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- PDB-4r7n: Fab C2E3 -

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Basic information

Entry
Database: PDB / ID: 4r7n
TitleFab C2E3
Components
  • Fab C2E3 Heavy chain
  • Fab C2E3 Light chain
KeywordsIMMUNE SYSTEM / TLR4 antibody
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.45 Å
AuthorsLoyau, J. / Didelot, G. / Malinge, P. / Ravn, U. / Magistrelli, G. / Depoisier, J.F. / Kosco-Vilbois, M. / Fischer, N. / Thore, S. / Rousseau, F.
CitationJournal: J.Mol.Biol. / Year: 2015
Title: Robust Antibody-Antigen Complexes Prediction Generated by Combining Sequence Analyses, Mutagenesis, In Vitro Evolution, X-ray Crystallography and In Silico Docking.
Authors: Loyau, J. / Didelot, G. / Malinge, P. / Ravn, U. / Magistrelli, G. / Depoisier, J.F. / Pontini, G. / Poitevin, Y. / Kosco-Vilbois, M. / Fischer, N. / Thore, S. / Rousseau, F.
History
DepositionAug 28, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 29, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 26, 2015Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fab C2E3 Heavy chain
B: Fab C2E3 Light chain
C: Fab C2E3 Heavy chain
D: Fab C2E3 Light chain
E: Fab C2E3 Heavy chain
F: Fab C2E3 Light chain
G: Fab C2E3 Heavy chain
H: Fab C2E3 Light chain
I: Fab C2E3 Heavy chain
J: Fab C2E3 Light chain
K: Fab C2E3 Heavy chain
L: Fab C2E3 Light chain
M: Fab C2E3 Heavy chain
N: Fab C2E3 Light chain
O: Fab C2E3 Heavy chain
P: Fab C2E3 Light chain
Q: Fab C2E3 Heavy chain
R: Fab C2E3 Light chain
S: Fab C2E3 Heavy chain
T: Fab C2E3 Light chain


Theoretical massNumber of molelcules
Total (without water)478,24420
Polymers478,24420
Non-polymers00
Water0
1
A: Fab C2E3 Heavy chain
B: Fab C2E3 Light chain


Theoretical massNumber of molelcules
Total (without water)47,8242
Polymers47,8242
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3380 Å2
ΔGint-25 kcal/mol
Surface area19680 Å2
MethodPISA
2
C: Fab C2E3 Heavy chain
D: Fab C2E3 Light chain


Theoretical massNumber of molelcules
Total (without water)47,8242
Polymers47,8242
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3370 Å2
ΔGint-22 kcal/mol
Surface area19660 Å2
MethodPISA
3
E: Fab C2E3 Heavy chain
F: Fab C2E3 Light chain


Theoretical massNumber of molelcules
Total (without water)47,8242
Polymers47,8242
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3400 Å2
ΔGint-24 kcal/mol
Surface area19910 Å2
MethodPISA
4
G: Fab C2E3 Heavy chain
H: Fab C2E3 Light chain


Theoretical massNumber of molelcules
Total (without water)47,8242
Polymers47,8242
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3300 Å2
ΔGint-24 kcal/mol
Surface area19680 Å2
MethodPISA
5
I: Fab C2E3 Heavy chain
J: Fab C2E3 Light chain


Theoretical massNumber of molelcules
Total (without water)47,8242
Polymers47,8242
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3300 Å2
ΔGint-23 kcal/mol
Surface area19740 Å2
MethodPISA
6
K: Fab C2E3 Heavy chain
L: Fab C2E3 Light chain


Theoretical massNumber of molelcules
Total (without water)47,8242
Polymers47,8242
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3280 Å2
ΔGint-25 kcal/mol
Surface area19860 Å2
MethodPISA
7
M: Fab C2E3 Heavy chain
N: Fab C2E3 Light chain


Theoretical massNumber of molelcules
Total (without water)47,8242
Polymers47,8242
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3410 Å2
ΔGint-25 kcal/mol
Surface area19690 Å2
MethodPISA
8
O: Fab C2E3 Heavy chain
P: Fab C2E3 Light chain


Theoretical massNumber of molelcules
Total (without water)47,8242
Polymers47,8242
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3180 Å2
ΔGint-23 kcal/mol
Surface area20790 Å2
MethodPISA
9
Q: Fab C2E3 Heavy chain
R: Fab C2E3 Light chain


Theoretical massNumber of molelcules
Total (without water)47,8242
Polymers47,8242
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3280 Å2
ΔGint-22 kcal/mol
Surface area19800 Å2
MethodPISA
10
S: Fab C2E3 Heavy chain
T: Fab C2E3 Light chain


Theoretical massNumber of molelcules
Total (without water)47,8242
Polymers47,8242
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3260 Å2
ΔGint-23 kcal/mol
Surface area19760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)178.100, 208.410, 214.380
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221
Detailsheterodimer with assembly identifier 2 / heterodimer with assembly identifier 1

