[English] 日本語
Yorodumi
- PDB-3auv: Predicting Amino Acid Preferences in the Complementarity Determin... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3auv
TitlePredicting Amino Acid Preferences in the Complementarity Determining Regions of an Antibody-Antigen Recognition Interface
Componentssc-dsFv derived from the G6-Fab
KeywordsIMMUNE SYSTEM / sc-dsFv (disulfide-stabilized scFv) / scFv / monovalent antibody / VEGF / antibody engineering
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsYu, C.M. / Peng, H.P. / Chen, I.C. / Lee, Y.C. / Chen, J.B. / Tsai, K.C. / Chen, C.T. / Chang, J.Y. / Yang, E.W. / Hsu, P.C. ...Yu, C.M. / Peng, H.P. / Chen, I.C. / Lee, Y.C. / Chen, J.B. / Tsai, K.C. / Chen, C.T. / Chang, J.Y. / Yang, E.W. / Hsu, P.C. / Jian, J.W. / Hsu, H.J. / Chang, H.J. / Hsu, W.L. / Huang, K.F. / Ma, A.C. / Yang, A.S.
CitationJournal: Plos One / Year: 2012
Title: Rationalization and design of the complementarity determining region sequences in an antibody-antigen recognition interface
Authors: Yu, C.M. / Peng, H.P. / Chen, I.C. / Lee, Y.C. / Chen, J.B. / Tsai, K.C. / Chen, C.T. / Chang, J.Y. / Yang, E.W. / Hsu, P.C. / Jian, J.W. / Hsu, H.J. / Chang, H.J. / Hsu, W.L. / Huang, K.F. ...Authors: Yu, C.M. / Peng, H.P. / Chen, I.C. / Lee, Y.C. / Chen, J.B. / Tsai, K.C. / Chen, C.T. / Chang, J.Y. / Yang, E.W. / Hsu, P.C. / Jian, J.W. / Hsu, H.J. / Chang, H.J. / Hsu, W.L. / Huang, K.F. / Ma, A.C. / Yang, A.S.
History
DepositionFeb 16, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 22, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 29, 2012Group: Database references
Revision 1.2Apr 25, 2012Group: Database references

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: sc-dsFv derived from the G6-Fab
B: sc-dsFv derived from the G6-Fab
C: sc-dsFv derived from the G6-Fab
D: sc-dsFv derived from the G6-Fab
E: sc-dsFv derived from the G6-Fab
F: sc-dsFv derived from the G6-Fab


Theoretical massNumber of molelcules
Total (without water)174,9386
Polymers174,9386
Non-polymers00
Water9,746541
1
A: sc-dsFv derived from the G6-Fab


Theoretical massNumber of molelcules
Total (without water)29,1561
Polymers29,1561
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: sc-dsFv derived from the G6-Fab


Theoretical massNumber of molelcules
Total (without water)29,1561
Polymers29,1561
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: sc-dsFv derived from the G6-Fab


Theoretical massNumber of molelcules
Total (without water)29,1561
Polymers29,1561
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: sc-dsFv derived from the G6-Fab


Theoretical massNumber of molelcules
Total (without water)29,1561
Polymers29,1561
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: sc-dsFv derived from the G6-Fab


Theoretical massNumber of molelcules
Total (without water)29,1561
Polymers29,1561
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: sc-dsFv derived from the G6-Fab


Theoretical massNumber of molelcules
Total (without water)29,1561
Polymers29,1561
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
A: sc-dsFv derived from the G6-Fab
C: sc-dsFv derived from the G6-Fab
E: sc-dsFv derived from the G6-Fab


Theoretical massNumber of molelcules
Total (without water)87,4693
Polymers87,4693
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4440 Å2
ΔGint-27 kcal/mol
Surface area25990 Å2
MethodPISA
8
B: sc-dsFv derived from the G6-Fab
D: sc-dsFv derived from the G6-Fab
F: sc-dsFv derived from the G6-Fab


Theoretical massNumber of molelcules
Total (without water)87,4693
Polymers87,4693
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4470 Å2
ΔGint-28 kcal/mol
Surface area26030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.063, 136.063, 169.004
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain A and (resseq 12:117 or resseq 136:253 )A12 - 117
121chain A and (resseq 12:117 or resseq 136:253 )A136 - 253
211chain B and (resseq 12:117 or resseq 136:253 )B12 - 117
