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- PDB-7ke3: Heavy chain ferritin with C-terminal EBNA1 epitope -

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Basic information

Entry
Database: PDB / ID: 7ke3
TitleHeavy chain ferritin with C-terminal EBNA1 epitope
ComponentsFerritin heavy chain,Epstein-Barr nuclear antigen 1
KeywordsOXIDOREDUCTASE / Protein nanoparticle / vaccine / virus like particle
Function / homology
Function and homology information


host cell PML body / symbiont-mediated suppression of host antigen processing and presentation / viral latency / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters / iron ion sequestering activity / enzyme-substrate adaptor activity / : / symbiont-mediated disruption of host cell PML body / autolysosome / Scavenging by Class A Receptors ...host cell PML body / symbiont-mediated suppression of host antigen processing and presentation / viral latency / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters / iron ion sequestering activity / enzyme-substrate adaptor activity / : / symbiont-mediated disruption of host cell PML body / autolysosome / Scavenging by Class A Receptors / Golgi Associated Vesicle Biogenesis / ferroxidase / regulation of DNA replication / intracellular sequestering of iron ion / ferroxidase activity / negative regulation of fibroblast proliferation / ferric iron binding / Iron uptake and transport / ferrous iron binding / tertiary granule lumen / iron ion transport / endonuclease activity / intracellular iron ion homeostasis / ficolin-1-rich granule lumen / iron ion binding / immune response / DNA-binding transcription factor activity / negative regulation of cell population proliferation / virus-mediated perturbation of host defense response / Neutrophil degranulation / positive regulation of DNA-templated transcription / DNA binding / extracellular exosome / extracellular region / identical protein binding / membrane / nucleus / cytoplasm / cytosol
Similarity search - Function
Epstein Barr virus nuclear antigen-1, DNA-binding / Epstein Barr virus nuclear antigen-1, DNA-binding domain / Epstein Barr virus nuclear antigen-1, DNA-binding domain superfamily / E2/EBNA1, C-terminal / Ferritin iron-binding regions signature 1. / Ferritin iron-binding regions signature 2. / Ferritin, conserved site / Ferritin / Ferritin-like diiron domain / Ferritin-like diiron domain profile. ...Epstein Barr virus nuclear antigen-1, DNA-binding / Epstein Barr virus nuclear antigen-1, DNA-binding domain / Epstein Barr virus nuclear antigen-1, DNA-binding domain superfamily / E2/EBNA1, C-terminal / Ferritin iron-binding regions signature 1. / Ferritin iron-binding regions signature 2. / Ferritin, conserved site / Ferritin / Ferritin-like diiron domain / Ferritin-like diiron domain profile. / Ferritin/DPS protein domain / Ferritin-like domain / Ferritin-like / Ferritin-like superfamily
Similarity search - Domain/homology
: / Ferritin heavy chain / Epstein-Barr nuclear antigen 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Epstein-Barr virus (Epstein-Barr virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsPederick, J.L. / Bruning, J.B.
CitationJournal: Vaccine / Year: 2021
Title: Immunogenicity study of engineered ferritins with C- and N-terminus insertion of Epstein-Barr nuclear antigen 1 epitope.
Authors: Qu, Y. / Zhang, B. / Wang, Y. / Yin, S. / Pederick, J.L. / Bruning, J.B. / Sun, Y. / Middelberg, A. / Bi, J.
History
DepositionOct 10, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 1, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 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: Ferritin heavy chain,Epstein-Barr nuclear antigen 1
B: Ferritin heavy chain,Epstein-Barr nuclear antigen 1
C: Ferritin heavy chain,Epstein-Barr nuclear antigen 1
D: Ferritin heavy chain,Epstein-Barr nuclear antigen 1
E: Ferritin heavy chain,Epstein-Barr nuclear antigen 1
F: Ferritin heavy chain,Epstein-Barr nuclear antigen 1
G: Ferritin heavy chain,Epstein-Barr nuclear antigen 1
H: Ferritin heavy chain,Epstein-Barr nuclear antigen 1
I: Ferritin heavy chain,Epstein-Barr nuclear antigen 1
J: Ferritin heavy chain,Epstein-Barr nuclear antigen 1
K: Ferritin heavy chain,Epstein-Barr nuclear antigen 1
L: Ferritin heavy chain,Epstein-Barr nuclear antigen 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)283,98038
Polymers282,13012
Non-polymers1,85026
Water12,809711
1
A: Ferritin heavy chain,Epstein-Barr nuclear antigen 1
B: Ferritin heavy chain,Epstein-Barr nuclear antigen 1
C: Ferritin heavy chain,Epstein-Barr nuclear antigen 1
D: Ferritin heavy chain,Epstein-Barr nuclear antigen 1
E: Ferritin heavy chain,Epstein-Barr nuclear antigen 1
F: Ferritin heavy chain,Epstein-Barr nuclear antigen 1
G: Ferritin heavy chain,Epstein-Barr nuclear antigen 1
H: Ferritin heavy chain,Epstein-Barr nuclear antigen 1
I: Ferritin heavy chain,Epstein-Barr nuclear antigen 1
J: Ferritin heavy chain,Epstein-Barr nuclear antigen 1
K: Ferritin heavy chain,Epstein-Barr nuclear antigen 1
L: Ferritin heavy chain,Epstein-Barr nuclear antigen 1
hetero molecules

