290.1123964122690.107017777035-0.269193528846-0.02792968427470.31875192867-0.0677975285391-0.02561649483510.271831402131-0.009991189200650.290742403245-10.7512907186-7.3545694240911.051195075
130.960774076830.190678988189-0.435855655171.01207186726-0.3173759702650.602370257391-0.2308106280160.323148403928-0.203663115138-0.1859202233730.1504948361190.06696683745070.249372250564-0.526715769350.06295714240720.33638585563-0.075347348531-0.02289111428020.343043215303-0.01741059461350.34069155534-22.3380751172-6.8808610962915.6767139593
144.93497900698-0.257088812727-0.5204323212683.82604416360.3199325509833.44203122703-0.08390532011990.322237863130.117309944691-0.5973215902630.07414627828960.092276925602-0.2894153752720.406938773392-0.001234022268370.327317552457-0.006674242771470.03007158077350.360405747041-0.00540151739430.21161251411619.370366827423.5778789343-9.5664921895
152.066536280652.330994784271.247082606934.49616952151.773049176221.288397177150.03012075278230.416694590224-0.0507561687409-0.381902393492-0.0126549026620.21337983273-0.015399824234-0.0299093874667-0.006051601418970.394740377917-0.0160447551636-0.04059591652730.46667310971-0.01070235511460.21896923135710.65477247311.7032965102-16.1889451773
162.629356801050.132456209057-0.2716487108810.716994990343-0.4757255268360.918592719066-0.05138000792140.432779009025-0.479966646749-0.3208461032240.0858587968306-0.08820657388230.0658775741273-0.008754619537680.005852493708030.3509210403810.02950712172710.05046558055480.344435646641-0.1001316784580.30365857133614.39235155060.731405915273-13.0247029622
172.5147701811-1.892216345690.1771939961163.44259189568-0.7530399886311.03568067889-0.2106743479950.218604348073-0.1352888368950.01289131727690.205927102597-0.05563427939850.1820162565850.102905533951-0.02729342428490.3189383056060.01799968594890.0309184384330.324835610078-0.06176645013280.28192119756825.24129501158.21893591632-8.44845570894
181.879143214891.00408001326-0.5132745121581.67044214069-0.1979887855270.63300697176-0.07748105564830.08095778394180.127604156149-0.1463755684960.05589093848380.1174694338440.188680720994-0.06317877345480.01288242451940.305021703798-0.00475087652581-0.004664564541440.299421793248-0.03394721168260.2553911323787.23264156656.10592340693-8.05638468346
194.540922067040.652017765106-1.452989387350.3928132163040.1204885539132.21232603838-0.04232033086320.0256413827262-0.273456397339-0.1618015893960.244189295614-0.0657210269640.463880487716-0.102534642863-0.1908452809860.404746652348-0.09223346530310.008405468269910.336390754919-0.04140676315680.3341952858833.12486457332-9.81964851893-6.03420971202
200.8191589959160.2325423011450.2233213695980.539031305284-0.07853124648860.557380185411-0.1689812019340.158386835374-0.273645337401-0.2001701364790.157215436136-0.2529953579520.2740501646270.1697567596610.001361435628550.4308855064280.0159486514460.07254059631060.250299564087-0.07284389390680.38773854656620.9596001242-8.55054508269-0.736789470079
213.57482633379-0.5387029727180.5906380425130.748114008565-0.02208339987420.865101039492-0.10879834128-0.346205602675-0.09350785200010.05344214652080.0718033924592-0.1395831622860.4116249930610.03891303023610.05191401131350.3879706569290.0461330545390.04308461802330.230429218868-0.02261374586440.3521428833819.1848427255-6.756371908327.09985930423