221chain B and (resseq 12:117 or resseq 136:253 )B136 - 253
311chain C and (resseq 12:117 or resseq 136:253 )C12 - 117
321chain C and (resseq 12:117 or resseq 136:253 )C136 - 253
411chain D and (resseq 12:117 or resseq 136:253 )D12 - 117
421chain D and (resseq 12:117 or resseq 136:253 )D136 - 253
511chain E and (resseq 12:117 or resseq 136:253 )E12 - 117
521chain E and (resseq 12:117 or resseq 136:253 )E136 - 253
611chain F and (resseq 12:117 or resseq 136:253 )F12 - 117
621chain F and (resseq 12:117 or resseq 136:253 )F136 - 253

-
Components

#1: Antibody
sc-dsFv derived from the G6-Fab


Mass: 29156.348 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 541 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.58 Å3/Da / Density % sol: 52.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 100mM Tris-HCl, 100mM MgCl2, 20% PEG 4000, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 0.97622 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 7, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97622 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. obs: 70426 / % possible obs: 99.1 % / Redundancy: 8.2 %
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 7.7 % / Num. unique all: 6598 / % possible all: 93.9

-
Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
PHENIX(phenix.refine: 1.7_648)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→29.319 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7142 / SU ML: 0.33 / σ(F): 0 / Phase error: 33.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2514 3233 5.06 %RANDOM
Rwork0.2158 ---
all0.2176 66802 --
obs0.2176 63877 89.92 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 26.313 Å2 / ksol: 0.324 e/Å3
Displacement parametersBiso max: 126.59 Å2 / Biso min: 6.01 Å2
Baniso -1Baniso -2Baniso -3
1--8.145 Å2-0 Å20 Å2
2---8.145 Å20 Å2
3---16.29 Å2
Refinement stepCycle: LAST / Resolution: 2.4→29.319 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10322 0 0 541 10863
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0210616
X-RAY DIFFRACTIONf_angle_d1.79214440
X-RAY DIFFRACTIONf_dihedral_angle_d14.2673658
X-RAY DIFFRACTIONf_chiral_restr0.1131586
X-RAY DIFFRACTIONf_plane_restr0.0081830
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1706X-RAY DIFFRACTIONPOSITIONAL0.065
12B1706X-RAY DIFFRACTIONPOSITIONAL0.065
13C1706X-RAY DIFFRACTIONPOSITIONAL0.086
14D1712X-RAY DIFFRACTIONPOSITIONAL0.091
15E1706X-RAY DIFFRACTIONPOSITIONAL0.142
16F1706X-RAY DIFFRACTIONPOSITIONAL0.096
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.4005-2.48620.39052680.3035516677
2.4862-2.58570.30362870.2758541281
2.5857-2.70330.31712960.2757563084
2.7033-2.84570.31833160.2479577287
2.8457-3.02390.26893400.2299599189
3.0239-3.2570.25083210.2294617592
3.257-3.58430.25943220.2295646595
3.5843-4.10180.23293720.1921656198
4.1018-5.16320.18113630.158664198
5.1632-29.32070.22583480.1954683197
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.12540.0381-0.17240.2861-0.18390.3037-0.1485-0.00180.12310.0014-0.0163-0.034-0.0092-0.0216-0.19360.2541-0.1938-0.090.2629-0.0790.211367.871487.5689154.9489
20.0429-0.05790.06970.0813-0.09430.16170.06510.02830.0473-0.0433-0.0269-0.151-0.03160.19170.00010.2658-0.0945-0.0720.2991-0.06040.521582.098895.9587147.3281
30.022-0.0113-0.00730.00630.00470.008-0.0541-0.0846-0.00180.0475-0.01890.01680.01450.0412-0.00090.4413-0.119-0.19880.27860.08940.440169.381580.1653156.2984
40.0029-0.0031-0.01580.02230.06840.19870.08510.06360.0561-0.00870.0888-0.07330.03860.0490.08490.0366-0.0227-0.07150.16260.0270.371669.456884.6617144.6881
50.0239-0.0162-0.00450.0234-0.02120.0488-0.0721-0.01190.057-0.0252-0.0547-0.0156-0.03850.01-0.08010.2601-0.1244-0.01650.201-0.00470.646465.865897.7444138.4807
60.0111-0.01460.01650.0198-0.02010.0260.0166-0.0125-0.04620.02210.0185-0.02950.02170.02250.03140.1127-0.0162-0.08260.187-0.10710.303672.063482.3102139.6374