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Components

#1: Antibody
Fab C2E3 Heavy chain


Mass: 24305.307 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): Ovary cells / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody
Fab C2E3 Light chain


Mass: 23519.068 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): Ovary cells / Production host: Cricetulus griseus (Chinese hamster)

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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: 4.16 Å3/Da / Density % sol: 70.43 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 20% PEG 3350, 0.1M Bis Tris Propane pH 8.5, 0.23M sodium citrate, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.99987 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 13, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99987 Å / Relative weight: 1
ReflectionResolution: 3.45→50 Å / Num. all: 105492 / Num. obs: 105387 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 3.45→3.54 Å / Redundancy: 7.2 % / Mean I/σ(I) obs: 2.2 / Num. unique all: 7717 / % possible all: 100

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Processing

Software
NameVersionClassification
StructureStudiodata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.45→48.775 Å / SU ML: 0.47 / σ(F): 1.35 / Phase error: 31.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.28 5001 4.75 %RANDOM
Rwork0.2358 ---
obs0.2379 105261 99.89 %-
all-105377 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.45→48.775 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms32933 0 0 0 32933
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00433832
X-RAY DIFFRACTIONf_angle_d0.8646041
X-RAY DIFFRACTIONf_dihedral_angle_d12.9412101
X-RAY DIFFRACTIONf_chiral_restr0.0545182
X-RAY DIFFRACTIONf_plane_restr0.0045865
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs
3.4501-3.48930.38151720.331733293329
3.4893-3.53030.34341640.320732953295
3.5303-3.57330.36491650.325433073307
3.5733-3.61850.33921520.299632883288
3.6185-3.66610.32051750.291532983298
3.6661-3.71640.38581660.294933373337
3.7164-3.76940.36841630.301432843884
3.7694-3.82570.35941660.286233223322
3.8257-3.88540.35341650.27932823282
3.8854-3.94910.29491680.268433253325
3.9491-4.01720.2831530.258232913291
4.0172-4.09020.28111680.258233323332
4.0902-4.16880.31221710.250933173317
4.1688-4.25380.28731610.234233283328
4.2538-4.34630.28111750.227633373337
4.3463-4.44730.27231630.207832993299
4.4473-4.55850.24961660.203333473347
4.5585-4.68160.25511600.20633253325
4.6816-4.81930.2371720.197433403340
4.8193-4.97470.23331590.192733443344
4.9747-5.15230.22651710.233183318
5.1523-5.35830.2471610.198133733373
5.3583-5.60190.25781670.206833393339
5.6019-5.89670.25881760.209533473347
5.8967-6.26550.24181640.215333603360
6.2655-6.74810.29881700.239533723372
6.7481-7.42510.27281720.240234193419
7.4251-8.49460.25191610.221434003400
8.4946-10.68370.23141730.200634303430
10.6837-48.77970.31841820.272635753575
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)
11.23960.4980.86060.62780.59871.43660.1476-0.1871-0.2975-0.1517-0.07570.028-0.07330.320200.6574-0.0090.11720.62020.07480.7415202.2189215.4853488.7245
20.8656-0.0428-0.1435-0.4220.8855-0.67510.00690.0521-0.163-0.0967-0.0758-0.0959-0.1929-0.080600.91370.04250.09810.90080.14150.8929184.4705227.2447479.4961
30.62410.1716-0.3507-0.007-1.0113-0.21280.05330.4103-0.01330.14480.11990.25450.0595-0.101-00.84160.1046-0.06490.77630.10970.9414177.0978230.1034473.4417
40.6738-0.65170.07090.7905-0.49540.63810.1642-0.52250.0156-0.30970.22070.2715-0.37780.234900.9555-0.09270.19520.8358-0.14460.7773203.6178238.9434496.481
