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- PDB-7rth: Crystal structure of an anti-lysozyme nanobody in complex with an... -

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Basic information

Entry
Database: PDB / ID: 7rth
TitleCrystal structure of an anti-lysozyme nanobody in complex with an anti-nanobody Fab "NabFab"
Components
  • (Fragment Antigen-Binding ...) x 2
  • NanobodySingle-domain antibody
KeywordsIMMUNE SYSTEM / Antigen / FAB / Single-Domain Antibody
Function / homologyDI(HYDROXYETHYL)ETHER / PHOSPHATE ION
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.19 Å
AuthorsFilippova, E.V. / Mukherjee, S. / Bloch, J.S. / Locher, K.P. / Kossiakoff, A.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2021
Title: Development of a universal nanobody-binding Fab module for fiducial-assisted cryo-EM studies of membrane proteins.
Authors: Joël S Bloch / Somnath Mukherjee / Julia Kowal / Ekaterina V Filippova / Martina Niederer / Els Pardon / Jan Steyaert / Anthony A Kossiakoff / Kaspar P Locher /
Abstract: With conformation-specific nanobodies being used for a wide range of structural, biochemical, and cell biological applications, there is a demand for antigen-binding fragments (Fabs) that ...With conformation-specific nanobodies being used for a wide range of structural, biochemical, and cell biological applications, there is a demand for antigen-binding fragments (Fabs) that specifically and tightly bind these nanobodies without disturbing the nanobody-target protein interaction. Here, we describe the development of a synthetic Fab (termed NabFab) that binds the scaffold of an alpaca-derived nanobody with picomolar affinity. We demonstrate that upon complementary-determining region grafting onto this parent nanobody scaffold, nanobodies recognizing diverse target proteins and derived from llama or camel can cross-react with NabFab without loss of affinity. Using NabFab as a fiducial and size enhancer (50 kDa), we determined the high-resolution cryogenic electron microscopy (cryo-EM) structures of nanobody-bound VcNorM and ScaDMT, both small membrane proteins of ∼50 kDa. Using an additional anti-Fab nanobody further facilitated reliable initial three-dimensional structure determination from small cryo-EM test datasets. Given that NabFab is of synthetic origin, is humanized, and can be conveniently expressed in in large amounts, it may be useful not only for structural biology but also for biomedical applications.
History
DepositionAug 13, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 1, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 16, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fragment Antigen-Binding Light Chain
B: Fragment Antigen-Binding Heavy Chain
C: Fragment Antigen-Binding Light Chain
D: Fragment Antigen-Binding Heavy Chain
E: Fragment Antigen-Binding Light Chain
F: Fragment Antigen-Binding Heavy Chain
G: Fragment Antigen-Binding Light Chain
H: Fragment Antigen-Binding Heavy Chain
I: Fragment Antigen-Binding Light Chain
J: Fragment Antigen-Binding Heavy Chain
K: Fragment Antigen-Binding Light Chain
L: Fragment Antigen-Binding Heavy Chain
M: Fragment Antigen-Binding Light Chain
N: Fragment Antigen-Binding Heavy Chain
O: Fragment Antigen-Binding Light Chain
P: Fragment Antigen-Binding Heavy Chain
Q: Fragment Antigen-Binding Light Chain
R: Fragment Antigen-Binding Heavy Chain
a: Nanobody
c: Nanobody
e: Nanobody
g: Nanobody
i: Nanobody
k: Nanobody
m: Nanobody
o: Nanobody
q: Nanobody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)574,950118
Polymers568,02627
Non-polymers6,92491
Water2,972165
1
A: Fragment Antigen-Binding Light Chain
B: Fragment Antigen-Binding Heavy Chain
a: Nanobody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,5629
Polymers63,1143
Non-polymers4486
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Fragment Antigen-Binding Light Chain
D: Fragment Antigen-Binding Heavy Chain
E: Fragment Antigen-Binding Light Chain
F: Fragment Antigen-Binding Heavy Chain
c: Nanobody
e: Nanobody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,41434
Polymers126,2286
Non-polymers2,18628
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
G: Fragment Antigen-Binding Light Chain
H: Fragment Antigen-Binding Heavy Chain
I: Fragment Antigen-Binding Light Chain
J: Fragment Antigen-Binding Heavy Chain
g: Nanobody
i: Nanobody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,28332
Polymers126,2286
Non-polymers2,05526
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
K: Fragment Antigen-Binding Light Chain
L: Fragment Antigen-Binding Heavy Chain
M: Fragment Antigen-Binding Light Chain
N: Fragment Antigen-Binding Heavy Chain
k: Nanobody
m: Nanobody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,49123
Polymers126,2286
Non-polymers1,26317
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
O: Fragment Antigen-Binding Light Chain
P: Fragment Antigen-Binding Heavy Chain
Q: Fragment Antigen-Binding Light Chain
R: Fragment Antigen-Binding Heavy Chain
o: Nanobody
q: Nanobody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,20120
Polymers126,2286
Non-polymers97214
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)225.530, 130.280, 223.980
Angle α, β, γ (deg.)90.000, 107.990, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Antibody , 3 types, 27 molecules ACEGIKMOQBDFHJLNPRacegikmoq

#1: Antibody
Fragment Antigen-Binding Light Chain /


Mass: 23258.783 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pRH2.2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): C43
#2: Antibody
Fragment Antigen-Binding Heavy Chain /


Mass: 25684.463 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pRH2.2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): C43
#3: Antibody
Nanobody / Single-domain antibody


Mass: 14170.781 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET26b+ / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)

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Non-polymers , 5 types, 256 molecules

#4: Chemical...