A: Ferritin heavy chain,Epstein-Barr nuclear antigen 1
B: Ferritin heavy chain,Epstein-Barr nuclear antigen 1
C: Ferritin heavy chain,Epstein-Barr nuclear antigen 1
D: Ferritin heavy chain,Epstein-Barr nuclear antigen 1
E: Ferritin heavy chain,Epstein-Barr nuclear antigen 1
F: Ferritin heavy chain,Epstein-Barr nuclear antigen 1
G: Ferritin heavy chain,Epstein-Barr nuclear antigen 1
H: Ferritin heavy chain,Epstein-Barr nuclear antigen 1
I: Ferritin heavy chain,Epstein-Barr nuclear antigen 1
J: Ferritin heavy chain,Epstein-Barr nuclear antigen 1
K: Ferritin heavy chain,Epstein-Barr nuclear antigen 1
L: Ferritin heavy chain,Epstein-Barr nuclear antigen 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)567,96076
Polymers564,26124
Non-polymers3,70052
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_777-y+2,-x+2,-z+21
Buried area97230 Å2
ΔGint-469 kcal/mol
Surface area130760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)217.882, 217.882, 147.203
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11C-304-

FE

21E-301-

FE

31C-450-

HOH

41E-455-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 23 through 48 or resid 50...
21(chain B and (resid 23 through 48 or resid 50...
31(chain C and (resid 23 through 48 or resid 50...
41(chain D and (resid 23 through 48 or resid 50...
51(chain E and (resid 23 through 48 or resid 50...
61(chain F and (resid 23 through 48 or resid 50...
71(chain G and (resid 23 through 48 or resid 50...
81(chain H and (resid 23 through 48 or resid 50...
91(chain I and (resid 23 through 48 or resid 50...
101(chain J and (resid 23 through 48 or resid 50...
111(chain K and (resid 23 through 48 or resid 50...
121(chain L and (resid 23 through 48 or resid 50...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 23 through 48 or resid 50...A23 - 48
121(chain A and (resid 23 through 48 or resid 50...A50 - 52
131(chain A and (resid 23 through 48 or resid 50...A53
141(chain A and (resid 23 through 48 or resid 50...A6 - 176
151(chain A and (resid 23 through 48 or resid 50...A6 - 176
161(chain A and (resid 23 through 48 or resid 50...A6 - 176
211(chain B and (resid 23 through 48 or resid 50...B23 - 48
221(chain B and (resid 23 through 48 or resid 50...B50 - 52
231(chain B and (resid 23 through 48 or resid 50...B53
241(chain B and (resid 23 through 48 or resid 50...B6 - 176
251(chain B and (resid 23 through 48 or resid 50...B6 - 176
261(chain B and (resid 23 through 48 or resid 50...B6 - 176
311(chain C and (resid 23 through 48 or resid 50...C23 - 48
321(chain C and (resid 23 through 48 or resid 50...C50 - 52
331(chain C and (resid 23 through 48 or resid 50...C53
341(chain C and (resid 23 through 48 or resid 50...C5 - 176
351(chain C and (resid 23 through 48 or resid 50...C5 - 176
361(chain C and (resid 23 through 48 or resid 50...C5 - 176
371(chain C and (resid 23 through 48 or resid 50...C5 - 176
381(chain C and (resid 23 through 48 or resid 50...C5 - 176
391(chain C and (resid 23 through 48 or resid 50...C5 - 176
411(chain D and (resid 23 through 48 or resid 50...D23 - 48
421(chain D and (resid 23 through 48 or resid 50...D50 - 52
431(chain D and (resid 23 through 48 or resid 50...D53
441(chain D and (resid 23 through 48 or resid 50...D6 - 176
451(chain D and (resid 23 through 48 or resid 50...D6 - 176
461(chain D and (resid 23 through 48 or resid 50...D6 - 176
511(chain E and (resid 23 through 48 or resid 50...E23 - 48
521(chain E and (resid 23 through 48 or resid 50...E50 - 52
531(chain E and (resid 23 through 48 or resid 50...E53
541(chain E and (resid 23 through 48 or resid 50...E5 - 176
551(chain E and (resid 23 through 48 or resid 50...E5 - 176
561(chain E and (resid 23 through 48 or resid 50...E5 - 176
571(chain E and (resid 23 through 48 or resid 50...E5 - 176
581(chain E and (resid 23 through 48 or resid 50...E5 - 176
611(chain F and (resid 23 through 48 or resid 50...F23 - 48
621(chain F and (resid 23 through 48 or resid 50...F50 - 60
631(chain F and (resid 23 through 48 or resid 50...F62
641(chain F and (resid 23 through 48 or resid 50...F65 - 67
651(chain F and (resid 23 through 48 or resid 50...F88 - 101
661(chain F and (resid 23 through 48 or resid 50...F5 - 176
671(chain F and (resid 23 through 48 or resid 50...F5 - 176
681(chain F and (resid 23 through 48 or resid 50...F5 - 176
691(chain F and (resid 23 through 48 or resid 50...F5 - 176
6101(chain F and (resid 23 through 48 or resid 50...F5 - 176
6111(chain F and (resid 23 through 48 or resid 50...F5 - 176
711(chain G and (resid 23 through 48 or resid 50...G23 - 48
721(chain G and (resid 23 through 48 or resid 50...G50 - 52
731(chain G and (resid 23 through 48 or resid 50...G53
741(chain G and (resid 23 through 48 or resid 50...G5 - 176
751(chain G and (resid 23 through 48 or resid 50...G5 - 176
761(chain G and (resid 23 through 48 or resid 50...G5 - 176
771(chain G and (resid 23 through 48 or resid 50...G5 - 176
781(chain G and (resid 23 through 48 or resid 50...G5 - 176
811(chain H and (resid 23 through 48 or resid 50...H23 - 48
821(chain H and (resid 23 through 48 or resid 50...H50 - 52
831(chain H and (resid 23 through 48 or resid 50...H53
841(chain H and (resid 23 through 48 or resid 50...H5 - 176
851(chain H and (resid 23 through 48 or resid 50...H5 - 176
861(chain H and (resid 23 through 48 or resid 50...H5 - 176
871(chain H and (resid 23 through 48 or resid 50...H5 - 176
881(chain H and (resid 23 through 48 or resid 50...H5 - 176
911(chain I and (resid 23 through 48 or resid 50...I23 - 48
921(chain I and (resid 23 through 48 or resid 50...I50 - 60
931(chain I and (resid 23 through 48 or resid 50...I62
941(chain I and (resid 23 through 48 or resid 50...I0
951(chain I and (resid 23 through 48 or resid 50...I5 - 176
961(chain I and (resid 23 through 48 or resid 50...I5 - 176
971(chain I and (resid 23 through 48 or resid 50...I5 - 176
981(chain I and (resid 23 through 48 or resid 50...I5 - 176
991(chain I and (resid 23 through 48 or resid 50...I5 - 176
9101(chain I and (resid 23 through 48 or resid 50...I5 - 176
9111(chain I and (resid 23 through 48 or resid 50...I5 - 176
1011(chain J and (resid 23 through 48 or resid 50...J23 - 48
1021(chain J and (resid 23 through 48 or resid 50...J50 - 52
1031(chain J and (resid 23 through 48 or resid 50...J53
1041(chain J and (resid 23 through 48 or resid 50...J5 - 176
1051(chain J and (resid 23 through 48 or resid 50...J5 - 176
1061(chain J and (resid 23 through 48 or resid 50...J5 - 176
1111(chain K and (resid 23 through 48 or resid 50...K23 - 48
1121(chain K and (resid 23 through 48 or resid 50...K50 - 52
1131(chain K and (resid 23 through 48 or resid 50...K53
1141(chain K and (resid 23 through 48 or resid 50...K5 - 176
1151(chain K and (resid 23 through 48 or resid 50...K5 - 176
1161(chain K and (resid 23 through 48 or resid 50...K5 - 176
1171(chain K and (resid 23 through 48 or resid 50...K5 - 176
1181(chain K and (resid 23 through 48 or resid 50...K5 - 176
1211(chain L and (resid 23 through 48 or resid 50...L23 - 48
1221(chain L and (resid 23 through 48 or resid 50...L50 - 52
1231(chain L and (resid 23 through 48 or resid 50...L53
1241(chain L and (resid 23 through 48 or resid 50...L5 - 176
1251(chain L and (resid 23 through 48 or resid 50...L5 - 176
1261(chain L and (resid 23 through 48 or resid 50...L5 - 176
1271(chain L and (resid 23 through 48 or resid 50...L5 - 176
1281(chain L and (resid 23 through 48 or resid 50...L5 - 176
1291(chain L and (resid 23 through 48 or resid 50...L5 - 176

