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- PDB-5ajk: Crystal structure of variola virus virulence factor F1L in comple... -

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Basic information

Entry
Database: PDB / ID: 5ajk
TitleCrystal structure of variola virus virulence factor F1L in complex with human Bak BH3 domain
Components
  • BCL-2 HOMOLOGOUS ANTAGONIST/KILLER
  • HOMOLOG OF VACCINIA VIRUS CDS F1L
KeywordsAPOPTOSIS / BCL-2 / POXVIRUS / BID
Function / homology
Function and homology information


Activation and oligomerization of BAK protein / fibroblast apoptotic process / B cell negative selection / BAK complex / post-embryonic camera-type eye morphogenesis / apoptotic process involved in blood vessel morphogenesis / limb morphogenesis / response to fungus / BH domain binding / establishment or maintenance of transmembrane electrochemical gradient ...Activation and oligomerization of BAK protein / fibroblast apoptotic process / B cell negative selection / BAK complex / post-embryonic camera-type eye morphogenesis / apoptotic process involved in blood vessel morphogenesis / limb morphogenesis / response to fungus / BH domain binding / establishment or maintenance of transmembrane electrochemical gradient / Release of apoptotic factors from the mitochondria / B cell apoptotic process / negative regulation of endoplasmic reticulum calcium ion concentration / response to mycotoxin / mitochondrial fusion / endocrine pancreas development / thymocyte apoptotic process / integral component of mitochondrial outer membrane / activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c / endoplasmic reticulum calcium ion homeostasis / positive regulation of endoplasmic reticulum unfolded protein response / activation of cysteine-type endopeptidase activity / suppression by virus of host apoptotic process / response to UV-C / regulation of mitochondrial membrane permeability / positive regulation of calcium ion transport into cytosol / myeloid cell homeostasis / Bcl-2 family protein complex / pore complex / positive regulation of IRE1-mediated unfolded protein response / positive regulation of proteolysis / vagina development / B cell homeostasis / blood vessel remodeling / positive regulation of release of cytochrome c from mitochondria / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / Pyroptosis / extrinsic apoptotic signaling pathway in absence of ligand / cellular response to unfolded protein / negative regulation of peptidyl-serine phosphorylation / animal organ regeneration / release of cytochrome c from mitochondria / heat shock protein binding / regulation of mitochondrial membrane potential / apoptotic signaling pathway / response to gamma radiation / positive regulation of protein-containing complex assembly / response to organic cyclic compound / cellular response to UV / response to hydrogen peroxide / intrinsic apoptotic signaling pathway in response to DNA damage / cell population proliferation / cellular response to mechanical stimulus / brain development / transmembrane transporter binding / chaperone binding / response to ethanol / mitochondrial outer membrane / aging / regulation of cell cycle / protein heterodimerization activity / positive regulation of apoptotic process / negative regulation of gene expression / negative regulation of cell population proliferation / response to xenobiotic stimulus => GO:0009410 / apoptotic process / protein-containing complex binding / endoplasmic reticulum / protein homodimerization activity / mitochondrion / identical protein binding / metal ion binding / cytosol
Similarity search - Function
Orthopoxvirus protein F1 / Apoptosis regulator M11L like / Poxvirus F1/C10 / Apoptosis regulator BAK / Apoptosis regulator, Bcl-2, BH3 motif, conserved site / Apoptosis regulator, Bcl-2 family BH3 motif signature. / Apoptosis regulator, Bcl-2, BH1 motif, conserved site / Apoptosis regulator, Bcl-2 family BH1 motif signature. / Apoptosis regulator, Bcl-2, BH2 motif, conserved site / Apoptosis regulator, Bcl-2 family BH2 motif signature. ...Orthopoxvirus protein F1 / Apoptosis regulator M11L like / Poxvirus F1/C10 / Apoptosis regulator BAK / Apoptosis regulator, Bcl-2, BH3 motif, conserved site / Apoptosis regulator, Bcl-2 family BH3 motif signature. / Apoptosis regulator, Bcl-2, BH1 motif, conserved site / Apoptosis regulator, Bcl-2 family BH1 motif signature. / Apoptosis regulator, Bcl-2, BH2 motif, conserved site / Apoptosis regulator, Bcl-2 family BH2 motif signature. / BCL (B-Cell lymphoma); contains BH1, BH2 regions / Bcl-2 family / BCL2-like apoptosis inhibitors family profile. / Bcl2-like / Apoptosis regulator proteins, Bcl-2 family / Bcl-2-like superfamily
Similarity search - Domain/homology
ACETATE ION / Bcl-2 homologous antagonist/killer / Apoptosis regulator Bcl-2 homolog
Similarity search - Component
Biological speciesVARIOLA VIRUS (smallpox virus)
HOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsKvansakul, M. / Colman, P.M.
CitationJournal: Cell Death Dis. / Year: 2015
Title: Variola Virus F1L is a Bcl-2-Like Protein that Unlike its Vaccinia Virus Counterpart Inhibits Apoptosis Independent of Bim.
Authors: Marshall, B. / Puthalakath, H. / Caria, S. / Chugh, S. / Doerflinger, M. / Colman, P.M. / Kvansakul, M.
History
DepositionFeb 25, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 25, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 8, 2015Group: Atomic model / Other