222.694784569441.3820971138-0.6708628151341.38668744336-0.2464808606491.23783284379-0.0928773966478-0.154852430086-0.297147859811-0.114829683675-0.121935517729-0.06655226004830.1984107295970.1057154221020.1761673519690.3215372315240.1369964591310.01262581352750.381664261773-0.0005082190235140.45481749233938.7283262995-3.0720837322112.7114226059
231.053111127070.9342789395070.2388187976643.56878967075-1.028086388150.61528002392-0.125831570898-0.0175530327944-0.13955343012-0.2995579712970.034639784725-0.5465118237160.1522661248790.2208288248490.0381534418530.3036329409340.0759476335730.08671278533280.340817876736-0.08216936930650.40099259442543.98176101435.879149427150.904506938144
241.70975904232-0.0145151399067-0.3481160072312.019377125260.1210360881551.36247058517-0.0440858087571-0.270413457454-0.03597200280180.110699673366-0.036444739844-0.2141955271950.2144092558180.6696081405830.1182264964510.3299273910780.0783931793435-0.04531863608820.5296714827060.04535572218970.30481506560643.069887078218.333673658935.729723026
251.51453109948-0.4135403293490.2146898960940.985748662644-0.2750478213690.909600957315-0.063315650326-0.444014859439-0.07589990436850.1700315367230.0585410375023-0.04084717304890.116056490717-0.05915604862370.004236684120180.3693778152680.04252733343250.002363319829170.3623632867620.00804992576730.31049681415623.864713723920.550434936447.1429424466
261.84976140585-0.664364444376-1.27964144140.8804178633371.118605968391.76342998183-0.2553502517960.0518250251476-0.351227023360.339125676484-0.04289733988650.1078758598130.480603716147-0.2148550624940.2363714917130.4426015677780.03141964441220.05201697165570.3774746597470.007551697527710.38203062726617.285312683610.060756764645.4778566068
270.763732449838-0.351631792238-0.5498647183141.435172400611.241307800082.23865223790.02106726691190.0767297768653-0.0623411489262-0.207191698483-0.1249731935980.292994586693-0.260644728669-0.3531339681070.1070294666150.2258730309460.0338791560297-0.04595366011510.2814892601920.03447920887860.284450246452-30.280363951822.921158266536.2864148969
280.04368903996440.01341551127310.1679060480680.2197944665220.3150411820310.866378432859-0.04494436992980.1458572576380.0408162167060.01164384080650.01304204579060.120509247607-0.0679477562615-0.1421195299180.03089345776240.2718014883480.01093085025550.03263588629360.2284046154880.03872733520810.284007459844-9.7322675613935.128725630542.8281496634
290.1786395024110.2465661633440.02166775204470.3224217308090.2914663140210.822257432618-0.01467124049830.01076768874420.0670858324871-0.02399546637060.00401129205240.0799490596798-0.0918876291942-0.1216120240580.02696168306620.2643157222270.01501284212010.03221006454780.2403992913470.0122920731370.239792338867-8.4910737157342.001242060851.1674163989
300.426934733387-0.0895971429686-0.1838775600750.5308727480620.1047244084080.792648040703-0.07777023067870.128581504890.0282958446662-0.1154303533770.007159024380910.13314004529-0.174660963936-0.1362492271520.06882473342960.3329762379710.04622375703320.001597327062410.251523258456-0.02582836955480.28768916923-12.620071554457.36203051748.1371118393
310.316629995994-0.07185264649950.3765756939560.826726183587-0.1422947054581.1767643742-0.0348241539001-0.01591677431920.101730033902-0.03707482436960.01381078279010.0313798824204-0.109275215787-0.06696105438560.04532233359370.2950789440280.01410236360460.04055383215710.198135430989-0.01420150996950.2345747941914.2205776113462.17055504956.4509231876