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 50 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical...
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 29 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 165 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.92 Å3/Da / Density % sol: 57.53 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8.8
Details: 0.02 M Citric acid, 0.08 M BIS-TRIS propane, 16 % (w/v) PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jun 11, 2021 / Details: 3.3 Undulator (Undulator A)
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 3.19→111.43 Å / Num. obs: 102005 / % possible obs: 99.4 % / Redundancy: 5.7 % / CC1/2: 0.98 / Rpim(I) all: 0.17 / Net I/σ(I): 9.5
Reflection shellResolution: 3.19→3.36 Å / Redundancy: 5.4 % / Mean I/σ(I) obs: 1.9 / Num. unique obs: 14566 / CC1/2: 0.47 / Rpim(I) all: 0.737

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX1.16_3549refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6JB9, 5C8J
Resolution: 3.19→90.907 Å / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 0.31 / Phase error: 26.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2671 5099 5.12 %
Rwork0.2159 94559 -
obs0.2185 99658 96.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 249.68 Å2 / Biso mean: 77.104 Å2 / Biso min: 7.32 Å2
Refinement stepCycle: final / Resolution: 3.19→90.907 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms37922 0 354 165 38441
Biso mean--82.41 30.83 -
Num. residues----4958
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.1905-3.22670.309165141144
3.2267-3.26470.32351410.3258679
3.2647-3.30450.34311610.2985309197
3.3045-3.34630.34351700.28293304100
3.3463-3.39040.33911690.28073187100
3.3904-3.43680.33231790.27163269100
3.4368-3.48590.311590.26173181100
3.4859-3.5380.28561920.25573251100
3.538-3.59320.27771820.25473224100
3.5932-3.65220.30541660.26023225100
3.6522-3.71510.31781860.25383242100
3.7151-3.78270.30431810.24993212100
3.7827-3.85540.33321780.23593211100
3.8554-3.93410.28951410.23443298100
3.9341-4.01970.25512000.22633169100
4.0197-4.11320.27591780.2133270100
4.1132-4.21610.28051920.21353211100
4.2161-4.330.23091530.19043276100
4.33-4.45750.25021940.1822317599
4.4575-4.60130.23461660.17043246100
4.6013-4.76580.20651500.1715321699
4.7658-4.95660.20831700.1699320298
4.9566-5.18210.23022010.17233238100
5.1821-5.45530.25531640.17493264100
5.4553-5.79710.27491850.18863239100
5.7971-6.24460.25281970.19853266100
6.2446-6.87280.23241610.20973280100
6.8728-7.86680.26071720.2053322199
7.8668-9.90940.21051730.1781326998
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)
11.39621.8530.95573.04451.65530.9120.40180.16570.05450.30630.2217-0.4416-0.0808-0.00490.13351.9830.48690.64870.39180.03560.797520.765372.3314-98.2239
23.2590.78030.59544.2305-2.22393.43550.40240.2850.58130.4970.08010.1269-0.5547-0.1144-0.07711.43350.04050.2270.29470.26730.495519.283561.725-92.3417
30.84330.6159-0.29552.0241-0.26440.10480.24620.44140.71580.59270.11590.7118-0.6379-0.3316-0.22951.33240.34570.3150.68340.36450.67189.671764.7204-94.0264
42.2229-0.9548-0.08772.51990.14141.2460.8150.16220.71540.6037-0.24520.3011-0.5204-0.22820.2521.8630.48080.62660.64030.19750.743218.758768.5889-92.0902
50.5711-0.00150.02921.0803-0.72220.48340.377-0.0810.80040.07240.43880.1652-1.22830.1649-0.10521.7507-0.10760.60390.6482-0.18610.78227.093470.6939-97.4061
61.68610.1475-1.08920.0144-0.080.9234-0.1189-0.0902-0.23810.14230.0895-0.140.07260.34020.36932.1025-1.19760.70851.755-0.6251.160161.169176.0503-92.8613
70.37340.16910.33491.07850.70270.57160.16430.124-0.04040.0742-0.0213-0.0834-0.48570.26050.04042.5398-0.83580.66220.4716-0.67260.872245.842879.1579-100.0594