50.38580.19560.14470.30290.2507-0.34990.59730.01940.28610.1182-0.34850.2133-0.03630.536301.09960.0770.07990.8602-0.16620.9688202.0078234.9738495.4888
60.683-0.3622-0.28680.45520.2597-0.38450.3159-0.11350.19-0.0555-0.3161-0.00620.08410.016200.87580.04540.05490.7529-0.051.1159171.4537238.6046484.7871
70.26480.0594-0.2950.11580.08631.20350.4322-0.13870.0976-0.0999-0.10130.1599-0.084-0.089100.8440.154-0.04930.8585-0.04721.1821165.6578237.7243485.6401
80.4177-0.0296-1.37210.23080.29490.60050.2838-0.30820.0581-0.10790.25340.3705-0.13680.2392-00.8364-0.0509-0.0921.0665-0.14531.1654121.8691304.7206479.5105
90.4151-0.2174-0.12110.47560.3143-0.0753-0.08790.6330.53550.53670.214-0.32960.0884-0.015-00.7786-0.0133-0.19590.8936-0.04611.1329121.7965305.9675474.9593
100.611-0.45040.10230.01910.18550.5245-0.3566-0.22240.21110.97030.5013-0.2779-0.0509-0.1665-01.07530.11810.08990.9450.17130.886995.4404289.7506490.6842
111.0851-0.4668-0.47690.1708-0.37460.0921-0.0660.1660.3449-0.08820.14950.07620.48070.187201.18550.07830.03520.75930.03760.955898.3111291.384491.2377
120.0687-0.2621-0.3724-0.0050.0024-0.2462-0.43661.1452-0.3167-0.28580.999-0.00760.6148-0.052101.00970.0615-0.21411.17340.01350.9874117.5889281.0417464.3422
130.10360.22660.37090.65450.06860.2060.31460.20590.10090.43770.22040.09620.22180.244900.98270.0661-0.12361.0643-0.15910.9046125.1333287.2831468.5386
140.1551-0.1380.07540.040.12680.142-0.040.7248-0.55160.17090.6635-0.17490.51630.946401.08660.1-0.14011.3061-0.43471.157131.1305281.0274475.1822
150.28370.05170.51280.2051-0.12120.0486-0.4419-0.12290.66230.42510.7176-0.31020.62020.17300.86680.1052-0.15190.9384-0.21771.1213123.3921280.4608469.0527
160.0111-0.0395-0.02110.06890.0004-0.07860.83020.2459-0.0746-0.780.1682-0.23380.48480.409600.677-0.1488-0.09040.8783-0.21550.8933127.9733296.2823463.8113
170.1739-0.00120.13520.0215-0.2688-0.09571.07190.18280.18140.685-0.57810.4369-0.21120.089900.7546-0.03280.03470.72520.04480.9373100.9358276.3499477.0182
18-0.0886-0.14230.01010.0296-0.20640.13980.13180.24160.720.3304-0.22430.54990.50030.539-01.1980.21970.20130.92840.07931.223884.8846292.6111487.5325
190.08720.19790.01290.33680.17460.00670.47850.6121-0.2621-0.018-0.03520.3230.9069-0.576200.9866-0.0038-0.02881.2421-0.0341.176292.1282279.6079475.006
200.0147-0.07090.01860.09460.16570.10170.4446-0.4640.32040.173-0.0161-0.1685-0.01-0.20800.8975-0.1430.06831.08110.10741.402283.9042287.6058474.482
210.03720.0667-0.10290.2166-0.14130.0134-0.08340.3284-0.00780.43630.07750.221-0.09710.308500.92880.0406-0.03030.93890.05581.103894.2383285.7945480.2399
220.12110.07040.5342-0.24020.47640.38660.3725-0.3255-0.9674-0.15840.19390.16240.0611-0.146501.0749-0.02440.29471.27270.04981.68681.853279.3091480.3163
230.0457-0.0736-0.04380.18310.14910.04-0.5004-0.3060.5921-0.045-0.0196-0.2031-0.0227-0.081201.2512-0.21760.28711.755-0.59031.018293.5411253.2488447.3525
24-0.18260.0598-0.10670.2569-0.1769-0.0123-0.45960.2565-0.03140.29230.28670.8313-0.08050.8122-01.1969-0.18270.1661.4222-0.36181.1193103.6242250.5035448.0055
250.50570.1002-0.02670.29210.01010.0543-0.56230.0581-0.65550.0977-0.00430.0399-0.25050.011701.5076-0.38890.35031.5413-0.38621.2653100.3861244.5349451.7859
260.0463-0.0227-0.21490.15510.062-0.0283-0.38441.2489-0.74630.1184-0.30670.29340.3772-0.5876-00.9898-0.2010.00421.4637-0.26020.7628107.8964255.3749446.7911
270.3186-0.3676-1.3288-0.01950.3450.925-0.36710.6075-0.2133-0.3660.12760.51480.2459-0.328601.1924-0.2124-0.12551.85-0.58771.392481.3432270.6232448.7712
280.1107-0.1875-0.10330.0360.07040.1341-0.48430.3660.65090.0888-1.08851.0757-0.8344-0.53201.3895-0.2407-1.13264.45240.14910.100684.2952286.8281442.3701