70.02370.01580.01860.01470.00160.04010.0360.033-0.0148-0.0380.01460.0167-0.0065-0.02820.00830.33830.0072-0.08970.44950.0010.186372.960583.0339134.2615
80.0728-0.0458-0.04760.03090.03490.04340.03170.1079-0.0974-0.01990.168-0.1118-0.01560.16040.11360.1877-0.1498-0.11880.30610.03550.521977.828884.8479142.0829
90.0543-0.0152-0.0030.02230.02850.0490.0789-0.0154-0.0778-0.0330.0828-0.05270.029-0.03480.48960.1318-0.0166-0.18350.34480.04490.459479.663991.6858142.9657
100.0107-0.0141-0.0020.0320.00650.0016-0.00030.02180.0241-0.0461-0.02930.0154-0.0380.0325-0.16960.0952-0.2803-0.33060.29630.15140.389271.000294.8963144.7466
110.11640.008-0.14430.0067-0.02150.21110.0691-0.08190.03290.00350.03220.0438-0.02390.03730.10340.094-0.086-0.08350.2927-0.14030.287462.884184.181149.2886
120.0079-0.0085-0.00870.01580.0060.058-0.03590.2112-0.0019-0.1514-0.0677-0.08540.0135-0.08060.00070.4524-0.2075-0.02110.5395-0.05060.413272.758798.9912141.3735
130.01280.0150.00650.01820.0010.0685-0.01460.03850.02940.0360.0063-0.0056-0.1017-0.03370.08010.1898-0.0218-0.06520.17790.00470.110253.22494.9078132.9964
140.0576-0.04580.02940.0385-0.03740.11390.052-0.0040.0078-0.00360.03060.0097-0.0346-0.00080.01020.39290.124-0.1450.2012-0.13080.437541.3481104.9533147.2986
150.2602-0.0301-0.08610.00780.00840.1730.0032-0.16620.14030.06880.0046-0.0179-0.1064-0.05110.06150.1457-0.00790.03510.1453-0.07570.093552.352289.2135138.1676
160.34360.0449-0.2360.1076-0.05810.3776-0.08630.10930.0195-0.03790.0263-0.00030.0511-0.1304-0.09730.01990.0083-0.15580.02460.01980.08951.335985.0819146.2561
170.0027-0.00980.01370.0376-0.04620.05820.0019-0.00290.0324-0.07370.03310.01310.00750.06580.03120.1678-0.1237-0.01130.1617-0.15050.11545.321890.298151.7089
180.0099-0.0483-0.01110.17190.05220.0126-0.03210.07-0.0569-0.00650.03880.01620.0899-0.01170.03130.06710.01250.01970.0003-0.1438-0.003444.222888.7606135.6639
190.0722-0.09290.05810.1038-0.06810.0475-0.0227-0.16260.18520.1144-0.09810.0475-0.0424-0.1469-0.10760.1793-0.03140.00690.1843-0.09360.276650.42196.517146.224
200.35790.0667-0.04390.31460.080.32220.0143-0.0314-0.07210.0837-0.0385-0.0138-0.01110.2752-0.20220.029-0.0782-0.0360.1007-0.01950.229858.382188.1827139.3733
210.00380.0012-0.00030.0032-0.01160.03370.02360.03820.11940.0293-0.0654-0.0899-0.09360.0087-0.04220.349-0.04450.13280.04270.08520.282943.2823108.680198.1598
220.0864-0.0129-0.03580.0194-0.01530.0367-0.0736-0.00920.0351-0.03080.02970.0278-0.0531-0.0559-0.04840.4629-0.0021-0.06770.17390.11730.291337.9295113.686100.1648
230.05750.00060.0880.0224-0.00560.13220.0073-0.0140.02830.01960.0107-0.0122-0.0713-0.12450.03190.2101-0.00430.00230.15890.01530.077437.238100.8989102.4029
240.04840.02430.01460.0161-0.00350.0448-0.080.01470.03380.0254-0.064-0.164-0.01610.1312-0.0990.1209-0.0602-0.0250.12250.13680.232345.7442104.8327111.7563
250.00180.0001-0.00160.00240.00170.0020.00840.03660.0167-0.01540.07330.0230.0143-0.0211-0.00020.30870.04380.06830.2286-0.05190.23233.2088103.8596112.2647
260.33790.213-0.11010.1856-0.03010.66880.1165-0.05450.170.18090.08570.0215-0.1365-0.00630.2010.26470.056-0.05140.0991-0.00330.286435.2145110.3597107.1713
270.04610.0042-0.040.02190.04140.1296-0.0006-0.03520.00950.02930.0139-0.0320.00610.0416-0.01130.3694-0.0085-0.00010.1172-0.17710.422445.521118.7104112.3428
280.00140.0051-0.0030.0205-0.00990.0049-0.0052-0.01980.02470.0155-0.0074-0.0308-0.03450.0561-0.03890.21590.074-0.00440.07370.18590.450446.6778108.7883105.4507
290.0268-0.01240.00890.0051-0.00650.0047-0.03660.00370.0061-0.01170.0235-0.026-0.09590.05960.03910.1482-0.0366-0.00350.25710.09660.007639.797493.7992101.5267
300.0184-0.0175-0.00410.0299-0.02850.071-0.05030.01-0.01180.0115-0.0665-0.0967-0.03730.0922-0.07850.29560.01330.14530.07140.2220.245748.9472110.7974100.9346
310.27020.1330.17140.06320.08180.1043-0.05430.14480.0513-0.09310.02990.003-0.1320.0981-0.04550.33360.0677-0.08080.12350.01970.268948.6609100.3228119.4983