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Components

#1: Protein
Ferritin heavy chain,Epstein-Barr nuclear antigen 1 / Ferritin H subunit / Cell proliferation-inducing gene 15 protein / EBV nuclear antigen 1


Mass: 23510.867 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Epstein-Barr virus (strain B95-8) (Epstein-Barr virus (strain B95-8))
Gene: FTH1, FTH, FTHL6, OK/SW-cl.84, PIG15, EBNA1, BKRF1 / Strain: B95-8 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P02794, UniProt: P03211, ferroxidase
#2: Chemical
ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: Fe
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 711 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.1 Å3/Da / Density % sol: 60.27 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / Details: 0.1M HEPES pH 7.0, 30% Jeffamine M-600 pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Oct 9, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.2→48.72 Å / Num. obs: 177978 / % possible obs: 99.9 % / Redundancy: 27.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.336 / Rpim(I) all: 0.065 / Rrim(I) all: 0.342 / Net I/σ(I): 8.9 / Num. measured all: 4871537
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.2-2.2427.62.54924013187030.9070.4932.5971.699.8
12.05-48.7225.20.05631305124110.0120.05729.898.6

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation8.38 Å48.72 Å
Translation8.38 Å48.72 Å

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.4data scaling
PHASER2.8.3phasing
PHENIX1.18.2-3874refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6J4A