81.7603-0.1035-1.27220.0739-0.24342.5394-0.1050.03120.04360.32650.3151-0.0768-0.60220.1849-0.08111.9705-0.55290.54230.8349-0.32090.727643.500776.8492-97.9911
93.02410.30670.270.98040.61721.23260.05440.215-0.2776-0.44490.3962-0.5006-0.52670.8580.0651.6846-1.15250.40951.1878-0.43941.119555.413173.9973-99.4855
103.08410.54151.30911.08920.74711.65110.2130.3153-0.2729-0.01710.1678-0.391-0.08930.4935-0.3932.0669-0.45570.74350.512-0.50980.87854.703181.8439-104.9752
113.96751.0958-1.70450.4151-0.45811.1389-0.03410.1199-0.0952-0.38790.1921-0.3546-0.53780.280.04172.5107-0.60520.99180.8884-0.22571.103850.016587.3358-102.9118
124.73440.9928-1.01052.9047-0.62774.16110.7251-0.3939-0.40150.8581-0.441-0.6805-0.25110.2778-0.28530.7775-0.1396-0.10720.37130.09190.743427.97446.8236-85.0468
133.0850.10591.52246.08225.2147.05080.4985-0.1495-0.91540.4919-0.0447-0.18110.03730.5293-0.24630.66320.0877-0.00890.3870.09160.584426.47345.0331-96.0576
142.73090.1997-0.18990.9348-0.23461.2071-0.2083-0.0352-0.41220.25350.0765-0.4168-0.22670.08880.14720.9025-0.0329-0.00920.51590.13430.717923.880347.8266-90.311
151.50120.79311.32880.9941.54932.53660.5529-0.46830.14291.10530.145-0.1804-0.9911.0169-0.08442.1449-0.71560.46681.5151-0.43640.763650.071270.8001-86.2764
160.3943-0.0614-0.32620.01930.04210.2660.0633-0.00360.0403-0.0571-0.15710.42850.02950.24170.06631.4702-0.2901-0.0951.4195-0.20320.56655.501567.0729-78.0819
175.40670.6382-0.32492.25510.08712.10170.06380.3867-0.2813-0.18750.03190.2235-0.0479-0.0386-0.07270.2416-0.0205-0.10310.24870.0130.4459-1.130588.5664-25.8545
187.05970.96631.23711.22690.23131.46-0.12420.66870.0556-0.32940.32550.2167-0.0818-0.2096-0.26120.3515-0.0158-0.04180.23720.0320.3447-8.359595.1202-28.5732
192.2295-0.24460.15544.6978-0.71892.1661-0.2552-0.05850.44020.02830.1535-0.0352-0.150.07520.06350.12070.00250.00330.43650.00730.4524-30.1597110.584-26.7021
200.7776-0.0877-1.51286.1489-1.27533.3601-0.11750.0305-0.04910.1277-0.3546-0.5092-0.3286-0.66140.23480.455-0.06880.05140.75810.11630.5124-26.7033114.0527-34.5788
212.1878-0.54130.06344.07810.1952.03080.2211-0.22420.2848-0.0861-0.14490.193-0.291-0.3478-0.10470.1863-0.0730.05120.49740.08390.4707-31.5147109.2773-29.2142
223.1883-0.92890.06282.2964-0.14413.5569-0.2179-0.74290.70490.7377-0.32390.0762-0.3069-0.00140.51550.381-0.1756-0.03870.7145-0.15240.87083.9663111.6733-12.0145
230.27780.2445-0.05413.40730.29844.7843-0.0854-0.3230.63110.27580.1074-0.19580.27280.7034-0.07320.2823-0.0613-0.08470.5558-0.06310.62529.5504104.7475-15.3137
245.08292.70130.32732.87870.34012.7407-0.11320.42280.35520.17050.0372-0.3658-0.41720.67080.10610.2098-0.1548-0.1180.26310.03330.785713.2528107.8376-24.6626
251.8757-1.8458-0.30123.68630.05330.7404-0.03720.26290.64860.4042-0.0949-0.4095-0.3030.16420.11060.2223-0.0203-0.06850.5653-0.05710.64089.9919105.5988-19.4832
261.2225-1.6025-0.57992.34-0.14163.2946-0.42-0.2870.5432-0.48650.17990.58850.0412-0.06260.19150.562-0.09370.02460.32070.00720.5718-32.1936112.9669-16.9406
272.9771.1309-0.01163.6350.0262.0380.2354-0.36360.52330.5092-0.16380.02050.23170.1765-0.01880.4397-0.0349-0.00590.3877-0.0120.4276-22.8438110.2008-11.453
280.5304-0.0840.3880.79670.37810.5320.3444-0.17560.71050.0482-0.2762-0.2906-0.4785-0.1032-0.09110.3726-0.06850.05690.32430.04230.6201-19.7972113.6126-20.1692
296.04022.5373-1.37532.63230.35661.2037-0.4067-0.1865-0.32690.2862-0.19170.47840.3116-0.26580.40430.3767-0.1114-0.01940.33350.03470.2554-40.7047102.2842-13.0662
304.36641.6175-1.88934.2803-0.57522.87380.4629-0.42340.41310.9777-0.04970.10340.0685-0.1878-0.37430.7544-0.07670.0150.7873-0.19270.4275-29.9536114.4433-7.7905
315.4223-2.2446-2.20833.04940.10821.31280.0375-0.2837-0.10740.09080.2265-0.25210.24210.299-0.23390.31910.0024-0.12660.60440.18990.5976-22.8593114.8221-43.2181