29-0.09430.06630.08580.0736-0.1459-0.0433-0.38031.0645-0.93470.20370.83631.27971.12290.297401.2383-0.1085-0.27352.4597-0.55191.50785.9661268.7075444.4614
30-0.1149-0.1576-0.2267-0.0428-0.13-0.081-0.2244-0.33380.48850.2079-0.5380.3728-0.90210.0371-01.1017-0.2327-0.23761.88320.06211.03787.4193273.9718449.4594
310.0937-0.06570.4405-0.1605-0.0514-0.3041-1.28841.6681-2.0852-0.6351-1.4638-1.14551.3264-0.1921-0-3.1565-0.4439-4.42212.96950.1924-3.100683.3229276.4214437.6397
320.6157-0.01920.19560.96931.18580.0837-0.30850.29130.17950.30890.34440.18040.19860.241801.0011-0.0027-0.04370.9925-0.11570.6799116.1052266.4911453.998
33-0.19490.4063-0.21550.3832-0.3914-0.2918-0.10550.15650.2988-0.01230.26040.26470.20640.281801.1690.0055-0.00621.1639-0.16110.9677113.7242270.0092454.5749
340.071-0.3625-0.03320.19640.61080.11120.07771.290.47660.54690.09120.1172-0.20.0887-00.93860.1624-0.14581.75150.23291.354683.3847285.3662452.5563
350.2156-0.15960.05070.0107-0.89640.22270.06680.64420.29480.27420.28640.18990.1082-0.259300.82370.1261-0.11921.47330.28821.351884.1733287.8034455.4632
360.824-0.24740.41310.78520.06470.2270.104-0.2494-0.0883-0.2085-0.1553-0.2442-0.0781-0.1266-00.7391-0.00810.02180.86940.12660.8917157.6405203.1847489.556
370.6202-0.1466-0.29320.1006-0.09690.3978-0.0713-0.16550.1259-0.0510.06480.0902-0.13740.1223-00.9557-0.015-0.08150.90460.00950.9012135.9902215.7732501.0638
380.40630.0296-0.37870.10490.29390.63770.1332-0.1129-0.14090.0239-0.1936-0.3718-0.0181-0.2174-00.8527-0.0313-0.09620.81770.21320.8476157.1522195.3894511.6564
390.55940.0137-0.3585-0.1420.48070.5054-0.0846-0.15040.13460.0690.1034-0.00450.1493-0.2006-01.0612-0.0071-0.081.28730.05180.7298127.6641209.1767511.0766
400.56450.7638-0.23541.0989-0.70870.5205-0.0352-0.1441-0.23140.02910.04020.16220.0069-0.255800.86680.02160.04231.24720.05931.0013119.7818207.5723510.1245
410.8286-0.14780.49520.6436-0.23920.21120.0230.08240.14420.12110.061-0.18390.141-0.2318-01.2985-0.01890.191.0759-0.35281.2273178.2221270.6445517.6156
420.1904-0.13890.06950.2347-0.02510.4011-0.3504-0.10240.1805-0.2050.34940.2987-0.20980.178501.36670.06550.2361.038-0.25261.337178.9339272.2481513.355
430.89581.0430.58440.55540.08790.56310.416-0.41150.48050.1363-0.3920.34660.2841-0.027901.2119-0.00270.15781.2855-0.06320.9687163.3508244.9268522.5616
440.4622-0.1114-0.30460.38710.89810.55690.1726-0.1661-0.1764-0.1720.08290.2118-0.18420.337401.1206-0.07090.18081.0337-0.18331.0386194.9205256.6087509.8538
45-0.01480.74150.07910.94230.45250.04840.2523-0.0805-0.20710.1412-0.2164-0.2583-0.4137-0.105301.06380.04350.08871.2874-0.02131.3048169.0911237.3514513.1049
460.38270.25170.05310.0884-0.44350.59960.06330.30480.04430.16260.20660.21430.10250.037300.8989-0.16630.06821.05690.01921.2812163.4428233.3938508.9364
470.3296-0.1079-0.41060.08090.00110.10660.1892-0.0458-0.2018-0.1244-0.1450.27890.2073-0.245201.4415-0.11-0.16371.30920.34251.1256130.6888173.3128544.714
480.0358-0.0267-0.0335-0.0159-0.0727-0.00730.15090.47690.26260.3641-0.7365-0.2545-0.1089-0.153301.3988-0.2236-0.0431.34620.49680.9732135.0019183.8182541.016
49-0.11-0.01210.01060.05210.0488-0.00010.54550.13750.52070.59650.3635-0.07580.7522-0.211801.47930.0190.05741.49190.27071.2546138.3669180.6182553.1124
500.0729-0.02390.13080.01520.0045-0.0952-0.1166-0.3590.08050.38580.02650.19620.213-0.355201.39710.00120.061.47520.30821.1906129.167176.2307551.6431
51-0.00180.0401-0.1671-0.4753-0.29240.40170.1305-0.5741-0.10460.1787-0.19660.07170.03710.077-01.1715-0.15130.02781.30490.25461.1285129.4701179.1056539.1294