320.01540.01550.01130.0378-0.01030.027-0.02210.0393-0.0050.010.0091-0.031-0.02110.04440.01660.1588-0.18460.09420.28710.0860.306363.136192.3728112.0386
330.0051-0.0070.00150.00990.00130.0043-0.05470.0184-0.0398-0.01240.0568-0.0022-0.01060.10130.00040.18740.01660.11090.20060.03920.352366.194986.099105.7676
340.0966-0.02810.04280.09470.02640.0297-0.02990.08890.1062-0.18440.052-0.04160.03320.04420.20050.11430.0202-0.0527-0.44440.4452-0.147649.469490.4486112.3271
350.0971-0.03870.01660.0168-0.00240.00230.01150.0147-0.01190.0572-0.104-0.0340.08120.0204-0.20280.01520.2266-0.0642-0.32750.205-0.030748.857986.8254102.7717
360.02320.00840.00320.00540.0020.0204-0.0362-0.01940.00940.06830.01590.0031-0.0456-0.02610.00390.10290.05590.00420.17030.07710.08655.767682.4116102.4425
370.02610.00150.0381-0.0006-0.00140.0553-0.0255-0.01690.0307-0.00320.0068-0.0307-0.0844-0.0645-0.05450.1827-0.0529-0.13320.09540.09920.004255.109282.7046115.4148
380.00640.0009-0.01690.0160.04430.1472-0.00550.0370.002-0.0825-0.0188-0.09050.03710.0631-0.15580.2494-0.01860.02060.15450.09250.115158.362991.7753104.0117
390.02820.0295-0.08710.2550.03260.3331-0.04490.1260.0059-0.0954-0.0821-0.015-0.09510.005-0.27160.05550.01-0.07420.14330.10430.056740.68794.3224112.6245
400.00840.0028-0.00840.0009-0.00050.0099-0.06060.0468-0.0048-0.0459-0.0404-0.07260.00840.0287-00.2316-0.15170.05630.27910.00320.267563.7895.2424107.0512
410.0121-0.00890.02440.0043-0.01450.0514-0.0426-0.00590.01310.0055-0.0123-0.0007-0.0807-0.017-0.04930.29440.0564-0.0780.0879-0.13950.159153.155749.0925155.4544
420.02090.0101-0.01190.11720.06540.05650.0419-0.0322-0.06750.01980.0548-0.02450.0987-0.01640.12050.34740.1084-0.2016-0.02350.02350.163953.383631.8023147.8227
430.00740.0037-0.01240.21450.09690.0777-0.049-0.02380.01540.0261-0.02610.04140.0471-0.0312-0.04790.39890.1078-0.06990.1803-0.1020.093346.225450.7975156.702
440.105-0.0323-0.02730.11240.02680.01540.0059-0.030.00220.0379-0.0597-0.0138-0.0047-0.1745-0.24730.20030.0211-0.06010.18450.0029-0.011949.954748.3801145.09
450.1274-0.02540.13710.06330.07560.3357-0.0939-0.01980.0317-0.0429-0.0938-0.0634-0.05950.0578-0.12190.15690.03450.03770.32130.20180.398163.021944.9124138.7715
460.12330.09220.07490.06990.05640.0450.0086-0.0087-0.02580.00980.0111-0.02190.0221-0.00380.08850.10280.05240.0628-0.00710.0650.097746.565547.2741140.0731
470.0392-0.03660.02810.0334-0.02690.02090.02730.0106-0.0029-0.03970.0175-0.0052-0.00550.02060.07550.3496-0.05470.09560.1566-0.1320.097246.689346.03134.6909
480.12260.00430.04750.0335-0.08560.25620.1184-0.0829-0.09270.06510.09190.12730.0018-0.13390.09180.1767-0.001-0.04550.0575-0.02220.111646.331540.0295144.4727
490.0196-0.01830.00380.0389-0.04710.0870.0281-0.0015-0.0170.0070.04470.0118-0.02610.00470.04740.3297-0.06640.12160.1842-0.07390.235156.775431.9574138.3139
500.0007-0.00350.00150.025-00.0226-0.01610.011-0.01860.0197-0.035-0.01750.01120.0247-0.06780.1739-0.05250.06640.05580.0680.299158.03441.9075145.1257
510.00240.02190.00330.26160.02910.00380.0059-0.0990.05770.07440.1362-0.0170.05520.1130.01940.1783-0.00280.0140.1833-0.00930.066851.26556.9356149.0515
520.0264-0.0295-0.01510.03160.02180.12380.01990.0352-0.0666-0.0208-0.09050.00190.17660.097-0.01360.30020.0027-0.0650.1242-0.06680.178660.502238.5013148.7279
530.00960.0122-0.01190.0289-0.01180.0105-0.07-0.10520.00310.051-0.0758-0.26260.05560.07190.00480.27160.07690.04970.3590.02210.676268.681357.1324134.0762
540.0581-0.0125-0.020.0105-0.0060.04860.007-0.0790.0063-0.01440.0315-0.00760.01330.1461-0.02350.1508-0.0542-0.09890.2932-0.03080.617775.495264.1278142.6138
550.04320.05240.00870.08490.03640.0177-0.0149-0.0119-0.09260.01080.0343-0.1824-0.04110.01320.06990.20820.05920.00060.0470.04620.168960.267660.0776138.3608
560.0377-0.03630.01510.09530.0660.1536-0.0621-0.02110.0434-0.0679-0.07050.0053-0.14850.0283-0.11730.1314-0.0007-0.1332-0.01220.1460.230959.404963.8804146.3615
570.0298-0.01310.04190.0127-0.00510.09090.03580.03660.0170.04440.0304-0.0232-0.0182-0.0440.0930.3209-0.0478-0.15680.32940.12440.389766.413166.12153.5327