6j4a


Resolution: 2.2→48.72 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 34.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2705 8841 5.01 %
Rwork0.2407 167570 -
obs0.2422 176411 99.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 88.63 Å2 / Biso mean: 26.4795 Å2 / Biso min: 15.41 Å2
Refinement stepCycle: final / Resolution: 2.2→48.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16158 0 68 711 16937
Biso mean--33.46 31.71 -
Num. residues----2001
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A7885X-RAY DIFFRACTION7.108TORSIONAL
12B7885X-RAY DIFFRACTION7.108TORSIONAL
13C7885X-RAY DIFFRACTION7.108TORSIONAL
14D7885X-RAY DIFFRACTION7.108TORSIONAL
15E7885X-RAY DIFFRACTION7.108TORSIONAL
16F7885X-RAY DIFFRACTION7.108TORSIONAL
17G7885X-RAY DIFFRACTION7.108TORSIONAL
18H7885X-RAY DIFFRACTION7.108TORSIONAL
19I7885X-RAY DIFFRACTION7.108TORSIONAL
110J7885X-RAY DIFFRACTION7.108TORSIONAL
111K7885X-RAY DIFFRACTION7.108TORSIONAL
112L7885X-RAY DIFFRACTION7.108TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2-2.230.32172940.28595522581699
2.23-2.250.37642760.35795463573998
2.25-2.280.35233030.32195415571898
2.28-2.310.32562670.27095574584199
2.31-2.340.30843100.257455425852100
2.34-2.370.28952830.2515587587099
2.37-2.40.27412780.249655425820100
2.4-2.440.282840.255155765860100
2.44-2.480.29132930.24455735866100
2.48-2.520.26242670.23855935860100
2.52-2.560.27443290.23755485877100
2.56-2.610.25742820.237555835865100
2.61-2.660.26282860.227156015887100
2.66-2.710.24982810.22755589587099
2.71-2.770.23953090.23645556586599
2.77-2.840.25032970.22815551584899
2.84-2.910.25052980.23025585588399
2.91-2.990.26332930.22685589588299
2.99-3.070.27743010.22955580588199
3.07-3.170.26622740.21185605587999
3.17-3.290.22613260.21745593591999
3.29-3.420.24662920.22045619591199
3.42-3.570.22862790.22575592587199
3.57-3.760.27792890.22925586587598
3.76-40.26432900.225607589799
4-4.310.25992980.21765645594399
4.31-4.740.22743270.21935620594799
4.74-5.420.28143170.255612592998
5.42-6.830.35323210.291957646085100
6.83-48.720.27082970.26275758605595
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.75-0.18510.12161.834-1.96321.22830.1330.0354-0.10070.11960.16260.4243-0.2369-0.2054-0.17290.235-0.0190.02080.2062-0.04810.218222.7324159.9763158.033
20.24771.1292-0.67244.2458-2.09522.021-0.08980.0766-0.0806-0.0760.0132-0.45670.08680.06940.08390.17930.0223-0.01080.3024-0.01470.2931230.7068167.4572150.7484
31.62550.20141.16521.9441-0.90841.60650.1853-0.1469-0.2049-0.23250.20230.61050.0243-0.2741-0.32570.2427-0.0120.06510.3459-0.02390.2687219.259158.5068154.3104
40.37291.5349-0.95074.0477-2.03551.77720.1738-0.10760.06880.0893-0.04830.4131-0.1658-0.1185-0.01650.18110.0250.03560.2791-0.04860.2957224.9446166.5658165.9341
50.671.1712-1.83591.4302-2.50064.4541-0.0921-0.12180.1151-0.0101-0.1465-0.2528-0.02910.07560.17790.2269-0.0078-0.02480.242-0.05790.2339232.998183.9013155.0022
66.51234.1769-1.89693.2632-0.80971.3828-0.72360.3983-0.9886-0.7971-0.1923-1.0226-0.0631-0.10410.36170.13880.0453-0.16630.19430.19610.1882223.7734177.2122124.8195
71.137-0.96330.53683.6505-2.57591.59880.17070.1927-0.0895-0.2561-0.05840.40920.25460.0974-0.12580.22040.0064-0.00840.2097-0.02260.2689223.5393154.3831143.3475
80.6078-2.66490.40929.0628-5.42384.2641-0.16790.06090.2115-0.0851-0.2063-0.83260.04340.15010.34330.1973-0.0211-0.02360.1915-0.00540.2331231.2824157.6888141.038
91.5226-0.538-1.36141.8936-0.33491.56080.2245-0.09120.09260.3620.31410.4926-0.2772-0.3216-0.53750.2242-0.1098-0.05730.2868-0.04060.2146219.4358163.5632140.3869
100.9608-1.70331.37878.6886-6.34896.45370.2267-0.1128-0.2949-0.39550.40721.00780.2512-0.126-0.58510.21880.0351-0.01320.2911-0.01410.269222.6414150.8568131.3585