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HOMOLOG OF VACCINIA VIRUS CDS F1L
B: BCL-2 HOMOLOGOUS ANTAGONIST/KILLER
C: HOMOLOG OF VACCINIA VIRUS CDS F1L
D: BCL-2 HOMOLOGOUS ANTAGONIST/KILLER
E: HOMOLOG OF VACCINIA VIRUS CDS F1L
F: BCL-2 HOMOLOGOUS ANTAGONIST/KILLER
G: HOMOLOG OF VACCINIA VIRUS CDS F1L
H: BCL-2 HOMOLOGOUS ANTAGONIST/KILLER
I: HOMOLOG OF VACCINIA VIRUS CDS F1L
J: BCL-2 HOMOLOGOUS ANTAGONIST/KILLER
K: HOMOLOG OF VACCINIA VIRUS CDS F1L
L: BCL-2 HOMOLOGOUS ANTAGONIST/KILLER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,45517
Polymers135,20712
Non-polymers2485
Water1,76598
1
A: HOMOLOG OF VACCINIA VIRUS CDS F1L
B: BCL-2 HOMOLOGOUS ANTAGONIST/KILLER
C: HOMOLOG OF VACCINIA VIRUS CDS F1L
D: BCL-2 HOMOLOGOUS ANTAGONIST/KILLER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1997
Polymers45,0694
Non-polymers1303
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10040 Å2
ΔGint-92.2 kcal/mol
Surface area15890 Å2
MethodPISA
2
E: HOMOLOG OF VACCINIA VIRUS CDS F1L
F: BCL-2 HOMOLOGOUS ANTAGONIST/KILLER
K: HOMOLOG OF VACCINIA VIRUS CDS F1L
L: BCL-2 HOMOLOGOUS ANTAGONIST/KILLER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1285
Polymers45,0694
Non-polymers591
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9770 Å2
ΔGint-92.1 kcal/mol
Surface area15570 Å2
MethodPISA
3
G: HOMOLOG OF VACCINIA VIRUS CDS F1L
H: BCL-2 HOMOLOGOUS ANTAGONIST/KILLER
I: HOMOLOG OF VACCINIA VIRUS CDS F1L
J: BCL-2 HOMOLOGOUS ANTAGONIST/KILLER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1285
Polymers45,0694
Non-polymers591
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9490 Å2
ΔGint-92.7 kcal/mol
Surface area15190 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)124.774, 68.762, 171.598
Angle α, β, γ (deg.)90.00, 109.43, 90.00
Int Tables number5
Space group name H-MI121

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Components

#1: Protein
HOMOLOG OF VACCINIA VIRUS CDS F1L


Mass: 19652.309 Da / Num. of mol.: 6 / Fragment: RESIDUES 39-201
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) VARIOLA VIRUS (smallpox virus) / Strain: BANGLADESH / Description: SYNTHETIC CDNA / Plasmid: PGEX-6P3 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: Q85365
#2: Protein/peptide
BCL-2 HOMOLOGOUS ANTAGONIST/KILLER / APOPTOSIS REGULATOR BAK / BCL-2-LIKE PROTEIN 7 / BCL2-L-7