321.241701696770.240010139335-0.0830346729470.2700865166050.1357321752270.379856765588-0.00380038903495-0.05237660806440.1064281685960.07398870039980.02489091293630.023239631831-0.06690219155230.0269662518077-0.01970952222650.292235330620.0322202462020.01766793144090.190587500218-0.02624607972910.232388140952.4332631086862.459712553968.8954204903
330.843556306135-0.0564448588793-0.1225228192150.3051044359020.1734272922420.522802780171-0.0160182106664-0.2350518362060.05428006086110.05469910214580.03217551722360.0457189698809-0.05161921597180.0624542406425-0.0144166185780.2759162057670.02537756986820.03146041560920.248560313851-0.01291919364970.211839980876-0.83371321942151.824371967172.6822253664
341.679951300360.0466516453455-0.5279357277130.6443805294660.3181244228450.345881228375-0.01379421210650.2799275342160.152041526403-0.07265495009040.01543998026150.00294919075817-0.06964653013660.06212659714380.02197940441760.206715311472-0.01241852283550.007352991062690.24084452074-0.01071570007030.2433890691615.216105352547.337563786544.977298418
350.5507180130340.249247822447-0.243069344610.7785445449160.07631405204660.406284829062-0.134279769435-0.0907963581486-0.1271395238080.1029887833650.07227229929730.09537407470760.0327170709805-0.03509613564710.05888646492610.2780259574930.01829904611450.02640683132780.2807696436230.01193574612060.221686571756-1.5577327747728.122666361163.3515275579
360.223558671409-0.0171121684028-0.04412742221220.2951108423960.21091179770.4539612218160.009957739024940.0136576817087-0.005453258098440.0180047273386-0.004054746090810.0888320558547-0.00646241334496-0.101137875842-0.01019199899380.19005395805-0.002419334404790.02005522900820.2351953451260.03903263455080.237806413709-22.956822831419.215160713149.9296375254
370.6603830953610.3870368790280.5373328062181.124129710050.7097636399531.274820447030.0730617677143-0.0656488357648-0.04734704857480.210618578768-0.02653154427210.2308316340090.134497665904-0.201046229026-0.01934833447280.252822803458-0.02981921759340.03999796150140.3054770260980.0436820067490.27837141479-31.831001038812.063252675762.5225048143
380.9603860047350.01640977341290.5483057546180.611781959440.2954748637661.101250988280.0781526839326-0.0954015412788-0.180389068310.132896874356-0.06571052671230.2157278286170.315592239453-0.26572042083-0.0198598810170.30833714919-0.05965917181810.01855619622830.2969733732080.02980525620370.330550313494-30.90690060780.54545027365157.4189964638
393.751362243250.35417142140.1109192889782.260753729260.2142725281824.129037141380.0726666383154-0.0651995794441-0.4042703165090.1792671028180.215113760775-0.249936267833-0.175738807473-0.0102515284289-0.2367458681320.2755800536970.02158737797120.03510063418110.394880483829-0.01275543419790.275105444221-2.8788575329943.232155106283.9010396517
404.443083796782.47844799071-1.281438939491.96448283458-1.051321121460.807083419252-0.0892612384121-0.357813467886-0.1418933962910.309550980673-0.04311924150870.01695697591260.126106463870.07524412953650.1392169623060.424427703049-0.01903087855970.04792054852420.3592606893240.04292980056650.284019643932-14.425135276433.773514586690.1449630313
410.5617886789590.359821047074-0.01766841952011.29396334414-0.005692427181410.4197545169060.100109495034-0.1258031261930.05639056210770.259613777394-0.1141036949010.1813888097010.0355775956734-0.02131392207970.01701499146070.3097340357630.01751265671220.08692812243970.324931969936-0.001780183066940.2716774359-24.139206511734.799915305682.7993715556