116.858-1.75492.83663.4424-1.24934.04540.20681.1897-0.1807-0.3049-0.0972-0.21310.22041.0748-0.08320.33010.0305-0.04480.3228-0.01480.2461229.0617164.2369123.4954
121.8902-2.03671.35346.7432-3.58173.60410.1745-0.10890.43490.5047-0.6014-0.4843-0.15050.58310.35720.17410.0149-0.02590.31010.00890.2475231.8235142.052134.052
135.26422.15352.39813.5104-0.98157.45020.31-1.1122-0.68720.32390.0030.2743-0.3861-0.7062-0.4220.28170.01550.01150.31160.01430.3105227.0071129.1072145.5309
141.420.1460.05254.2252-2.07354.7681-0.0174-0.1160.0957-0.02970.0788-0.1735-0.0218-0.2732-0.13230.28830.09530.00570.27450.00730.1348236.7752135.1149147.0149
152.7342-2.4477-0.16162.34120.93262.6354-0.13410.11550.0540.31610.17930.29720.04850.27760.04960.3031-0.0578-0.01350.1863-0.00940.1723257.9205109.7357125.1721
162.69040.20282.13171.1611-0.14541.82360.2121-0.0386-0.19250.09310.0058-0.00630.20070.0335-0.16470.26950.01240.06570.2511-0.02770.212281.3708109.8867143.3157
177.53052.40564.11840.38911.17213.3229-0.3063-0.07660.8163-0.02-0.06720.2671-0.2348-0.1340.31350.25880.03220.02040.19040.00350.3232278.0068117.5657141.0631
181.94751.15060.33030.6842-0.98421.1042-0.1307-0.059-0.590.04940.25860.15040.0047-0.2559-0.13640.2121-0.0170.00560.2507-0.08670.3227272.1774105.7761140.3973
195.03990.9892.64790.76681.24022.4978-0.09150.1666-0.2019-0.15720.071-0.05610.07080.1926-0.00640.2687-0.00720.08430.1558-0.02290.2464280.143111.2454128.5683
202.08921.24832.43860.84081.06683.8003-0.05290.05240.17440.0256-0.1188-0.2685-0.06330.02510.12530.28180.00480.05550.2350.01880.2842297.7989119.0869139.4623
211.42650.5066-0.39561.8170.46820.3304-0.08760.07090.0631-0.2242-0.09730.25010.06020.36990.33150.1870.0066-0.06510.35120.08650.334290.9281110.1339169.7949
223.4939-0.48442.85010.3839-0.20482.38240.075-0.116-0.55280.04310.18320.1301-0.0771-0.0861-0.24960.19580.00140.03870.16440.00940.2484268.0461109.9161151.2984
237.6473-2.54253.7725-0.0017-0.87052.1162-0.3096-0.09190.47410.0161-0.0524-0.2445-0.2525-0.07510.39410.23110.01840.01030.20280.00190.2865271.2155117.7156153.7024
241.5221-1.0677-1.55971.59811.31921.6409-0.23810.3193-0.497-0.15390.1860.03320.03050.8305-0.14470.3016-0.09720.0813-0.01210.04930.2992277.1973105.7783154.1975
256.9317-1.49916.03970.6168-1.50495.54330.107-0.4572-0.8093-0.14340.29110.1518-0.2447-0.3939-0.46060.29370.03460.0150.26410.00770.2729264.4187109.0881163.0219
263.5876-0.54050.47211.93390.2442.4953-0.1675-0.22840.16160.4171-0.00820.0431-0.2038-0.04070.13840.34180.03440.04890.29680.06150.2694277.9885115.4197171.1132
271.5774-1.53731.18680.6026-1.44552.3031-0.03740.2825-0.1726-0.1250.0335-0.1727-0.15940.00830.04520.25930.0220.00750.16830.00260.1783251.5511119.1909155.0904
281.6273-1.16520.3611.11610.10151.4891-0.6750.68040.07330.43170.0578-0.14370.75270.2423-0.05590.4086-0.0153-0.27310.376-0.08620.1596241.5611162.550999.087
290.590.53510.65861.64851.26162.173-0.0326-0.00610.0873-0.2365-0.05270.1511-0.1825-0.09250.1370.1730.0074-0.01480.19450.03640.2523243.0324187.3404116.0112
300.14480.5225-0.71994.94515.85516.83220.14390.0334-0.04450.15360.1027-0.26820.23410.0879-0.20890.22830.06620.0160.25720.01760.2465246.8102179.9299118.8409
310.00080.4914-0.60941.6165-0.28141.4193-0.0192-0.023-0.0479-0.7191-0.0359-0.1293-0.2947-0.11250.12560.16940.0371-0.03420.27650.01090.1715243.0517183.231106.9888
321.0770.81441.20073.53633.10742.61340.1145-0.02310.1661-0.0021-0.22390.34520.0384-0.29470.09840.22290.02860.02680.27150.05640.1847233.8391175.4871115.9211
331.53141.93851.72822.99851.94733.1114-0.0157-0.00550.12170.02190.12440.0784-0.05680.0649-0.18370.20680.0164-0.00240.2360.05040.2342236.8731187.8233133.8645
341.41591.6126-1.26111.824-1.05276.19250.27310.420.62880.4170.27310.20130.1177-0.2469-0.3940.29620.0597-0.03450.21660.05090.3676256.3501210.6843122.7467