323.17520.28460.23446.64342.6973.04470.3468-0.4378-0.29260.1571-0.1243-0.62190.3251-0.0235-0.19840.3037-0.0074-0.00060.45760.16710.4564-14.8652124.1768-47.2745
330.45270.7572-0.30752.6254-0.07590.73090.20080.116-0.20790.33420.19050.10410.2038-0.0399-0.35860.4460.1383-0.09520.55510.09390.5283-21.1358120.0063-46.9127
345.1302-2.17930.38563.2842-1.10341.91830.05320.52980.2036-0.3304-0.2438-0.12360.3251-0.36830.18430.3916-0.0421-0.07420.4008-0.08650.3545-11.603286.1701-47.9997
356.0712-2.93162.59535.4422-3.18596.91450.10860.64990.2445-0.2445-0.04510.0044-0.5098-0.4304-0.07860.4451-0.0372-0.0230.5071-0.03250.3614-15.453494.7994-47.6217
365.1083-0.8794-0.61151.6502-0.33711.0854-0.20520.0667-0.8423-0.07040.20710.12070.26120.02870.02450.3946-0.0211-0.11220.3998-0.07820.6529-11.801280.7561-43.6948
370.0452-0.1585-0.20851.90552.22382.6503-0.1002-0.2604-0.4702-0.97420.1728-1.0047-0.18360.6859-0.05090.4982-0.03190.19150.52760.13740.94361.6067124.5519-57.0715
383.96951.16090.7625.10540.95633.2409-0.1038-0.18270.04490.392-0.1284-1.0209-0.02590.15240.23290.3571-0.0528-0.00420.53460.05920.8631.6028124.6262-45.3213
392.5198-1.6468-0.40964.92970.841.6666-0.1457-0.2694-0.06590.02310.3404-1.14730.04070.25-0.18710.3637-0.0102-0.03860.3965-00.6101-0.1749125.0998-51.2606
401.6476-1.66710.61822.0623-0.03532.8947-0.09810.4309-0.0631-1.0541-0.14970.1379-0.1003-0.31410.18320.7946-0.0565-0.06290.90620.01460.3245-8.896584.2779-58.389
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1284.0524-0.649-0.3063.32821.09662.64350.1162-0.1738-0.5372-0.128-0.3070.4069-0.33450.35790.24430.37010.2053-0.1890.63810.01740.404162.105810.4363-13.9501
1291.321-1.61040.9784.2814-0.28023.36430.50340.16190.2218-0.0511-0.04950.21640.1796-0.0021-0.28010.40560.1499-0.22540.4041-0.04140.647161.654112.8001-20.4879
1301.13540.08020.11191.8423-0.44553.033-0.3098-0.48690.04230.2861-0.0958-0.2172-0.50750.38450.23160.1951-0.0289-0.12580.47490.06490.392163.020923.0636-12.8683
1310.272-0.43371.05543.2808-0.77014.40070.1928-0.52310.13580.4461-0.0414-0.9914-0.45730.0396-0.09820.6025-0.1302-0.18720.475-0.19370.776523.472586.2688-45.702
1321.4991-0.5042-0.62391.0022-1.45523.6006-0.24620.30370.0546-0.81650.3648-1.2604-0.60940.87830.14750.7136-0.18660.31770.5704-0.20521.020329.18189.9769-56.6485
1336.49686.4265-5.13326.3961-5.10184.09670.04790.58360.0356-0.780.4756-1.2587-0.38360.1978-0.40750.9522-0.09770.05860.7067-0.28960.645925.4211100.0295-62.2015
1341.20721.1429-1.89421.0814-1.79372.97850.47530.49250.2566-0.4444-0.02970.1002-0.3971-0.0253-0.33290.6507-0.12130.06590.6708-0.03420.637314.728390.2267-59.8346
1350.9595-1.5161-0.4922.4210.42515.9224-0.0257-0.23980.1179-0.40410.5188-0.1657-1.09060.7344-0.47470.94260.05210.35340.4195-0.03520.765924.292297.8311-53.0877
1360.6568-0.4176-1.28965.3296-1.66573.74280.14190.38860.1590.16070.2401-0.8359-0.4713-0.0006-0.31760.654-0.16060.12910.49920.02690.740321.947791.662-50.1828
1372.9436-2.0084-0.28261.81780.26870.35360.12650.01910.16340.1853-0.02260.1878-0.0731-0.09240.03670.8622-0.10870.41660.2817-0.08310.578724.166782.2152-51.9956
1382.4384-0.02061.39630.3223-0.92213.3484-0.28570.71340.8778-0.4836-0.0706-0.6337-0.39810.60840.41040.9714-0.34720.12520.9952-0.01890.903835.047191.4042-61.735
1391.9178-0.8073-0.71.4433-2.11075.5821-0.51280.02490.439-0.99750.1628-0.6495-0.19380.33910.35030.9099-0.33550.02910.3889-0.01321.061828.584385.8196-59.295
1405.39630.4089-3.91374.21613.42416.14660.86440.07280.40680.13340.3270.0913-0.36080.316-0.88110.4072-0.0521-0.08590.94190.12250.8012.888327.335429.1786
1414.78352.80180.29858.62131.34638.3097-0.1066-0.3786-0.1529-0.0873-0.18340.009-0.1223-0.55250.20860.5573-0.1093-0.09120.57520.00730.265118.58110.322333.2299
1420.67360.7708-0.21281.24910.55851.82360.67470.6441-0.2528-0.3799-0.20661.1705-0.5964-1.1465-0.35260.96340.3018-0.33910.89240.11821.2573-1.851719.048226.8491