580.03850.00830.02490.08580.02590.0207-0.03070.0017-0.0362-0.0286-0.0553-0.1574-0.02940.0334-0.03880.1123-0.0354-0.00430.16960.0350.439466.374468.0483137.2459
590.04180.09280.02360.3195-0.12260.2204-0.0519-0.0890.00890.1929-0.1023-0.3579-0.09620.0724-0.06270.1381-0.0176-0.06410.20340.00240.463869.771258.971146.317
600.12980.0631-0.06090.8689-0.09040.7018-0.07440.0285-0.02150.0081-0.0133-0.25130.0549-0.1218-0.26290.13530.0024-0.01610.1049-0.03420.116557.589656.1603139.2064
610.009-0.02260.00810.0502-0.02030.0079-0.010.01-0.0211-0.05320.02740.0897-0.04480.04950.01740.0568-0.1152-0.19110.29530.04330.278215.946570.380594.9101
620.00190.00270.00690.00410.00730.03260.0177-0.03770.06550.0477-0.04990.0770.004-0.1073-0.09470.1017-0.0656-0.10130.1969-0.12650.44710.8961.9203102.586
630.0017-0.0022-0.00460.00310.0060.01130.02540.0185-0.0255-0.05230.0237-0.02650.03960.01360.00040.17520.00950.02770.3894-0.05910.208420.907865.237593.688
640.00690.00370.00470.00380.00850.0114-0.004-0.0829-0.11090.07150.0268-0.04320.1434-0.08250.00010.1622-0.0430.0540.1637-0.00970.285716.959467.2849105.3036
650.028-0.0317-0.00340.04230.00980.0133-0.0404-0.00610.0469-0.0186-0.06170.0347-0.0502-0.0529-0.14760.0669-0.0323-0.14690.1095-0.06990.28399.731873.5633111.4792
660.01420.00370.00590.00940.00710.0067-0.05810.0012-0.03330.0518-0.03790.00960.00040.0401-0.00860.2116-0.0238-0.14150.17020.09690.294419.306661.0515110.8787
670.01340.03080.00780.10530.04030.01280.08-0.1702-0.09960.112-0.08990.20740.06530.07730.01580.196-0.0454-0.02850.2563-0.07130.197312.929161.0736107.3805
680.0029-0.0002-0.00050.00140.0003-0.00040.055-0.010.0053-0.01090.03660.0072-0.0735-0.03950.00020.2776-0.13920.02230.3925-0.05010.3764-0.041763.1989111.5881
690.0121-0.0045-0.00020.0094-0.00670.0057-0.1091-0.02580.001-0.0032-0.061-0.0715-0.0670.0058-0.00020.1689-0.0294-0.00080.174-0.08130.45057.297271.0243105.2552
700.08090.04190.00990.02230.0110.21290.04720.0687-0.00590.0310.03480.00080.0652-0.00630.14390.0957-0.0466-0.14310.2410.06880.06523.703672.694101.3169
710.008-0.0043-0.00060.008-0.00610.1018-0.04690.03670.0379-0.01930.0045-0.0145-0.0860.0249-0.00640.1322-0.0601-0.13520.2982-0.09920.15374.399372.0489100.7898
720.1102-0.1154-0.03530.3467-0.01870.02520.02020.1187-0.1065-0.0201-0.07990.20590.0777-0.28-0.0130.2345-0.18550.01170.5599-0.10010.28427.849173.7848116.4224
730.09560.0179-0.05360.04170.04640.11140.04190.01620.04110.0007-0.02450.0206-0.0157-0.11320.02820.20890.0831-0.02710.2619-0.03140.074514.016291.9625112.8377
740.28190.05710.11490.1426-0.06920.10870.0423-0.01390.0273-0.0026-0.02810.0118-0.0951-0.0544-0.00420.28310.09450.00350.1223-0.00480.37717.766797.2917107.6757
750.0869-0.0238-0.06920.16970.04810.05180.0276-0.04970.01670.04-0.13550.1381-0.04640.04320.0470.02520.044-0.10130.11170.07140.062221.920382.1131111.9748
760.35690.007-0.10480.4951-0.00190.6393-0.039-0.1369-0.00620.0936-0.09710.0121-0.07030.0805-0.53380.0520.03870.03510.0504-0.08210.003625.627383.2354103.9703
770.19460.0194-0.02010.2384-0.01890.01510.0388-0.069-0.02950.054-0.0147-0.04030.04760.03790.0652-0.00430.0509-0.21320.02780.0941-0.183424.764390.8091100.3726
780.10320.1242-0.00110.1492-0.0018-0.00010.076-0.25520.01170.1658-0.13530.01890.03120.0254-0.01020.16230.04090.06570.24550.00990.036125.674691.3687115.4037
790.19240.07870.03990.36490.19810.28630.0276-0.147-0.08310.1583-0.0717-0.09460.11560.0715-0.1883-0.11460.06250.00580.14360.03660.051816.174789.7489104.001
800.23150.1051-0.02350.13980.19280.46370.10520.1182-0.00940.0522-0.00830.00570.1907-0.16880.1910.06870.00580.02610.2164-0.01520.06919.401278.6386110.7551
810.03180.0064-0.00210.025-0.02270.0209-0.0268-0.0041-0.03590.0434-0.00490.02470.03420.0866-0.02880.15330.10350.13820.42040.10140.437826.201680.7009155.0685
820.0081-0.00020.01190.00930.01150.0238-0.032-0.0074-0.0425-0.0471-0.03720.0886-0.0467-0.0825-0.05980.20450.14520.0330.2931-0.09720.140511.193389.3667146.3454