420.588035195136-0.06027710806450.3042323675731.10268535276-0.4161716599660.3593816491120.124806874043-0.1015873413630.1753109811510.166498507659-0.1235793508290.304043679527-0.156880292002-0.170906784591-0.01309567741140.2799691595330.05981836700940.09700292217080.40913406741-0.01828650904790.421693121984-34.811950566343.4720416274.564064838
430.6111753697390.232425485858-0.05356439168572.83297413208-0.198133334170.7539774022280.01302850220650.0500124297170.119096704326-0.130756113375-0.09860394707790.0326010586515-0.16249999716-0.2937045059130.09021920971420.2600929073780.06463888998570.04099729429770.3774436279580.01067750487860.398061664682-31.888039716747.994311201865.1391762788
443.450924683941.136469426350.8344199417051.80258711350.2455008680771.53209105703-0.0621202569444-0.2673538585360.5397475252430.0177710032945-0.1273530257110.396706427228-0.202617182008-0.2500661535710.1719172772730.3183291348670.0633152551860.0594235407720.238654287171-0.03793235823180.389039620579-21.330723431867.174731974373.6088456434
453.225498754290.917253076675-1.95064900064.941305324260.1625900151981.331398991350.09930174968120.4329670514090.275524711517-0.431683869733-0.0969111797470.325881763856-0.192091301845-0.1013067572580.02327403710030.413453815010.0322058524026-0.01095163550340.4384210599960.0536707316960.362062304709-6.2496936623361.416064192730.1908431504
462.637978790970.69641369050.4683212695261.704216042780.3744544625421.48848487658-0.0844476029043-0.03584612541550.199116067161-0.182521937719-0.0131429869494-0.00366650891398-0.480108141509-0.1717636384850.08679580804120.4589881570910.0377747835313-0.0219652495120.2534134322220.04303636747090.287313247881-9.0460030819369.41051819541.6829928178
470.9287594071140.0147355131901-0.2365672455190.07472738044570.1992429226960.6489434538960.0213962247063-0.09354831018990.0856439316377-0.09666427095970.0121473015508-0.04840202936820.0618662767318-0.0435503035108-0.0263727953920.39670089980.0311164238055-0.002873366869970.337596784733-0.003610051991420.353236155913-6.2366573744546.504095473732.9158847267
481.85400359727-1.495616315661.468534431074.02700572282-2.471072391932.695859630890.111139609940.344214966517-0.0628661576288-0.563992703493-0.3942788824790.0346465998695-0.29506348997-0.2933455224620.28297430990.5462328440940.0903557490415-0.03962353449730.561849913366-0.06303109250890.362857989768-4.4202489237844.866006460721.9116409648
490.9393226459490.00383385053476-0.6661146303111.401233032310.2683682640440.9210864495980.0110362438889-0.0101058016317-0.013542320882-0.322053948017-0.1471492127950.152512480105-0.04421449791330.03402013074090.1341912042980.3427670762350.0252787681433-0.02301894462650.3319340798030.007177836565790.353330473547-5.2702569271452.764067386129.5811600731
503.51989710986-1.22348506159-1.039130375464.748924288362.466089314163.7860007407-0.09319760710880.499135836385-0.474329769737-0.608778763057-0.2348280582090.122891518924-0.0224331962633-0.4095636388280.3195967124850.3733579382390.02000651282640.01684443685310.455681660525-0.04399129824130.381487976812-10.450443127439.482550186621.6464481592
510.776604957633-0.574547439703-0.8444715959131.071492411950.5699572572190.972346949555-0.1718446759740.054827124533-0.3910002261340.263276843224-0.1741447166650.4100968348040.193126364081-0.2200364135340.3391098539690.327576616835-0.009433267402450.04493683640220.355419888866-0.1035855427520.406153193639-13.642076488539.379480397130.3379693741