520.2064-0.09260.21890.0096-0.05350.0546-0.2484-0.3944-1.1-0.4210.55290.0438-0.1366-0.2903-01.8937-0.3761-0.15741.53210.15951.8491112.3638170.6402506.0652
53-0.02330.25770.1045-0.08630.02130.1524-0.7115-0.3326-0.3829-0.05950.45840.88070.2313-0.55501.3483-0.1368-0.07221.59180.17451.5391116.0784173.1835520.9668
540.0867-0.3171-0.0394-0.17220.1364-0.057-0.4712-0.1250.2292-0.59080.72940.1547-0.06710.245801.4334-0.1455-0.08821.57740.16911.3044118.5551173.8076515.8612
550.24240.11540.0816-0.0989-0.04850.0084-0.0719-0.3161-0.48840.10460.6604-0.01310.7289-0.346101.5624-0.27610.09372.01340.11431.5873112.0961166.7761521.4558
560.37720.3607-0.17710.89060.82420.38050.00360.05770.17830.1341-0.1271-0.2764-0.0268-0.2324-01.0705-0.1626-0.14491.13780.23750.8931148.761182.0762529.1752
570.5287-0.370.2698-0.45420.11650.18980.2770.1975-0.30330.0563-0.0408-0.0164-0.165-0.315901.1271-0.1232-0.05211.30330.22960.9315142.7332182.0368525.0156
580.1453-0.55270.35910.2342-0.50320.26550.0188-0.4626-0.1576-0.21570.0927-0.129-0.14-0.253200.8594-0.2191-0.11241.39440.3521.1222114.9056183.1114507.8474
590.36330.2154-0.24280.70060.18610.56340.0464-0.07980.3845-0.0325-0.0294-0.13290.1979-0.235-00.9324-0.2484-0.22931.53080.28220.993117.2801184.1193507.0105
60-0.06120.0522-0.32740.5901-0.67470.51460.47460.25791.3680.0273-1.02830.36560.56930.0582-00.8602-0.04890.00150.77570.01510.9849167.2406313.4929490.0338
610.0927-0.63450.49790.76411.02010.75710.13810.3058-0.1808-0.0037-0.2404-0.1162-0.0711-0.215700.836-0.1136-0.04490.7689-0.00370.902166.9813304.8936489.6736
62-0.31890.1558-0.6830.4487-0.40490.5963-0.091-0.07020.0840.1867-0.1040.33840.2163-0.0041-00.8922-0.0725-0.0790.9998-0.1621.1882147.0203317.3728500.8454
630.3760.59250.22590.06870.2242-0.0401-0.25050.35650.62820.331-0.057-0.07180.28020.06801.05230.0697-0.13011.0588-0.12341.1294142.1305328.5366503.2839
640.4383-0.65010.51970.2143-0.18120.5168-0.1595-0.0876-0.99670.52720.04660.17550.3070.036701.7561-0.28260.0690.82070.1280.993164.7022295.0329513.3304
650.61760.3602-0.48890.5322-0.0750.5130.0395-0.0402-0.04450.1013-0.1486-0.27940.0039-0.077201.3-0.1174-0.16140.84720.16520.8199169.1245304.0218512.8794
660.13420.15340.0460.14170.05180.10550.43640.23890.47490.0725-0.1474-0.53420.6232-0.730401.4918-0.03970.1020.7780.15870.7517165.7256301.1232508.9042
670.29460.33380.2135-0.253-0.523-0.0288-1.38710.3074-0.11152.6414-0.47530.77042.8506-0.77270-0.6694-0.6677-0.10331.3863-0.65211.0953137.6079315.6604511.0554
680.39880.0489-0.31320.07370.22370.158-1.20891.0659-0.17381.6378-0.17230.59330.8009-0.8181-01.1794-0.57810.51241.8937-0.43781.7224130.9483310.8475511.637
690.1033-0.3085-0.10070.05970.29020.10931.00870.1114-0.00790.5105-0.33290.56090.04820.349501.4737-0.25710.24881.38380.07281.3921142.6134310.6119511.4534
70-0.00830.2885-0.10150.14880.06540.1557-0.31660.4729-0.43750.4453-0.92260.8720.9168-0.6212-00.8402-0.09040.22851.8314-0.22371.5609125.226314.6338510.2182
710.1088-0.4672-0.44890.1879-0.2374-0.4982-0.69391.1422-1.09981.09292.056-0.558-0.05251.046101.3774-0.10870.48791.20621.06681.0996142.5054282.3896546.0923
720.18650.98790.00510.34240.3410.2963-0.45520.1086-0.31780.06090.4062-0.3734-0.2385-0.3641-01.21210.16680.20811.27370.4291.1013142.0051285.304547.5309
730.01490.21230.0025-0.16080.2266-0.07051.477-0.0314-0.411-0.3794-1.6987-0.71760.20110.52203.5901-0.7125-0.08942.0281-0.21992.6882122.2031275.8379509.0076
740.3860.52550.46780.05330.347-0.0406-0.5735-0.0526-0.32130.44870.2679-0.0750.7969-0.737802.3114-0.56450.20371.78010.42522.2479126.3183277.0656523.1372
750.3890.1449-0.11370.4633-0.11870.7026-0.2388-0.1550.1325-0.32130.2602-0.32850.2436-0.5608-01.4699-0.23040.19410.99940.19621.0263157.796287.8426530.7076