830.03330.00860.02730.0768-0.04050.0543-0.0278-0.033-0.03320.0254-0.0768-0.0164-0.0630.0087-0.05880.24010.0620.08530.49350.00220.112330.860786.2435155.844
840.0113-0.0083-0.00790.00770.00620.034-0.0257-0.003-0.02540.00370.0060.0935-0.0149-0.04300.14590.00850.00880.1491-0.01380.198328.235583.4462144.7481
850.06050.01720.09850.1242-0.00640.17460.03380.031-0.1776-0.0121-0.05030.07570.0643-0.0739-0.0149-0.053-0.0686-0.0736-0.0199-0.0930.162722.514978.3045138.6662
860.0013-0.00260.00110.014-0.00260.00120.0507-0.0077-0.01490.0161-0.01620.0040.0023-0.00280.02540.26450.01140.04490.12450.11090.241829.573488.6927137.8975
870.02850.0063-0.02850.02450.04170.15590.1119-0.01370.1098-0.0355-0.0065-0.0289-0.08780.01130.07550.14260.076-0.05130.1965-0.05820.441324.006289.8919140.6394
880.1935-0.02240.14170.0817-0.03370.11430.1127-0.0160.04210.01690.0817-0.0701-0.00990.11290.53670.0521-0.0366-0.06670.166-0.23030.282617.009588.6505142.9558
890.0224-0.0155-0.00920.01190.0060.0231-0.02860.00110.0119-0.0094-0.00650.0092-0.00260.012-0.07960.1620.1375-0.07680.1239-0.20030.530818.618479.5731144.9619
900.466-0.19070.38140.1821-0.19940.33120.0649-0.0793-0.1352-0.07350.02980.01430.1394-0.1820.02490.1158-0.04760.10350.2757-0.04630.175935.078878.2614148.9001
910.0294-0.0052-0.00890.0911-0.06430.0497-0.0632-0.0728-0.0763-0.0402-0.1171-0.11360.12180.0067-0.06550.21170.08970.18040.2884-0.02660.453915.743578.7242149.4886
920.05060.03130.05960.0190.04110.06690.0939-0.05540.00630.00720.0461-0.03690.0256-0.1519-0.0090.44650.2411-0.17140.4179-0.05220.604724.940573.3342131.1272
930.02170.0141-0.0350.0316-0.00650.06940.0169-0.0088-0.06630.0219-0.04840.02260.0513-0.04930.00030.2977-0.1494-0.12710.45910.1690.791824.723757.0078139.0368
940.09720.03170.04130.3021-0.04820.16250.0425-0.051-0.04360.0498-0.05410.07410.1434-0.0766-0.14660.2323-0.0021-0.06220.1490.18510.405329.242853.4425143.5228
950.4702-0.23150.09850.85-0.0750.1633-0.0792-0.0915-0.21990.01530.18580.53820.0675-0.15780.09330.03520.1558-0.0185-0.056-0.00810.331933.287668.4812138.6438
960.02650.0383-0.02070.1094-0.00880.0443-0.0104-0.05010.02860.19950.0480.0909-0.0014-0.08060.02540.12330.09050.00070.0220.08970.285135.899368.2671146.1688
970.02510.00530.01280.00170.00340.0069-0.0014-0.00490.02810.0707-0.00430.053-0.0255-0.0376-0.0990.29340.08840.35050.11360.04420.181937.784462.4954151.9292
980.0149-0.00550.00620.03770.01640.01280.0647-0.0046-0.0644-0.1179-0.07930.05250.01560.0307-0.04780.20120.1091-0.1192-0.03490.09770.023937.117559.1749137.8593
990.0218-0.01350.00930.0066-0.01620.0018-0.1011-0.1821-0.22870.14160.11560.25720.0248-0.0976-0.09630.11220.1220.17450.19590.13650.556527.653861.1065146.9338
1000.24730.12480.1260.33440.16170.16130.04-0.1469-0.1884-0.01240.09910.2672-0.1491-0.0475-0.00590.137-0.04410.02890.10640.00080.305631.201872.8067139.3214
1010.08090.0108-0.02770.0395-0.01370.0518-0.0110.078-0.0079-0.03730.00780.0450.0117-0.0776-0.01310.21250.18090.02490.23380.00910.266856.775562.868595.3397
1020.11020.0847-0.00150.08970.0240.0230.0699-0.01780.1086-0.01310.1583-0.171-0.02610.10550.23910.16740.1740.1290.35070.03290.289170.49355.8374103.0476
1030.01460.00970.00580.03060.00760.01030.03860.07390.0921-0.0696-0.0456-0.0238-0.11870.10170.02290.18090.0377-0.05190.24890.07550.29658.445871.205599.2049
1040.01350.01250.00690.0244-0.00320.009-0.10140.00530.0038-0.0422-0.10320.1370.10270.0175-0.00110.1670.02860.05570.13890.0340.320255.231254.8403110.5433
1050.01510.0278-0.01930.0576-0.03050.03630.0075-0.0527-0.01720.02560.01860.0443-0.02980.01720.05650.061-0.1150.03380.17270.06080.034360.690768.3316110.744
1060.0392-0.00810.020.04180.05030.0837-0.004-0.0444-0.0156-0.02180.03570.0394-0.0501-0.02330.08120.23090.01490.060.44120.17660.071261.537967.5516116.1535
1070.0063-0.00350.01670.0022-0.00770.0446-0.2349-0.1086-0.0461-0.02810.1282-0.0201-0.02880.1992-0.00090.160.0167-0.01410.34840.05880.121166.467665.8105108.3804