350.4297-0.21280.08933.17321.12530.3634-0.04640.1056-0.0259-0.37480.0960.2147-0.0791-0.0712-0.07040.2796-0.0276-0.00110.2610.02990.1881255.2118185.6285106.1625
360.8407-1.5315-1.41017.39555.63953.4336-0.096-0.18960.12680.496-0.0058-0.25570.2350.10980.09810.21720.0085-0.07120.27630.02380.1638259.0492185.9491114.2261
372.8775-0.6658-0.20512.3352.78413.17690.2020.01760.13-0.2208-0.73880.2012-0.2781-0.91450.35330.32220.0132-0.03640.24860.11490.2323250.6167194.7447109.8451
38-0.0966-0.3896-0.32464.57572.31132.44590.17470.0540.0196-0.3109-0.0423-0.2616-0.1947-0.1527-0.08720.1593-0.01340.01010.20180.02170.2109265.743196.3497108.0469
390.87690.6878-0.44054.76721.76720.91910.07640.20260.07050.085-0.28280.21870.125-0.22030.18960.2233-0.0226-0.03790.27860.01630.2985270.7121175.742101.4669
401.2883-0.82572.1870.6355-1.10656.9111-0.09040.23070.350.19380.12050.3225-0.3903-0.0787-0.21230.17410.04360.03670.19330.07020.2363256.4542111.4547171.7705
41-0.02650.58590.2353.71982.10811.02030.11070.0083-0.03340.4457-0.1647-0.20270.1605-0.16720.05170.1813-0.0022-0.00510.22830.02390.2221255.4336136.4932188.309
421.18691.31580.58275.41695.50432.9964-0.230.0980.0241-0.90240.4971-0.1219-0.30410.4555-0.20410.339-0.0088-0.02430.260.00970.2145259.3057135.8233179.9226
433.5197-0.485-1.1210.53060.15881.17570.1309-0.0647-0.26530.2173-0.27540.01070.0366-0.81920.30970.24180.0383-0.010.23210.05950.157249.8734128.6084186.0149
440.02740.33970.68064.49762.62361.50440.1137-0.0123-0.0585-0.0173-0.0404-0.249-0.0299-0.1375-0.05240.2711-0.0502-0.01540.25140.04760.2058265.9173125.7699186.3652
450.2094-1.30410.20275.20540.39140.1746-0.00960.03820.06860.06050.04150.0073-0.12870.017-0.06630.1924-0.03960.01940.22630.03710.2464270.9058146.2218192.9861
468.71072.7579-2.78095.037-1.56630.9499-0.445-1.2683-0.39010.4435-0.4742-0.0932-0.1799-0.1310.57080.3324-0.0547-0.0060.2036-0.04290.2558241.9376159.5472195.444
470.4363-0.5348-0.24432.35431.94822.03710.07030.184-0.02780.217-0.2017-0.03690.3476-0.04190.110.20080.01910.00570.25860.00820.2368241.9599137.9909181.6062
483.8869-0.4592-1.19772.4578-2.63723.6334-0.4685-0.3742-0.4251-0.72340.1246-0.21010.34030.12630.09670.40820.00740.02320.2944-0.03470.2655248.1502121.3494165.822
490.2558-0.11040.92924.86755.11346.2006-0.13050.08090.15540.56150.16780.17060.48780.3852-0.09670.2361-0.05640.05770.23390.02430.2149246.9749142.1454175.7793
501.1529-0.01560.3430.4463-0.94881.92510.3767-0.5795-0.1346-0.1505-0.5608-0.16020.1191-0.33050.10260.3306-0.01920.00940.30150.02910.2547243.5476139.6432188.2094
511.5326-0.7686-1.87445.42214.39934.70310.2048-0.0544-0.09050.3342-0.23570.0760.1904-0.39970.1040.19150.0395-0.02210.23250.04420.218232.4534141.1153176.9961
522.4823-0.56070.7654.21441.62342.82770.0562-0.17570.6373-0.12950.1708-0.5971-0.32680.4919-0.15830.19720.00890.01180.3351-0.030.26236.8068156.6462181.9593
530.7979-1.0411-1.11112.66582.76252.28540.0317-0.0336-0.0517-0.11540.0056-0.0071-0.1006-0.04820.00620.23610.0389-0.00430.24280.05040.174236.991134.4034160.7307
541.5346-0.3139-1.42020.2330.12030.8277-0.0360.1184-0.1445-0.0184-0.0705-0.04670.0455-0.03440.09910.2710.0057-0.05350.2419-0.01630.294240.0572141.7841111.6233
553.4817-0.1729-2.97371.2387-0.87771.96990.25540.32320.00360.0596-0.0330.0003-0.2282-0.366-0.15870.237-0.0326-0.04250.2637-0.00760.1734253.433144.2373111.6152
560.96290.2928-1.01982.72911.0370.6554-0.03720.5674-0.3275-0.1681-0.11050.2463-0.0101-0.42280.23020.35220.0562-0.02850.35010.00240.137240.62136.8425109.9232
573.7065-0.1924-1.71951.2641-0.2682.0231-0.075-0.00060.12910.06020.12610.04480.0694-0.1061-0.06270.2666-0.0325-0.05930.21550.02210.1821239.2803151.9712108.1964
585.0928-0.4781-1.23580.7262-0.19990.5497-0.009-0.14850.1193-0.01880.0439-0.07020.1540.0558-0.06260.2299-0.03-0.03680.2258-0.02060.1734259.5189156.9638101.7383