76-0.05650.0830.00320.29440.61180.0254-1.83780.3630.57840.33661.30811.51341.56832.128900.7954-1.5322-0.58980.83830.88722.0111127.9607288.466509.1197
770.4042-0.12540.4750.3101-0.15230.2527-0.22520.00290.4355-0.0367-0.05880.22150.0710.1296-01.06390.132-0.13790.9264-0.10341.5922138.9884255.2983496.3692
781.54520.3233-0.09210.59020.47270.0448-0.04750.00950.12090.03380.15310.05290.1842-0.066301.04530.0787-0.04761.02520.09981.0757131.9633228.1741479.7442
790.02820.262-0.16930.0821-0.1383-0.0835-0.57631.01981.37530.18580.37440.110.0874-0.1165-01.55490.0338-0.56951.56960.36562.3782135.709261.6263469.4971
800.12580.0428-0.04210.0547-0.0099-0.01940.38510.76560.2851-0.08730.2708-0.4044-0.3399-0.899-01.94280.0419-0.4711.51630.0352.5879139.9952271.6303476.2008
810.0349-0.02120.24050.0249-0.0322-0.1177-2.2350.7590.59840.27-0.50370.20561.4077-0.806301.0890.2598-0.66230.90930.56571.8996142.023255.6593479.3635
820.0520.0164-0.00910.0407-0.07860.0612-0.72660.0058-0.07910.3819-0.59710.6647-0.87060.758401.5921-0.2232-0.13731.32730.33912.0123151.0465260.8126474.9165
83-0.12570.18860.09010.04520.0625-0.0351-0.44170.1283-0.41380.45350.3077-0.6004-0.5642-0.090801.84-0.3774-0.50391.61810.49261.8748142.5771261.7745472.0068
84-0.06380.08230.0261-0.0103-0.06730.0053-0.7464-0.14320.40750.63990.0809-0.19540.5481-0.338201.72930.1479-0.47780.8852-0.00771.9322138.7482268.6077486.2247
850.047-0.06990.01020.05240.02950.25630.34960.64250.26420.5634-0.2312-0.26580.3040.245701.2238-0.0035-0.02261.21910.27891.2388131.648241.3222464.0649
86-0.06160.04060.21730.24970.49770.75030.1708-0.02750.2259-0.2013-0.15090.0924-0.0687-0.4934-00.93570.0737-0.03531.37860.31921.1801119.7706230.923470.8456
870.2052-0.13640.3840.0525-0.24240.5020.3269-0.70270.20430.0458-0.70210.4462-0.31450.511801.22120.0962-0.21471.40820.08171.4588123.5217236.0395472.792
880.0719-0.10550.03440.07140.0441-0.00920.0113-0.1757-0.52720.01710.33290.212-0.9836-0.525501.3445-0.1975-0.07121.41960.32031.401113.2211225.8401467.5501
890.09860.18290.34620.0619-0.0123-0.06390.13150.3842-0.33090.30640.31890.1855-0.468-0.2817-01.5027-0.2513-0.23231.65550.47291.1748120.8745228.1787461.6767
90-0.00140.12310.04280.15050.12880.0827-0.38530.08540.4023-0.8568-0.29670.8499-0.69030.953102.24070.2468-0.7312.3072-0.17092.369146.7484353.1367497.7288
910.0786-0.21810.00170.2568-0.03440.0240.7467-0.59890.87022.24590.26051.2472-2.15032.0343-00.92280.8084-2.7891.5174-0.55443.0367158.0483359.6295500.2999
920.28340.1848-0.30280.0548-0.1582-0.0816-0.175-1.34950.2997-1.7092-1.43920.3410.27740.073302.20750.7445-1.45151.4811-1.31112.895149.0245365.547498.439
93-0.0215-0.08770.31520.14890.33310.26840.0042-1.9580.419-2.35920.08680.0556-1.12690.0828-01.25680.3735-0.95421.7373-0.52782.8868145.5121359.5385497.372
94-0.00220.0794-0.0314-0.0078-0.0108-0.0035-0.57580.55021.41450.16440.0271-0.6126-0.95310.4723-03.59330.1733-1.36970.8868-1.21922.2352157.817364.4601489.0873
950.50490.27290.18150.4086-0.02410.0185-0.433-0.15580.1517-0.17210.3862-0.21040.4052-0.054-01.75090.0277-0.89191.6165-0.39552.858137.5011336.1906482.7611
96-0.0616-0.32750.15910.2774-0.04920.0722-0.1027-1.81490.9289-1.4486-0.7339-0.12550.5612-0.542501.86260.0897-0.89611.99640.11273.0703141.2379337.0589483.1077
97-0.038-0.20030.11040.01680.01910.14850.0322-0.15180.7054-1.68240.52590.85210.551-0.4687-02.5208-0.2335-0.8271.8868-0.28652.3763141.0882336.9889477.3584
980.1268-0.09090.19080.1564-0.17340.04710.4775-0.4248-1.1349-0.23210.71390.3417-0.7880.4103-02.01420.0592-0.28021.9891-0.14931.4571144.5572331.1127485.9667
99-0.00450.0672-0.11780.0106-0.0762-0.01720.1970.8290.27360.5838-0.9772-0.11580.07160.685702.9090.5078-1.65371.7993-0.4853.4788147.2518368.8994470.1938