Mass: 2882.151 Da / Num. of mol.: 6 / Fragment: RESIDUES 67-92
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q16611
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 98 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.21 Å3/Da / Density % sol: 49 % / Description: NONE
Crystal growpH: 5.2 / Details: 1.7 M MGSO4, 0.1 M NA-ACETATE PH 5.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.975
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 17, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.975 Å / Relative weight: 1
ReflectionResolution: 2.55→40 Å / Num. obs: 45043 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 4.1 % / Biso Wilson estimate: 52.46 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 12
Reflection shellHighest resolution: 2.55 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 2.2 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4D2M
Resolution: 2.55→39.702 Å / SU ML: 0.32 / σ(F): 1.34 / Phase error: 26.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2405 2293 5.1 %
Rwork0.1968 --
obs0.199 44915 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.55→39.702 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7935 0 14 98 8047
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0038060
X-RAY DIFFRACTIONf_angle_d0.5710875
X-RAY DIFFRACTIONf_dihedral_angle_d12.4883048
X-RAY DIFFRACTIONf_chiral_restr0.0271250
X-RAY DIFFRACTIONf_plane_restr0.0021391
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.55-2.60540.31511610.27892630X-RAY DIFFRACTION100
2.6054-2.6660.30121180.2722635X-RAY DIFFRACTION100
2.666-2.73270.32431530.26152637X-RAY DIFFRACTION100
2.7327-2.80660.31181420.24782654X-RAY DIFFRACTION100
2.8066-2.88910.28691580.24412637X-RAY DIFFRACTION100
2.8891-2.98230.30521270.24492670X-RAY DIFFRACTION100
2.9823-3.08890.32921220.23612680X-RAY DIFFRACTION100
3.0889-3.21250.27831440.23182641X-RAY DIFFRACTION100
3.2125-3.35870.27691390.2192672X-RAY DIFFRACTION100
3.3587-3.53560.23581610.21252639X-RAY DIFFRACTION100
3.5356-3.7570.22021550.20422629X-RAY DIFFRACTION98
3.757-4.04680.20811480.16942668X-RAY DIFFRACTION100
4.0468-4.45360.2091270.15482692X-RAY DIFFRACTION100
4.4536-5.09690.21281380.15752689X-RAY DIFFRACTION100
5.0969-6.41710.25441520.2092715X-RAY DIFFRACTION100
6.4171-39.70670.20091480.172734X-RAY DIFFRACTION98
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)
13.67850.9561.00773.89630.87643.63290.24860.14810.23190.2464-0.69350.6298-0.4349-0.60.30430.5630.05960.15540.8099-0.16520.5424-10.954228.431868.4568
23.848-0.7541-0.00465.60511.70552.682-0.10680.2315-0.31110.0202-0.15570.70950.1809-0.39370.22070.3886-0.03560.01550.4131-0.06340.4404-6.999330.840451.8023
36.57931.59560.35651.4221-0.55171.01360.48161.0812-0.1457-0.0627-0.04360.13240.09510.2991-0.21710.47620.0420.03790.4604-0.12980.5501-2.674211.819138.301
44.0712-0.1468-1.17194.37953.12976.3417-0.1162-0.37880.9741-0.1187-0.40350.8594-1.0113-0.61470.24880.49030.0068-0.00340.673-0.15270.7113-22.66079.890647.3791
50.32150.13780.00281.26990.85751.3930.151-1.1485-0.1481.32950.0406-0.064-0.2145-0.63820.26150.9101-0.1036-0.01640.81850.05490.5233-12.9833.973258.242