1435.09280.30660.38114.81790.24124.1515-0.11490.79830.1874-0.8236-0.11470.4630.42170.26010.27270.50050.0139-0.07320.7445-0.04460.51416.086713.296119.2732
1441.11850.57581.79115.5761-0.53413.9977-0.53070.0646-0.42160.25040.39710.2906-0.1976-0.51850.10970.3523-0.00650.08090.48150.10890.5548.487611.498327.9096
1452.1756-3.633-1.29746.69452.27610.89240.14720.00590.0362-0.0440.15720.1095-0.1715-0.1031-0.20930.4067-0.1041-0.00660.89320.25070.677414.528718.467625.0109
1460.2908-0.4838-0.32521.69471.13450.9376-0.01930.99140.5202-0.453-0.80.4715-0.2182-0.15630.77290.48670.1443-0.12690.7678-0.11160.77425.040321.026917.6577
1471.28541.09811.30792.3956-0.39372.86810.5461-0.20340.48820.01770.0492-0.0877-0.1197-0.6167-0.45780.56270.0293-0.05880.463-0.0260.540850.55690.357242.7678
1482.01540.78871.06070.71211.28495.14190.177-0.34990.19980.2556-0.46860.2922-0.1629-1.02120.30510.28870.0123-0.18160.7674-0.27540.466349.875688.700551.9985
1493.0380.29160.5713.6873-0.77520.7136-0.4539-0.05480.33561.0339-0.3541.09710.30310.17530.64750.78330.0896-0.05640.6741-0.19910.44852.135584.928454.3684
1500.9566-0.2764-1.83674.19331.1733.62420.01520.34140.2090.0018-0.03540.7695-0.4863-0.49770.06080.80520.0584-0.21540.8106-0.35390.759353.406899.849656.4074
1515.21481.321-1.95445.6241.21346.14090.3107-0.48111.29580.2131-0.05980.6151-1.02240.1163-0.29170.5893-0.05820.13150.43-0.18790.674854.390295.763847.2172
1521.97561.2937-0.71619.12920.1472.22930.0366-0.58780.22050.8426-0.0105-0.8467-0.47960.4442-0.02460.337-0.12350.08720.5425-0.08650.320861.888885.172645.144
1531.5252-0.1061-2.28212.16471.40094.1401-0.1355-0.15160.32460.3715-0.2570.6197-0.3002-0.62650.15560.64570.365-0.06930.7093-0.45660.556446.224487.688850.1432
1541.94060.194-0.20132.1041.42023.7511-0.6857-0.48670.48370.8794-0.03360.23850.1143-0.64750.60840.57840.24220.04840.7709-0.16090.625948.034587.204854.5072
1554.1156-0.38890.25131.56520.83253.9362-0.64240.1250.1149-0.7115-0.25580.15860.3722-0.0680.86181.8354-0.5533-0.32691.00470.33051.036768.05440.7993-88.572
1562.6654-0.1544-1.64861.8734-0.74682.45050.0855-0.5087-0.2192-0.05170.2910.86370.1158-0.3116-0.3341.2067-0.240.00021.36140.62721.054667.236843.7266-78.7092
1570.9933-0.0529-0.76940.8032-1.34273.0147-0.15460.3676-0.0118-0.43790.09920.04730.3566-0.6708-0.34711.4913-0.4537-0.14490.99040.56870.775967.514944.7401-86.1294
1582.8760.0523-1.33340.9005-1.41183.9709-0.3203-0.7049-0.4809-0.64990.3383-0.50370.96370.15730.04231.4447-0.39530.09010.9840.33220.875573.837840.4619-78.1139
1592.9852-0.9489-0.27270.3037-0.00513.09080.2867-0.0660.29850.08210.12550.24380.54430.6813-0.42921.19560.25290.13290.6831-0.03931.089146.856847.1709-117.1787
1602.0017-0.4935-0.32851.10790.79890.77960.1528-0.3711-0.58211.07530.3059-0.10910.52670.089-0.1192.22710.17220.05230.40910.03711.1871146.242836.4074-127.5412
1610.2561-0.3651-0.56891.24091.25171.53910.26130.3008-0.38460.0044-0.33060.3887-0.0223-0.2092-0.02081.42320.1830.4980.4665-0.01211.2838141.686446.5379-130.7552
1622.3725-0.42670.0362.87410.90852.42130.4169-0.16410.56240.17520.38960.0135-0.4937-0.0228-0.66521.02870.18490.16930.7904-0.1431.0529153.649145.1755-130.4508
1636.6243-0.52930.29930.0930.45244.34820.1894-0.28070.3007-0.43690.3972-0.13340.48650.2593-0.38961.01060.1529-0.15680.6126-0.10731.64150.489447.9806-121.8951
1642.7716-2.1877-0.64542.88261.55671.9401-0.0525-0.1776-0.21920.72390.32670.15520.81530.0351-0.03661.4590.22570.28350.2127-0.00310.6686141.976340.5705-125.5644
1650.13610.08030.21250.71880.90641.2556-0.14110.00490.1610.0757-0.32180.00680.9049-0.17210.34341.37720.21580.34970.585-0.09690.8652141.739740.1796-131.2012
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 23 )A5 - 23
2X-RAY DIFFRACTION2chain 'A' and (resid 24 through 48 )A24 - 48