521.104708287840.6714540648141.731021268640.5665024018590.5959116165634.00343700415-0.178908427910.300002275475-0.258141493823-0.648947362034-0.009630389886790.283693255954-0.0075117771509-0.7895433660320.1765863769030.586227537415-0.0488460251179-0.07412027555010.888085797159-0.1233046465290.571053938874-30.275607933451.655131075728.9329714347
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 12 through 45 )
2X-RAY DIFFRACTION2chain 'A' and (resid 46 through 96 )
3X-RAY DIFFRACTION3chain 'A' and (resid 97 through 230 )
4X-RAY DIFFRACTION4chain 'A' and (resid 231 through 260 )
5X-RAY DIFFRACTION5chain 'A' and (resid 261 through 292 )
6X-RAY DIFFRACTION6chain 'A' and (resid 293 through 352 )
7X-RAY DIFFRACTION7chain 'A' and (resid 353 through 403 )
8X-RAY DIFFRACTION8chain 'A' and (resid 404 through 484 )
9X-RAY DIFFRACTION9chain 'A' and (resid 485 through 526 )
10X-RAY DIFFRACTION10chain 'B' and (resid 4 through 36 )
11X-RAY DIFFRACTION11chain 'B' and (resid 37 through 312 )
12X-RAY DIFFRACTION12chain 'B' and (resid 313 through 344 )
13X-RAY DIFFRACTION13chain 'B' and (resid 345 through 395 )
14X-RAY DIFFRACTION14chain 'C' and (resid 2 through 10 )
15X-RAY DIFFRACTION15chain 'C' and (resid 11 through 25 )
16X-RAY DIFFRACTION16chain 'C' and (resid 26 through 40 )
17X-RAY DIFFRACTION17chain 'C' and (resid 41 through 53 )
18X-RAY DIFFRACTION18chain 'C' and (resid 54 through 72 )
19X-RAY DIFFRACTION19chain 'C' and (resid 73 through 87 )
20X-RAY DIFFRACTION20chain 'C' and (resid 88 through 125 )
21X-RAY DIFFRACTION21chain 'C' and (resid 126 through 144 )
22X-RAY DIFFRACTION22chain 'C' and (resid 145 through 152 )
23X-RAY DIFFRACTION23chain 'C' and (resid 153 through 169 )
24X-RAY DIFFRACTION24chain 'D' and (resid 2 through 36 )
25X-RAY DIFFRACTION25chain 'D' and (resid 37 through 82 )
26X-RAY DIFFRACTION26chain 'D' and (resid 83 through 133 )
27X-RAY DIFFRACTION27chain 'E' and (resid 12 through 45 )
28X-RAY DIFFRACTION28chain 'E' and (resid 46 through 96 )
29X-RAY DIFFRACTION29chain 'E' and (resid 97 through 260 )
30X-RAY DIFFRACTION30chain 'E' and (resid 261 through 331 )
31X-RAY DIFFRACTION31chain 'E' and (resid 332 through 382 )
32X-RAY DIFFRACTION32chain 'E' and (resid 383 through 441 )
33X-RAY DIFFRACTION33chain 'E' and (resid 442 through 526 )
34X-RAY DIFFRACTION34chain 'F' and (resid 4 through 36 )
35X-RAY DIFFRACTION35chain 'F' and (resid 37 through 66 )
36X-RAY DIFFRACTION36chain 'F' and (resid 67 through 312 )
37X-RAY DIFFRACTION37chain 'F' and (resid 313 through 344 )
38X-RAY DIFFRACTION38chain 'F' and (resid 345 through 395 )
39X-RAY DIFFRACTION39chain 'G' and (resid 2 through 10 )
40X-RAY DIFFRACTION40chain 'G' and (resid 11 through 25 )
41X-RAY DIFFRACTION41chain 'G' and (resid 26 through 87 )
42X-RAY DIFFRACTION42chain 'G' and (resid 88 through 125 )
43X-RAY DIFFRACTION43chain 'G' and (resid 126 through 152 )
44X-RAY DIFFRACTION44chain 'G' and (resid 153 through 169 )
45X-RAY DIFFRACTION45chain 'H' and (resid 2 through 10 )
46X-RAY DIFFRACTION46chain 'H' and (resid 11 through 36 )
47X-RAY DIFFRACTION47chain 'H' and (resid 37 through 45 )
48X-RAY DIFFRACTION48chain 'H' and (resid 46 through 63 )
49X-RAY DIFFRACTION49chain 'H' and (resid 64 through 82 )
50X-RAY DIFFRACTION50chain 'H' and (resid 83 through 95 )
51X-RAY DIFFRACTION51chain 'H' and (resid 96 through 125 )
52X-RAY DIFFRACTION52chain 'H' and (resid 126 through 138 )

+
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://pdbjlvh1.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