592.3454-0.1036-1.01440.55250.20731.5499-0.24290.2251-0.3271-0.00180.07680.04690.2185-0.17540.11660.24770.00060.00170.2008-0.01160.2172257.0587128.0168109.3193
603.8406-0.5754-4.29810.2728-0.02584.09750.24710.08560.18580.0001-0.0449-0.0781-0.20380.0802-0.19130.2019-0.0185-0.02340.2382-0.04320.198251.8367133.3872120.8089
611.36290.09461.12871.2066-1.03111.6396-0.58390.00370.6777-0.4880.61230.34960.6102-0.0776-0.08650.2713-0.0514-0.00040.2566-0.05080.2078253.0853129.6371106.4027
623.4016-0.4993-3.32631.06980.16973.065-0.17790.18560.0733-0.25560.0943-0.03010.2169-0.18620.06410.29580.0201-0.00830.2315-0.03590.1952260.1723120.1188115.9245
632.7905-1.8429-1.85591.30771.66112.3653-0.0418-0.2453-0.2005-0.022-0.03820.01760.01060.02940.07710.24330.0115-0.04660.2271-0.00090.1639247.8628123.2154133.9654
643.9393-1.4916-1.1961.7730.74932.966-0.21330.38280.043-0.79240.0562-0.1346-0.3649-0.84310.00280.265-0.18610.12740.3092-0.04350.2157307.4806159.335298.9755
650.88040.7298-1.11043.0686-1.62112.3223-0.0405-0.0487-0.2447-0.2022-0.1295-0.2367-0.03010.17110.18270.19490.00840.00690.2187-0.0210.2304307.624138.0797112.5746
660.23980.256-0.50392.8676-3.0212.162-0.0629-0.0187-0.0616-0.0540.015-0.08260.0198-0.1844-0.01520.2645-0.01250.01820.2118-0.02910.2652302.4194138.6874120.057
67-0.48990.25770.55421.53241.24021.1220.10010.1764-0.0775-0.6269-0.05490.08390.50180.23290.1310.18460.05470.03330.3549-0.02420.2751305.883137.455106.2384
680.45130.2828-0.58872.9419-2.54043.54540.0568-0.0996-0.01080.0691-0.1144-0.052-0.1310.20710.13820.1620.02050.00530.2897-0.03310.2355315.4495146.498115.761
691.31051.3422-1.07943.1667-2.80022.8131-0.0136-0.06750.062-0.01850.07490.15780.12170.018-0.14190.2490.01980.02910.2545-0.04840.3267312.518134.2355133.7684
701.0180.3713-0.03121.4687-0.29270.9581-0.06870.1143-0.0812-0.18290.0827-0.07310.1425-0.05040.00760.27260.02140.05620.2579-0.02580.1783293.8049126.404111.5354
710.7757-0.870.3353.5827-3.26541.744-0.034-0.12650.03420.0593-0.092-0.0222-0.1180.110.10520.2918-0.02770.02730.2028-0.04880.1898291.1055140.0501111.3282
722.06940.2805-1.01931.3417-0.8722.2161-0.0280.048-0.0868-0.134-0.328-0.26260.18630.47160.16350.25280.0180.02120.2203-0.08070.1537298.6931127.1895109.8723
73-0.0325-0.0443-0.04433.8223-1.44211.50170.0761-0.0115-0.0129-0.0578-0.1849-0.02570.03470.10460.0920.1888-0.03420.01690.2308-0.03710.2494283.6763125.6035108.1755
740.53340.40930.55454.5087-0.89330.6030.03670.2181-0.19670.3011-0.1393-0.1275-0.18330.18110.07120.2436-0.05470.08040.2668-0.03830.2841278.6341145.9466101.6598
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 41 )A6 - 41
2X-RAY DIFFRACTION2chain 'A' and (resid 42 through 75 )A42 - 75
3X-RAY DIFFRACTION3chain 'A' and (resid 76 through 95 )A76 - 95
4X-RAY DIFFRACTION4chain 'A' and (resid 96 through 137 )A96 - 137
5X-RAY DIFFRACTION5chain 'A' and (resid 138 through 176 )A138 - 176
6X-RAY DIFFRACTION6chain 'B' and (resid 6 through 13 )B6 - 13
7X-RAY DIFFRACTION7chain 'B' and (resid 14 through 48 )B14 - 48
8X-RAY DIFFRACTION8chain 'B' and (resid 49 through 75 )B49 - 75
9X-RAY DIFFRACTION9chain 'B' and (resid 76 through 95 )B76 - 95
10X-RAY DIFFRACTION10chain 'B' and (resid 96 through 123 )B96 - 123
11X-RAY DIFFRACTION11chain 'B' and (resid 124 through 137 )B124 - 137
12X-RAY DIFFRACTION12chain 'B' and (resid 138 through 158 )B138 - 158
13X-RAY DIFFRACTION13chain 'B' and (resid 159 through 163 )B159 - 163
14X-RAY DIFFRACTION14chain 'B' and (resid 164 through 176 )B164 - 176
15X-RAY DIFFRACTION15chain 'C' and (resid 5 through 13 )C5 - 13
16X-RAY DIFFRACTION16chain 'C' and (resid 14 through 48 )C14 - 48
17X-RAY DIFFRACTION17chain 'C' and (resid 49 through 75 )C49 - 75
18X-RAY DIFFRACTION18chain 'C' and (resid 76 through 95 )C76 - 95
19X-RAY DIFFRACTION19chain 'C' and (resid 96 through 137 )C96 - 137
20X-RAY DIFFRACTION20chain 'C' and (resid 138 through 176 )C138 - 176