3X-RAY DIFFRACTION3chain 'A' and (resid 49 through 75 )A49 - 75
4X-RAY DIFFRACTION4chain 'A' and (resid 76 through 91 )A76 - 91
5X-RAY DIFFRACTION5chain 'A' and (resid 92 through 115 )A92 - 115
6X-RAY DIFFRACTION6chain 'A' and (resid 116 through 128 )A116 - 128
7X-RAY DIFFRACTION7chain 'A' and (resid 129 through 150 )A129 - 150
8X-RAY DIFFRACTION8chain 'A' and (resid 151 through 172 )A151 - 172
9X-RAY DIFFRACTION9chain 'A' and (resid 173 through 187 )A173 - 187
10X-RAY DIFFRACTION10chain 'A' and (resid 188 through 198 )A188 - 198
11X-RAY DIFFRACTION11chain 'A' and (resid 199 through 211 )A199 - 211
12X-RAY DIFFRACTION12chain 'B' and (resid 1 through 40 )B1 - 40
13X-RAY DIFFRACTION13chain 'B' and (resid 41 through 67 )B41 - 67
14X-RAY DIFFRACTION14chain 'B' and (resid 71 through 111 )B71 - 111
15X-RAY DIFFRACTION15chain 'B' and (resid 114 through 186 )B114 - 186
16X-RAY DIFFRACTION16chain 'B' and (resid 201 through 211 )B201 - 211
17X-RAY DIFFRACTION17chain 'C' and (resid 5 through 91 )C5 - 91
18X-RAY DIFFRACTION18chain 'C' and (resid 92 through 113 )C92 - 113
19X-RAY DIFFRACTION19chain 'C' and (resid 114 through 150 )C114 - 150
20X-RAY DIFFRACTION20chain 'C' and (resid 151 through 163 )C151 - 163
21X-RAY DIFFRACTION21chain 'C' and (resid 164 through 213 )C164 - 213
22X-RAY DIFFRACTION22chain 'D' and (resid 1 through 17 )D1 - 17
23X-RAY DIFFRACTION23chain 'D' and (resid 18 through 44 )D18 - 44
24X-RAY DIFFRACTION24chain 'D' and (resid 45 through 64 )D45 - 64
25X-RAY DIFFRACTION25chain 'D' and (resid 65 through 113 )D65 - 113
26X-RAY DIFFRACTION26chain 'D' and (resid 114 through 141 )D114 - 141
27X-RAY DIFFRACTION27chain 'D' and (resid 142 through 164 )D142 - 164
28X-RAY DIFFRACTION28chain 'D' and (resid 165 through 182 )D165 - 182
29X-RAY DIFFRACTION29chain 'D' and (resid 183 through 189 )D183 - 189
30X-RAY DIFFRACTION30chain 'D' and (resid 190 through 215 )D190 - 215
31X-RAY DIFFRACTION31chain 'E' and (resid 5 through 24 )E5 - 24
32X-RAY DIFFRACTION32chain 'E' and (resid 25 through 49 )E25 - 49
33X-RAY DIFFRACTION33chain 'E' and (resid 50 through 114 )E50 - 114
34X-RAY DIFFRACTION34chain 'E' and (resid 115 through 151 )E115 - 151
35X-RAY DIFFRACTION35chain 'E' and (resid 152 through 175 )E152 - 175
36X-RAY DIFFRACTION36chain 'E' and (resid 176 through 213 )E176 - 213
37X-RAY DIFFRACTION37chain 'F' and (resid 1 through 39 )F1 - 39
38X-RAY DIFFRACTION38chain 'F' and (resid 40 through 66 )F40 - 66
39X-RAY DIFFRACTION39chain 'F' and (resid 67 through 116 )F67 - 116
40X-RAY DIFFRACTION40chain 'F' and (resid 117 through 141 )F117 - 141
41X-RAY DIFFRACTION41chain 'F' and (resid 142 through 216 )F142 - 216
42X-RAY DIFFRACTION42chain 'G' and (resid 5 through 24 )G5 - 24
43X-RAY DIFFRACTION43chain 'G' and (resid 25 through 49 )G25 - 49
44X-RAY DIFFRACTION44chain 'G' and (resid 50 through 114 )G50 - 114
45X-RAY DIFFRACTION45chain 'G' and (resid 115 through 213 )G115 - 213
46X-RAY DIFFRACTION46chain 'H' and (resid 1 through 17 )H1 - 17
47X-RAY DIFFRACTION47chain 'H' and (resid 18 through 50 )H18 - 50
48X-RAY DIFFRACTION48chain 'H' and (resid 51 through 63 )H51 - 63
49X-RAY DIFFRACTION49chain 'H' and (resid 64 through 126 )H64 - 126
50X-RAY DIFFRACTION50chain 'H' and (resid 127 through 142 )H127 - 142
51X-RAY DIFFRACTION51chain 'H' and (resid 143 through 214 )H143 - 214
52X-RAY DIFFRACTION52chain 'I' and (resid 5 through 113 )I5 - 113
53X-RAY DIFFRACTION53chain 'I' and (resid 114 through 213 )I114 - 213
54X-RAY DIFFRACTION54chain 'J' and (resid 1 through 86 )J1 - 86
55X-RAY DIFFRACTION55chain 'J' and (resid 87 through 214 )J87 - 214
56X-RAY DIFFRACTION56chain 'K' and (resid 2 through 19 )K2 - 19
57X-RAY DIFFRACTION57chain 'K' and (resid 20 through 34 )K20 - 34
58X-RAY DIFFRACTION58chain 'K' and (resid 35 through 90 )K35 - 90