1080.2865-0.0009-0.120.0940.11290.1803-0.0168-0.05740.0502-0.00020.1028-0.022-0.0178-0.01090.3520.06010.02420.05720.23880.09080.142868.285958.9653107.4478
1090.0333-0.022-0.00050.10030.0470.0244-0.03580.0143-0.04370.0161-0.0170.0580.04860.0129-0.14950.09760.09180.09120.23050.15090.354459.627555.7865105.4932
1100.01530.0142-0.00910.0286-0.00260.00680.0129-0.0304-0.0427-0.031-0.00940.06090.0318-0.0041-0.01640.2160.0351-0.0040.26230.0730.141350.749671.4557101.8778
1110.0301-0.0098-0.01250.00840.01050.03370.03790.0213-0.0155-0.00780.00270.0084-0.0088-0.01650.02380.32750.1010.13810.3664-0.2240.500952.805760.420999.689
1120.0636-0.03220.00830.116-0.03720.01360.0062-0.08030.0259-0.08420.02060.10120.1293-0.0291-0.10710.34180.06760.05930.36930.24720.400458.754652.8379109.9868
1130.0015-0.00180.00020.0027-0.00250.0026-0.0388-0.0462-0.1518-0.0475-0.03820.08570.06410.026300.28860.021-0.04430.29630.06510.725338.018551.1869112.3151
1140.00930.00340.00520.0027-0.00670.0143-0.00260.0148-0.0362-0.1342-0.04120.07960.131-0.07910.00090.3341-0.02010.05360.3123-0.05860.56631.676151.9063106.998
1150.33720.0773-0.1160.55820.18110.29220.05860.0072-0.57140.0627-0.0967-0.14050.1680.0264-0.16770.07310.0462-0.04960.1698-0.04310.323142.681762.9736111.7943
1160.16410.0884-0.00210.0548-0.02240.0463-0.08560.2504-0.0848-0.08660.0647-0.0558-0.00010.0054-0.01430.1440.02990.04340.2209-0.02890.129541.17765.0634104.2506
1170.00580.0110.01790.07080.05960.0595-0.03430.0798-0.0219-0.0415-0.01320.00810.0375-0.0221-0.13230.0322-0.0658-0.07050.2201-0.20910.0935.230463.75498.5188
1180.1070.00940.01520.0451-0.00540.07370.0474-0.0851-0.07280.0378-0.03260.065-0.0307-0.02830.0640.04730.02950.01980.174-0.01140.354132.709561.6254112.5923
1190.16970.0998-0.03820.0853-0.11550.28770.09430.2816-0.4778-0.1918-0.19890.14390.08540.0509-0.09020.20930.0443-0.01620.2311-0.08930.413940.136656.4879104.4791
1200.22920.0714-0.04130.0458-0.04980.21290.1164-0.0323-0.285-0.0126-0.1263-0.00950.0850.1626-0.05720.0715-0.017-0.1540.1487-0.01750.408247.480862.3448111.136
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 12:20)
2X-RAY DIFFRACTION2(chain A and resid 21:33)
3X-RAY DIFFRACTION3(chain A and resid 34:39)
4X-RAY DIFFRACTION4(chain A and resid 40:49)
5X-RAY DIFFRACTION5(chain A and resid 50:56)
6X-RAY DIFFRACTION6(chain A and resid 57:63)
7X-RAY DIFFRACTION7(chain A and resid 64:68)
8X-RAY DIFFRACTION8(chain A and resid 69:80)
9X-RAY DIFFRACTION9(chain A and resid 81:93)
10X-RAY DIFFRACTION10(chain A and resid 94:99)
11X-RAY DIFFRACTION11(chain A and resid 100:113)
12X-RAY DIFFRACTION12(chain A and resid 114:135)
13X-RAY DIFFRACTION13(chain A and resid 136:144)
14X-RAY DIFFRACTION14(chain A and resid 145:151)
15X-RAY DIFFRACTION15(chain A and resid 152:176)
16X-RAY DIFFRACTION16(chain A and resid 177:194)
17X-RAY DIFFRACTION17(chain A and resid 195:203)
18X-RAY DIFFRACTION18(chain A and resid 204:217)
19X-RAY DIFFRACTION19(chain A and resid 218:232)
20X-RAY DIFFRACTION20(chain A and resid 233:253)
21X-RAY DIFFRACTION21(chain B and resid 11:27)
22X-RAY DIFFRACTION22(chain B and resid 28:35)
23X-RAY DIFFRACTION23(chain B and resid 36:49)
24X-RAY DIFFRACTION24(chain B and resid 50:60)
25X-RAY DIFFRACTION25(chain B and resid 61:66)
26X-RAY DIFFRACTION26(chain B and resid 67:88)
27X-RAY DIFFRACTION27(chain B and resid 89:93)
28X-RAY DIFFRACTION28(chain B and resid 94:99)
29X-RAY DIFFRACTION29(chain B and resid 100:109)
30X-RAY DIFFRACTION30(chain B and resid 110:116)
31X-RAY DIFFRACTION31(chain B and resid 117:138)
32X-RAY DIFFRACTION32(chain B and resid 139:146)
33X-RAY DIFFRACTION33(chain B and resid 147:154)
34X-RAY DIFFRACTION34(chain B and resid 155:176)
35X-RAY DIFFRACTION35(chain B and resid 177:198)
36X-RAY DIFFRACTION36(chain B and resid 199:205)
37X-RAY DIFFRACTION37(chain B and resid 206:217)
38X-RAY DIFFRACTION38(chain B and resid 218:232)
39X-RAY DIFFRACTION39(chain B and resid 233:246)
40X-RAY DIFFRACTION40(chain B and resid 247:252)