62.70020.7495-0.06284.44841.38993.62490.2361-0.0082-0.40640.0478-0.0255-0.20890.36870.0462-0.27030.3403-0.0128-0.06910.3408-0.06020.4372-6.92557.898949.2044
78.0065-1.0772-2.17025.71131.2593.15940.1881-0.3582-1.26150.0649-0.72070.20170.3057-0.57790.32990.5717-0.0355-0.04040.3755-0.02180.569-17.33720.00544.1776
82.6134-0.57750.48134.49181.05062.120.2395-0.27810.0351-0.21290.0536-0.42560.05550.3504-0.18310.4005-0.0340.04080.5004-0.0430.54860.263216.708147.8329
92.48740.69050.23861.91780.40072.39660.0473-0.23620.05020.0058-0.07280.0269-0.11850.250.00240.384-0.04210.04180.4195-0.08270.47220.753336.539458.589
107.9157-3.97313.87519.231-6.13248.5341-0.1966-0.39140.84240.4633-0.277-1.14-0.3697-0.03660.40310.4855-0.13460.05760.5952-0.13580.61068.482644.867463.1522
113.91950.22060.91893.66010.36212.59560.22682.01850.2183-0.628-0.5272-0.2302-0.08960.93010.46810.59920.07010.0361.57690.11860.9687-36.630825.583845.3083
122.908-0.84942.15561.1875-0.89532.8309-0.30650.27550.35170.0706-0.0928-0.0172-0.21190.16950.36890.44850.018-0.00840.66620.05070.5868-48.489733.502564.3664
134.79880.16851.45810.7876-1.09055.5773-0.38660.4870.0017-0.25480.2629-0.0067-0.44781.34110.00560.4817-0.03250.05080.8848-0.04250.5027-30.306920.583770.7574
141.351-0.98880.69292.06981.98096.1057-0.06450.1008-1.15840.17880.0826-0.13490.89230.8885-0.1460.62440.0558-0.02890.7917-0.01460.6648-41.941911.331670.8868
153.9178-0.94441.16283.3421-1.05465.07890.0312-0.2346-0.34140.0829-0.1190.10540.16060.2025-0.00250.33340.0037-0.02160.58450.01690.3406-45.536620.821772.6427
166.2737-2.6142-3.49095.47213.64087.7143-0.4043-1.0286-0.64880.12960.40550.42760.40041.4608-0.10450.42540.0671-0.04960.77810.13020.4676-35.568518.95281.6742
174.3042-0.1258-0.28794.83980.33922.68940.27820.54750.5676-0.1028-0.0218-0.5409-0.19460.557-0.19830.52210.08850.1060.50420.06720.58522.083737.848430.154
184.8603-1.5397-0.45282.8912-0.91852.4212-0.0393-0.6949-0.3461-0.0367-0.1894-0.13660.00930.21330.17240.50890.08020.03640.4849-0.10790.46844.88816.047125.8516
191.53040.85770.7120.86710.53231.5303-0.0471.78050.1368-0.83690.4791-0.18260.10640.788-0.02450.9290.28990.08390.96350.12050.60447.623321.03638.641
203.1802-0.4928-1.07845.7833-0.39953.53480.12230.569-0.0335-0.7065-0.05160.1134-0.0379-0.17110.05340.58050.18320.0330.4295-0.01350.51051.644218.492117.9101
217.37212.6811-1.31469.2509-3.62497.04340.019-0.0555-0.5739-0.3875-0.3788-0.72170.24650.3552-0.15240.57030.20390.09610.56560.00480.451511.56299.032516.7235
222.27790.1801-0.07854.40122.40323.51860.1733-0.00390.5118-0.3919-0.59980.7605-0.154-0.65210.30850.55380.1198-0.02630.5657-0.030.6833-5.267624.120324.5754
234.7-0.261-0.48182.81490.47133.45650.1501-0.67040.1777-0.1634-0.00530.6668-0.2931-0.557-0.20190.64180.0292-0.03110.30230.03910.7759-8.993643.883234.2228
243.88021.25490.40472.26140.98583.1350.55630.89110.8884-0.83170.00140.1529-0.5385-0.47860.05521.13740.25810.13750.61970.23430.6608-8.321952.35219.1551
254.2996-1.6771-0.35153.84231.82715.5670.40990.18940.3664-0.8062-0.3228-0.0267-0.7422-0.0716-0.15930.69510.13840.08250.42290.10820.6166-4.063545.922427.3833
263.1411.5007-1.01615.27090.55085.32590.84020.00970.68760.0168-0.45250.68060.5777-0.6225-0.1560.95930.19020.03550.6623-0.05531.3232-14.849855.177929.8979