59X-RAY DIFFRACTION59chain 'K' and (resid 91 through 102 )K91 - 102
60X-RAY DIFFRACTION60chain 'K' and (resid 103 through 114 )K103 - 114
61X-RAY DIFFRACTION61chain 'K' and (resid 115 through 129 )K115 - 129
62X-RAY DIFFRACTION62chain 'K' and (resid 130 through 164 )K130 - 164
63X-RAY DIFFRACTION63chain 'K' and (resid 165 through 213 )K165 - 213
64X-RAY DIFFRACTION64chain 'L' and (resid 1 through 17 )L1 - 17
65X-RAY DIFFRACTION65chain 'L' and (resid 18 through 67 )L18 - 67
66X-RAY DIFFRACTION66chain 'L' and (resid 68 through 126 )L68 - 126
67X-RAY DIFFRACTION67chain 'L' and (resid 127 through 152 )L127 - 152
68X-RAY DIFFRACTION68chain 'L' and (resid 153 through 195 )L153 - 195
69X-RAY DIFFRACTION69chain 'L' and (resid 196 through 214 )L196 - 214
70X-RAY DIFFRACTION70chain 'M' and (resid 5 through 24 )M5 - 24
71X-RAY DIFFRACTION71chain 'M' and (resid 25 through 62 )M25 - 62
72X-RAY DIFFRACTION72chain 'M' and (resid 63 through 76 )M63 - 76
73X-RAY DIFFRACTION73chain 'M' and (resid 77 through 102 )M77 - 102
74X-RAY DIFFRACTION74chain 'M' and (resid 103 through 129 )M103 - 129
75X-RAY DIFFRACTION75chain 'M' and (resid 130 through 151 )M130 - 151
76X-RAY DIFFRACTION76chain 'M' and (resid 152 through 211 )M152 - 211
77X-RAY DIFFRACTION77chain 'N' and (resid 1 through 20 )N1 - 20
78X-RAY DIFFRACTION78chain 'N' and (resid 21 through 42 )N21 - 42
79X-RAY DIFFRACTION79chain 'N' and (resid 43 through 70 )N43 - 70
80X-RAY DIFFRACTION80chain 'N' and (resid 71 through 103 )N71 - 103
81X-RAY DIFFRACTION81chain 'N' and (resid 104 through 116 )N104 - 116
82X-RAY DIFFRACTION82chain 'N' and (resid 117 through 159 )N117 - 159
83X-RAY DIFFRACTION83chain 'N' and (resid 160 through 175 )N160 - 175
84X-RAY DIFFRACTION84chain 'N' and (resid 176 through 206 )N176 - 206
85X-RAY DIFFRACTION85chain 'N' and (resid 207 through 213 )N207 - 213
86X-RAY DIFFRACTION86chain 'O' and (resid 5 through 23 )O5 - 23
87X-RAY DIFFRACTION87chain 'O' and (resid 29 through 49 )O29 - 49
88X-RAY DIFFRACTION88chain 'O' and (resid 50 through 76 )O50 - 76
89X-RAY DIFFRACTION89chain 'O' and (resid 77 through 129 )O77 - 129
90X-RAY DIFFRACTION90chain 'O' and (resid 130 through 164 )O130 - 164
91X-RAY DIFFRACTION91chain 'O' and (resid 165 through 187 )O165 - 187
92X-RAY DIFFRACTION92chain 'O' and (resid 188 through 199 )O188 - 199
93X-RAY DIFFRACTION93chain 'O' and (resid 200 through 211 )O200 - 211
94X-RAY DIFFRACTION94chain 'P' and (resid 0 through 19 )P0 - 19
95X-RAY DIFFRACTION95chain 'P' and (resid 20 through 126 )P20 - 126
96X-RAY DIFFRACTION96chain 'P' and (resid 134 through 195 )P134 - 195
97X-RAY DIFFRACTION97chain 'P' and (resid 196 through 214 )P196 - 214
98X-RAY DIFFRACTION98chain 'Q' and (resid 5 through 62 )Q5 - 62
99X-RAY DIFFRACTION99chain 'Q' and (resid 63 through 114 )Q63 - 114
100X-RAY DIFFRACTION100chain 'Q' and (resid 115 through 213 )Q115 - 213
101X-RAY DIFFRACTION101chain 'R' and (resid 1 through 19 )R1 - 19
102X-RAY DIFFRACTION102chain 'R' and (resid 20 through 51 )R20 - 51
103X-RAY DIFFRACTION103chain 'R' and (resid 52 through 67 )R52 - 67
104X-RAY DIFFRACTION104chain 'R' and (resid 71 through 98 )R71 - 98
105X-RAY DIFFRACTION105chain 'R' and (resid 99 through 113 )R99 - 113
106X-RAY DIFFRACTION106chain 'R' and (resid 114 through 126 )R114 - 126
107X-RAY DIFFRACTION107chain 'R' and (resid 135 through 164 )R135 - 164
108X-RAY DIFFRACTION108chain 'R' and (resid 165 through 200 )R165 - 200
109X-RAY DIFFRACTION109chain 'R' and (resid 201 through 214 )R201 - 214
110X-RAY DIFFRACTION110chain 'a' and (resid 3 through 59 )a3 - 59
111X-RAY DIFFRACTION111chain 'a' and (resid 60 through 87 )a60 - 87
112X-RAY DIFFRACTION112chain 'a' and (resid 88 through 113 )a88 - 113
113X-RAY DIFFRACTION113chain 'c' and (resid 3 through 17 )c3 - 17