41X-RAY DIFFRACTION41(chain C and resid 11:20)
42X-RAY DIFFRACTION42(chain C and resid 21:33)
43X-RAY DIFFRACTION43(chain C and resid 34:39)
44X-RAY DIFFRACTION44(chain C and resid 40:49)
45X-RAY DIFFRACTION45(chain C and resid 50:56)
46X-RAY DIFFRACTION46(chain C and resid 57:63)
47X-RAY DIFFRACTION47(chain C and resid 64:68)
48X-RAY DIFFRACTION48(chain C and resid 69:88)
49X-RAY DIFFRACTION49(chain C and resid 89:93)
50X-RAY DIFFRACTION50(chain C and resid 94:99)
51X-RAY DIFFRACTION51(chain C and resid 100:109)
52X-RAY DIFFRACTION52(chain C and resid 110:117)
53X-RAY DIFFRACTION53(chain C and resid 135:146)
54X-RAY DIFFRACTION54(chain C and resid 147:156)
55X-RAY DIFFRACTION55(chain C and resid 157:176)
56X-RAY DIFFRACTION56(chain C and resid 177:194)
57X-RAY DIFFRACTION57(chain C and resid 195:201)
58X-RAY DIFFRACTION58(chain C and resid 202:217)
59X-RAY DIFFRACTION59(chain C and resid 218:232)
60X-RAY DIFFRACTION60(chain C and resid 233:252)
61X-RAY DIFFRACTION61(chain D and resid 11:20)
62X-RAY DIFFRACTION62(chain D and resid 21:33)
63X-RAY DIFFRACTION63(chain D and resid 34:39)
64X-RAY DIFFRACTION64(chain D and resid 40:49)
65X-RAY DIFFRACTION65(chain D and resid 50:59)
66X-RAY DIFFRACTION66(chain D and resid 60:65)
67X-RAY DIFFRACTION67(chain D and resid 66:86)
68X-RAY DIFFRACTION68(chain D and resid 87:93)
69X-RAY DIFFRACTION69(chain D and resid 94:99)
70X-RAY DIFFRACTION70(chain D and resid 100:109)
71X-RAY DIFFRACTION71(chain D and resid 110:116)
72X-RAY DIFFRACTION72(chain D and resid 117:137)
73X-RAY DIFFRACTION73(chain D and resid 138:146)
74X-RAY DIFFRACTION74(chain D and resid 147:156)
75X-RAY DIFFRACTION75(chain D and resid 157:176)
76X-RAY DIFFRACTION76(chain D and resid 177:194)
77X-RAY DIFFRACTION77(chain D and resid 195:205)
78X-RAY DIFFRACTION78(chain D and resid 206:217)
79X-RAY DIFFRACTION79(chain D and resid 218:232)
80X-RAY DIFFRACTION80(chain D and resid 233:253)
81X-RAY DIFFRACTION81(chain E and resid 11:21)
82X-RAY DIFFRACTION82(chain E and resid 22:32)
83X-RAY DIFFRACTION83(chain E and resid 33:39)
84X-RAY DIFFRACTION84(chain E and resid 40:49)
85X-RAY DIFFRACTION85(chain E and resid 50:60)
86X-RAY DIFFRACTION86(chain E and resid 61:66)
87X-RAY DIFFRACTION87(chain E and resid 67:80)
88X-RAY DIFFRACTION88(chain E and resid 81:93)
89X-RAY DIFFRACTION89(chain E and resid 94:99)
90X-RAY DIFFRACTION90(chain E and resid 100:109)
91X-RAY DIFFRACTION91(chain E and resid 110:116)
92X-RAY DIFFRACTION92(chain E and resid 117:138)
93X-RAY DIFFRACTION93(chain E and resid 139:146)
94X-RAY DIFFRACTION94(chain E and resid 147:156)
95X-RAY DIFFRACTION95(chain E and resid 157:176)
96X-RAY DIFFRACTION96(chain E and resid 177:191)
97X-RAY DIFFRACTION97(chain E and resid 192:201)
98X-RAY DIFFRACTION98(chain E and resid 202:217)
99X-RAY DIFFRACTION99(chain E and resid 218:232)
100X-RAY DIFFRACTION100(chain E and resid 233:252)
101X-RAY DIFFRACTION101(chain F and resid 11:21)
102X-RAY DIFFRACTION102(chain F and resid 22:34)
103X-RAY DIFFRACTION103(chain F and resid 35:46)
104X-RAY DIFFRACTION104(chain F and resid 47:56)
105X-RAY DIFFRACTION105(chain F and resid 57:63)
106X-RAY DIFFRACTION106(chain F and resid 64:68)
107X-RAY DIFFRACTION107(chain F and resid 69:80)
108X-RAY DIFFRACTION108(chain F and resid 81:93)
109X-RAY DIFFRACTION109(chain F and resid 94:99)
110X-RAY DIFFRACTION110(chain F and resid 100:106)
111X-RAY DIFFRACTION111(chain F and resid 107:113)
112X-RAY DIFFRACTION112(chain F and resid 114:137)
113X-RAY DIFFRACTION113(chain F and resid 138:146)
114X-RAY DIFFRACTION114(chain F and resid 147:156)
115X-RAY DIFFRACTION115(chain F and resid 157:176)
116X-RAY DIFFRACTION116(chain F and resid 177:191)
117X-RAY DIFFRACTION117(chain F and resid 192:201)
118X-RAY DIFFRACTION118(chain F and resid 202:217)
119X-RAY DIFFRACTION119(chain F and resid 218:234)
120X-RAY DIFFRACTION120(chain F and resid 235:252)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more