21X-RAY DIFFRACTION21chain 'D' and (resid 6 through 13 )D6 - 13
22X-RAY DIFFRACTION22chain 'D' and (resid 14 through 48 )D14 - 48
23X-RAY DIFFRACTION23chain 'D' and (resid 49 through 75 )D49 - 75
24X-RAY DIFFRACTION24chain 'D' and (resid 76 through 95 )D76 - 95
25X-RAY DIFFRACTION25chain 'D' and (resid 96 through 123 )D96 - 123
26X-RAY DIFFRACTION26chain 'D' and (resid 124 through 137 )D124 - 137
27X-RAY DIFFRACTION27chain 'D' and (resid 138 through 176 )D138 - 176
28X-RAY DIFFRACTION28chain 'E' and (resid 5 through 13 )E5 - 13
29X-RAY DIFFRACTION29chain 'E' and (resid 14 through 48 )E14 - 48
30X-RAY DIFFRACTION30chain 'E' and (resid 49 through 75 )E49 - 75
31X-RAY DIFFRACTION31chain 'E' and (resid 76 through 95 )E76 - 95
32X-RAY DIFFRACTION32chain 'E' and (resid 96 through 137 )E96 - 137
33X-RAY DIFFRACTION33chain 'E' and (resid 138 through 176 )E138 - 176
34X-RAY DIFFRACTION34chain 'F' and (resid 5 through 13 )F5 - 13
35X-RAY DIFFRACTION35chain 'F' and (resid 14 through 48 )F14 - 48
36X-RAY DIFFRACTION36chain 'F' and (resid 49 through 75 )F49 - 75
37X-RAY DIFFRACTION37chain 'F' and (resid 76 through 95 )F76 - 95
38X-RAY DIFFRACTION38chain 'F' and (resid 96 through 137 )F96 - 137
39X-RAY DIFFRACTION39chain 'F' and (resid 138 through 176 )F138 - 176
40X-RAY DIFFRACTION40chain 'G' and (resid 5 through 13 )G5 - 13
41X-RAY DIFFRACTION41chain 'G' and (resid 14 through 48 )G14 - 48
42X-RAY DIFFRACTION42chain 'G' and (resid 49 through 76 )G49 - 76
43X-RAY DIFFRACTION43chain 'G' and (resid 77 through 95 )G77 - 95
44X-RAY DIFFRACTION44chain 'G' and (resid 96 through 137 )G96 - 137
45X-RAY DIFFRACTION45chain 'G' and (resid 138 through 176 )G138 - 176
46X-RAY DIFFRACTION46chain 'H' and (resid 5 through 13 )H5 - 13
47X-RAY DIFFRACTION47chain 'H' and (resid 14 through 41 )H14 - 41
48X-RAY DIFFRACTION48chain 'H' and (resid 42 through 48 )H42 - 48
49X-RAY DIFFRACTION49chain 'H' and (resid 49 through 75 )H49 - 75
50X-RAY DIFFRACTION50chain 'H' and (resid 76 through 95 )H76 - 95
51X-RAY DIFFRACTION51chain 'H' and (resid 96 through 123 )H96 - 123
52X-RAY DIFFRACTION52chain 'H' and (resid 124 through 137 )H124 - 137
53X-RAY DIFFRACTION53chain 'H' and (resid 138 through 176 )H138 - 176
54X-RAY DIFFRACTION54chain 'I' and (resid 5 through 41 )I5 - 41
55X-RAY DIFFRACTION55chain 'I' and (resid 42 through 75 )I42 - 75
56X-RAY DIFFRACTION56chain 'I' and (resid 76 through 95 )I76 - 95
57X-RAY DIFFRACTION57chain 'I' and (resid 96 through 137 )I96 - 137
58X-RAY DIFFRACTION58chain 'I' and (resid 138 through 176 )I138 - 176
59X-RAY DIFFRACTION59chain 'J' and (resid 5 through 41 )J5 - 41
60X-RAY DIFFRACTION60chain 'J' and (resid 42 through 75 )J42 - 75
61X-RAY DIFFRACTION61chain 'J' and (resid 76 through 95 )J76 - 95
62X-RAY DIFFRACTION62chain 'J' and (resid 96 through 137 )J96 - 137
63X-RAY DIFFRACTION63chain 'J' and (resid 138 through 176 )J138 - 176
64X-RAY DIFFRACTION64chain 'K' and (resid 5 through 13 )K5 - 13
65X-RAY DIFFRACTION65chain 'K' and (resid 14 through 41 )K14 - 41
66X-RAY DIFFRACTION66chain 'K' and (resid 42 through 76 )K42 - 76
67X-RAY DIFFRACTION67chain 'K' and (resid 77 through 95 )K77 - 95
68X-RAY DIFFRACTION68chain 'K' and (resid 96 through 137 )K96 - 137
69X-RAY DIFFRACTION69chain 'K' and (resid 138 through 176 )K138 - 176
70X-RAY DIFFRACTION70chain 'L' and (resid 5 through 41 )L5 - 41
71X-RAY DIFFRACTION71chain 'L' and (resid 42 through 75 )L42 - 75
72X-RAY DIFFRACTION72chain 'L' and (resid 76 through 95 )L76 - 95
73X-RAY DIFFRACTION73chain 'L' and (resid 96 through 137 )L96 - 137
74X-RAY DIFFRACTION74chain 'L' and (resid 138 through 176 )L138 - 176

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  • 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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