1000.17180.4174-0.07060.1243-0.51860.1105-0.02320.68161.0305-1.59250.48831.00650.8570.327803.1975-0.0078-1.39532.0380.26912.8708155.566367.0946475.7111
1010.5956-0.6364-1.03410.24850.60860.0764-0.22840.3641-0.0786-0.050.17310.2703-0.2601-0.512802.41140.0228-0.98462.2712-0.12632.1088138.9902347.0705474.9417
102-0.0028-0.04390.1619-0.0310.05950.1089-0.39470.2777-0.4998-0.5229-1.32040.4509-0.3367-0.0196-02.53970.0706-0.82322.569-1.0444.2384128.6235342.3652467.6747
1030.0419-0.08710.05790.0686-0.20610.4202-0.79721.1795-0.2794-0.72690.23050.4415-0.1523-0.5164-02.3908-0.1348-0.13162.215-0.43783.1114131.1188337.9026471.0662
104-0.14670.13510.0338-0.0538-0.1104-0.0847-1.28430.12120.0325-0.083-1.10190.3443-0.3725-0.7922-02.3589-0.5734-0.5593.0076-0.35871.5101130.8512335.7407460.6117
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 96 )
2X-RAY DIFFRACTION2chain 'A' and (resid 97 through 162 )
3X-RAY DIFFRACTION3chain 'A' and (resid 163 through 218 )
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 75 )
5X-RAY DIFFRACTION5chain 'B' and (resid 76 through 101 )
6X-RAY DIFFRACTION6chain 'B' and (resid 102 through 150 )
7X-RAY DIFFRACTION7chain 'B' and (resid 151 through 211 )
8X-RAY DIFFRACTION8chain 'C' and (resid 1 through 45 )
9X-RAY DIFFRACTION9chain 'C' and (resid 46 through 124 )
10X-RAY DIFFRACTION10chain 'C' and (resid 125 through 162 )
11X-RAY DIFFRACTION11chain 'C' and (resid 163 through 218 )
12X-RAY DIFFRACTION12chain 'D' and (resid 1 through 18 )
13X-RAY DIFFRACTION13chain 'D' and (resid 19 through 49 )
14X-RAY DIFFRACTION14chain 'D' and (resid 50 through 61 )
15X-RAY DIFFRACTION15chain 'D' and (resid 62 through 89 )
16X-RAY DIFFRACTION16chain 'D' and (resid 90 through 101 )
17X-RAY DIFFRACTION17chain 'D' and (resid 102 through 118 )
18X-RAY DIFFRACTION18chain 'D' and (resid 119 through 136 )
19X-RAY DIFFRACTION19chain 'D' and (resid 137 through 150 )
20X-RAY DIFFRACTION20chain 'D' and (resid 151 through 163 )
21X-RAY DIFFRACTION21chain 'D' and (resid 164 through 186 )
22X-RAY DIFFRACTION22chain 'D' and (resid 187 through 211 )
23X-RAY DIFFRACTION23chain 'E' and (resid 1 through 16 )
24X-RAY DIFFRACTION24chain 'E' and (resid 17 through 52 )
25X-RAY DIFFRACTION25chain 'E' and (resid 53 through 91 )
26X-RAY DIFFRACTION26chain 'E' and (resid 92 through 111 )
27X-RAY DIFFRACTION27chain 'E' and (resid 112 through 134 )
28X-RAY DIFFRACTION28chain 'E' and (resid 135 through 148 )
29X-RAY DIFFRACTION29chain 'E' and (resid 149 through 162 )
30X-RAY DIFFRACTION30chain 'E' and (resid 163 through 182 )
31X-RAY DIFFRACTION31chain 'E' and (resid 183 through 218 )
32X-RAY DIFFRACTION32chain 'F' and (resid 1 through 61 )
33X-RAY DIFFRACTION33chain 'F' and (resid 62 through 114 )
34X-RAY DIFFRACTION34chain 'F' and (resid 115 through 150 )
35X-RAY DIFFRACTION35chain 'F' and (resid 151 through 211 )
36X-RAY DIFFRACTION36chain 'G' and (resid 1 through 98 )
37X-RAY DIFFRACTION37chain 'G' and (resid 99 through 218 )
38X-RAY DIFFRACTION38chain 'H' and (resid 1 through 101 )
39X-RAY DIFFRACTION39chain 'H' and (resid 102 through 144 )
40X-RAY DIFFRACTION40chain 'H' and (resid 145 through 211 )
41X-RAY DIFFRACTION41chain 'I' and (resid 1 through 45 )
42X-RAY DIFFRACTION42chain 'I' and (resid 46 through 124 )
43X-RAY DIFFRACTION43chain 'I' and (resid 125 through 218 )
44X-RAY DIFFRACTION44chain 'J' and (resid 1 through 101 )
45X-RAY DIFFRACTION45chain 'J' and (resid 102 through 144 )
46X-RAY DIFFRACTION46chain 'J' and (resid 145 through 211 )
47X-RAY DIFFRACTION47chain 'K' and (resid 1 through 40 )