270.3922-0.08291.51460.0846-0.78178.9458-0.04450.12930.0921-0.3729-0.01980.55991.0174-0.9452-0.19730.73120.0849-0.02111.31610.1720.998-64.422824.508565.2951
283.2886-0.91792.95920.2476-1.14953.6552-0.26460.41170.74920.1084-0.1866-0.0005-0.55150.44050.22270.5242-0.0688-0.06060.64160.1370.584-51.204135.347755.9687
292.5276-1.5406-0.02833.6552-0.84021.48920.97221.691-1.5102-0.8676-0.76420.75461.38110.8322-0.34530.76580.3606-0.20261.1501-0.22270.8257-55.22622.833240.261
302.7615-0.28531.57752.1905-0.46353.11750.09551.85640.6355-0.3792-0.3261-0.29240.20850.89530.1160.37940.0749-0.02141.13830.31340.5767-49.420132.606444.0864
313.4615-0.30470.3483.5752-0.3114.4984-0.37351.49350.6938-0.64070.3314-0.4982-0.11871.52860.02740.4284-0.024-0.05451.41070.36570.5808-59.44737.491636.0921
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 46 THROUGH 65 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 66 THROUGH 96 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 97 THROUGH 118 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 119 THROUGH 132 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 133 THROUGH 149 )
6X-RAY DIFFRACTION6CHAIN 'A' AND (RESID 150 THROUGH 201 )
7X-RAY DIFFRACTION7CHAIN 'B' AND (RESID 68 THROUGH 90 )
8X-RAY DIFFRACTION8CHAIN 'C' AND (RESID 63 THROUGH 96 )
9X-RAY DIFFRACTION9CHAIN 'C' AND (RESID 97 THROUGH 201 )
10X-RAY DIFFRACTION10CHAIN 'D' AND (RESID 68 THROUGH 90 )
11X-RAY DIFFRACTION11CHAIN 'E' AND (RESID 47 THROUGH 72 )
12X-RAY DIFFRACTION12CHAIN 'E' AND (RESID 73 THROUGH 118 )
13X-RAY DIFFRACTION13CHAIN 'E' AND (RESID 119 THROUGH 136 )
14X-RAY DIFFRACTION14CHAIN 'E' AND (RESID 137 THROUGH 148 )
15X-RAY DIFFRACTION15CHAIN 'E' AND (RESID 149 THROUGH 201 )
16X-RAY DIFFRACTION16CHAIN 'F' AND (RESID 68 THROUGH 90 )
17X-RAY DIFFRACTION17CHAIN 'G' AND (RESID 64 THROUGH 96 )
18X-RAY DIFFRACTION18CHAIN 'G' AND (RESID 97 THROUGH 132 )
19X-RAY DIFFRACTION19CHAIN 'G' AND (RESID 133 THROUGH 149 )
20X-RAY DIFFRACTION20CHAIN 'G' AND (RESID 150 THROUGH 200 )
21X-RAY DIFFRACTION21CHAIN 'H' AND (RESID 68 THROUGH 90 )
22X-RAY DIFFRACTION22CHAIN 'I' AND (RESID 65 THROUGH 96 )
23X-RAY DIFFRACTION23CHAIN 'I' AND (RESID 97 THROUGH 131 )
24X-RAY DIFFRACTION24CHAIN 'I' AND (RESID 132 THROUGH 153 )
25X-RAY DIFFRACTION25CHAIN 'I' AND (RESID 154 THROUGH 201 )
26X-RAY DIFFRACTION26CHAIN 'J' AND (RESID 68 THROUGH 90 )
27X-RAY DIFFRACTION27CHAIN 'K' AND (RESID 64 THROUGH 72 )
28X-RAY DIFFRACTION28CHAIN 'K' AND (RESID 73 THROUGH 131 )
29X-RAY DIFFRACTION29CHAIN 'K' AND (RESID 132 THROUGH 148 )
30X-RAY DIFFRACTION30CHAIN 'K' AND (RESID 149 THROUGH 201 )
31X-RAY DIFFRACTION31CHAIN 'L' AND (RESID 69 THROUGH 90 )

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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

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Jun 16, 2017. Omokage search with filter

Omokage search with filter

Result of Omokage search can be filtered by keywords and the database types

Related info.:Omokage search

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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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