114X-RAY DIFFRACTION114chain 'c' and (resid 18 through 39 )c18 - 39
115X-RAY DIFFRACTION115chain 'c' and (resid 40 through 52 )c40 - 52
116X-RAY DIFFRACTION116chain 'c' and (resid 53 through 72 )c53 - 72
117X-RAY DIFFRACTION117chain 'c' and (resid 73 through 79 )c73 - 79
118X-RAY DIFFRACTION118chain 'c' and (resid 80 through 87 )c80 - 87
119X-RAY DIFFRACTION119chain 'c' and (resid 88 through 99 )c88 - 99
120X-RAY DIFFRACTION120chain 'c' and (resid 100 through 113 )c100 - 113
121X-RAY DIFFRACTION121chain 'e' and (resid 3 through 17 )e3 - 17
122X-RAY DIFFRACTION122chain 'e' and (resid 18 through 52 )e18 - 52
123X-RAY DIFFRACTION123chain 'e' and (resid 53 through 95 )e53 - 95
124X-RAY DIFFRACTION124chain 'e' and (resid 96 through 112 )e96 - 112
125X-RAY DIFFRACTION125chain 'g' and (resid 3 through 17 )g3 - 17
126X-RAY DIFFRACTION126chain 'g' and (resid 18 through 39 )g18 - 39
127X-RAY DIFFRACTION127chain 'g' and (resid 40 through 59 )g40 - 59
128X-RAY DIFFRACTION128chain 'g' and (resid 60 through 72 )g60 - 72
129X-RAY DIFFRACTION129chain 'g' and (resid 73 through 87 )g73 - 87
130X-RAY DIFFRACTION130chain 'g' and (resid 88 through 113 )g88 - 113
131X-RAY DIFFRACTION131chain 'i' and (resid 3 through 17 )i3 - 17
132X-RAY DIFFRACTION132chain 'i' and (resid 18 through 52 )i18 - 52
133X-RAY DIFFRACTION133chain 'i' and (resid 53 through 59 )i53 - 59
134X-RAY DIFFRACTION134chain 'i' and (resid 60 through 66 )i60 - 66
135X-RAY DIFFRACTION135chain 'i' and (resid 67 through 72 )i67 - 72
136X-RAY DIFFRACTION136chain 'i' and (resid 73 through 87 )i73 - 87
137X-RAY DIFFRACTION137chain 'i' and (resid 88 through 90 )i88 - 90
138X-RAY DIFFRACTION138chain 'i' and (resid 91 through 99 )i91 - 99
139X-RAY DIFFRACTION139chain 'i' and (resid 100 through 113 )i100 - 113
140X-RAY DIFFRACTION140chain 'k' and (resid 1 through 7 )k1 - 7
141X-RAY DIFFRACTION141chain 'k' and (resid 8 through 17 )k8 - 17
142X-RAY DIFFRACTION142chain 'k' and (resid 18 through 32 )k18 - 32
143X-RAY DIFFRACTION143chain 'k' and (resid 33 through 72 )k33 - 72
144X-RAY DIFFRACTION144chain 'k' and (resid 73 through 87 )k73 - 87
145X-RAY DIFFRACTION145chain 'k' and (resid 88 through 90 )k88 - 90
146X-RAY DIFFRACTION146chain 'k' and (resid 91 through 112 )k91 - 112
147X-RAY DIFFRACTION147chain 'm' and (resid 3 through 32 )m3 - 32
148X-RAY DIFFRACTION148chain 'm' and (resid 33 through 39 )m33 - 39
149X-RAY DIFFRACTION149chain 'm' and (resid 40 through 52 )m40 - 52
150X-RAY DIFFRACTION150chain 'm' and (resid 53 through 59 )m53 - 59
151X-RAY DIFFRACTION151chain 'm' and (resid 60 through 79 )m60 - 79
152X-RAY DIFFRACTION152chain 'm' and (resid 80 through 87 )m80 - 87
153X-RAY DIFFRACTION153chain 'm' and (resid 88 through 96 )m88 - 96
154X-RAY DIFFRACTION154chain 'm' and (resid 97 through 113 )m97 - 113
155X-RAY DIFFRACTION155chain 'o' and (resid 3 through 32 )o3 - 32
156X-RAY DIFFRACTION156chain 'o' and (resid 33 through 72 )o33 - 72
157X-RAY DIFFRACTION157chain 'o' and (resid 73 through 95 )o73 - 95
158X-RAY DIFFRACTION158chain 'o' and (resid 96 through 113 )o96 - 113
159X-RAY DIFFRACTION159chain 'q' and (resid 3 through 24 )q3 - 24
160X-RAY DIFFRACTION160chain 'q' and (resid 25 through 39 )q25 - 39
161X-RAY DIFFRACTION161chain 'q' and (resid 40 through 52 )q40 - 52
162X-RAY DIFFRACTION162chain 'q' and (resid 53 through 72 )q53 - 72
163X-RAY DIFFRACTION163chain 'q' and (resid 73 through 87 )q73 - 87
164X-RAY DIFFRACTION164chain 'q' and (resid 88 through 96 )q88 - 96
165X-RAY DIFFRACTION165chain 'q' and (resid 97 through 111 )q97 - 111

+
About Yorodumi

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News

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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

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