48X-RAY DIFFRACTION48chain 'K' and (resid 41 through 52 )
49X-RAY DIFFRACTION49chain 'K' and (resid 53 through 64 )
50X-RAY DIFFRACTION50chain 'K' and (resid 65 through 84 )
51X-RAY DIFFRACTION51chain 'K' and (resid 85 through 124 )
52X-RAY DIFFRACTION52chain 'K' and (resid 125 through 139 )
53X-RAY DIFFRACTION53chain 'K' and (resid 140 through 162 )
54X-RAY DIFFRACTION54chain 'K' and (resid 163 through 196 )
55X-RAY DIFFRACTION55chain 'K' and (resid 197 through 218 )
56X-RAY DIFFRACTION56chain 'L' and (resid 1 through 75 )
57X-RAY DIFFRACTION57chain 'L' and (resid 76 through 113 )
58X-RAY DIFFRACTION58chain 'L' and (resid 114 through 155 )
59X-RAY DIFFRACTION59chain 'L' and (resid 156 through 211 )
60X-RAY DIFFRACTION60chain 'M' and (resid 1 through 34 )
61X-RAY DIFFRACTION61chain 'M' and (resid 35 through 98 )
62X-RAY DIFFRACTION62chain 'M' and (resid 99 through 182 )
63X-RAY DIFFRACTION63chain 'M' and (resid 183 through 218 )
64X-RAY DIFFRACTION64chain 'N' and (resid 1 through 33 )
65X-RAY DIFFRACTION65chain 'N' and (resid 34 through 75 )
66X-RAY DIFFRACTION66chain 'N' and (resid 76 through 101 )
67X-RAY DIFFRACTION67chain 'N' and (resid 102 through 128 )
68X-RAY DIFFRACTION68chain 'N' and (resid 129 through 155 )
69X-RAY DIFFRACTION69chain 'N' and (resid 156 through 174 )
70X-RAY DIFFRACTION70chain 'N' and (resid 175 through 211 )
71X-RAY DIFFRACTION71chain 'O' and (resid 1 through 52 )
72X-RAY DIFFRACTION72chain 'O' and (resid 53 through 124 )
73X-RAY DIFFRACTION73chain 'O' and (resid 125 through 141 )
74X-RAY DIFFRACTION74chain 'O' and (resid 142 through 218 )
75X-RAY DIFFRACTION75chain 'P' and (resid 1 through 102 )
76X-RAY DIFFRACTION76chain 'P' and (resid 103 through 211 )
77X-RAY DIFFRACTION77chain 'Q' and (resid 1 through 124 )
78X-RAY DIFFRACTION78chain 'Q' and (resid 125 through 218 )
79X-RAY DIFFRACTION79chain 'R' and (resid 1 through 18 )
80X-RAY DIFFRACTION80chain 'R' and (resid 19 through 32 )
81X-RAY DIFFRACTION81chain 'R' and (resid 33 through 44 )
82X-RAY DIFFRACTION82chain 'R' and (resid 45 through 64 )
83X-RAY DIFFRACTION83chain 'R' and (resid 65 through 90 )
84X-RAY DIFFRACTION84chain 'R' and (resid 91 through 101 )
85X-RAY DIFFRACTION85chain 'R' and (resid 102 through 118 )
86X-RAY DIFFRACTION86chain 'R' and (resid 119 through 155 )
87X-RAY DIFFRACTION87chain 'R' and (resid 156 through 186 )
88X-RAY DIFFRACTION88chain 'R' and (resid 187 through 197 )
89X-RAY DIFFRACTION89chain 'R' and (resid 198 through 213 )
90X-RAY DIFFRACTION90chain 'S' and (resid 1 through 16 )
91X-RAY DIFFRACTION91chain 'S' and (resid 17 through 34 )
92X-RAY DIFFRACTION92chain 'S' and (resid 35 through 76 )
93X-RAY DIFFRACTION93chain 'S' and (resid 77 through 98 )
94X-RAY DIFFRACTION94chain 'S' and (resid 99 through 111 )
95X-RAY DIFFRACTION95chain 'S' and (resid 112 through 139 )
96X-RAY DIFFRACTION96chain 'S' and (resid 140 through 162 )
97X-RAY DIFFRACTION97chain 'S' and (resid 163 through 196 )
98X-RAY DIFFRACTION98chain 'S' and (resid 197 through 218 )
99X-RAY DIFFRACTION99chain 'T' and (resid 1 through 25 )
100X-RAY DIFFRACTION100chain 'T' and (resid 26 through 90 )
101X-RAY DIFFRACTION101chain 'T' and (resid 91 through 136 )
102X-RAY DIFFRACTION102chain 'T' and (resid 137 through 163 )
103X-RAY DIFFRACTION103chain 'T' and (resid 164 through 197 )
104X-RAY DIFFRACTION104chain 'T' and (resid 198 through 211 )

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  • 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

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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

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