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- PDB-3k2m: Crystal Structure of Monobody HA4/Abl1 SH2 Domain Complex -

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Basic information

Entry
Database: PDB / ID: 3k2m
TitleCrystal Structure of Monobody HA4/Abl1 SH2 Domain Complex
Components
  • Monobody HA4
  • Proto-oncogene tyrosine-protein kinase ABL1
KeywordsSIGNALING PROTEIN/PROTEIN BINDING / Engineered Binding Protein / Antibody Mimic / Protein-Protein complex / SH2 domain / ATP-binding / Phosphoprotein / Tyrosine-protein kinase / SIGNALING PROTEIN / SIGNALING PROTEIN-PROTEIN BINDING COMPLEX
Function / homology
Function and homology information


: / positive regulation of actin filament binding / positive regulation of oxidoreductase activity / protein localization to cytoplasmic microtubule plus-end / DNA conformation change / podocyte apoptotic process / DN4 thymocyte differentiation / Role of ABL in ROBO-SLIT signaling / response to epinephrine / transitional one stage B cell differentiation ...: / positive regulation of actin filament binding / positive regulation of oxidoreductase activity / protein localization to cytoplasmic microtubule plus-end / DNA conformation change / podocyte apoptotic process / DN4 thymocyte differentiation / Role of ABL in ROBO-SLIT signaling / response to epinephrine / transitional one stage B cell differentiation / activation of protein kinase C activity / nicotinate-nucleotide adenylyltransferase activity / regulation of modification of synaptic structure / positive regulation of microtubule binding / delta-catenin binding / B cell proliferation involved in immune response / positive regulation of extracellular matrix organization / neuroepithelial cell differentiation / microspike assembly / positive regulation of Wnt signaling pathway, planar cell polarity pathway / cerebellum morphogenesis / positive regulation of blood vessel branching / B-1 B cell homeostasis / mitochondrial depolarization / neuropilin signaling pathway / negative regulation of ubiquitin-protein transferase activity / neuropilin binding / bubble DNA binding / negative regulation of protein serine/threonine kinase activity / activated T cell proliferation / cellular response to dopamine / regulation of cell motility / regulation of Cdc42 protein signal transduction / proline-rich region binding / positive regulation of dendrite development / mitogen-activated protein kinase binding / myoblast proliferation / syntaxin binding / regulation of hematopoietic stem cell differentiation / alpha-beta T cell differentiation / cardiac muscle cell proliferation / regulation of T cell differentiation / regulation of axon extension / HDR through Single Strand Annealing (SSA) / positive regulation of cell migration involved in sprouting angiogenesis / negative regulation of cell-cell adhesion / Fc-gamma receptor signaling pathway involved in phagocytosis / Myogenesis / positive regulation of osteoblast proliferation / regulation of microtubule polymerization / RUNX2 regulates osteoblast differentiation / platelet-derived growth factor receptor-beta signaling pathway / negative regulation of cellular senescence / positive regulation of focal adhesion assembly / associative learning / Bergmann glial cell differentiation / regulation of endocytosis / neuromuscular process controlling balance / negative regulation of mitotic cell cycle / actin monomer binding / negative regulation of BMP signaling pathway / negative regulation of long-term synaptic potentiation / endothelial cell migration / RHO GTPases Activate WASPs and WAVEs / positive regulation of T cell migration / signal transduction in response to DNA damage / BMP signaling pathway / negative regulation of double-strand break repair via homologous recombination / regulation of cell adhesion / mismatch repair / negative regulation of endothelial cell apoptotic process / canonical NF-kappaB signal transduction / four-way junction DNA binding / peptidyl-tyrosine autophosphorylation / positive regulation of substrate adhesion-dependent cell spreading / positive regulation of vasoconstriction / spleen development / positive regulation of stress fiber assembly / cellular response to transforming growth factor beta stimulus / ruffle / positive regulation of establishment of T cell polarity / ERK1 and ERK2 cascade / positive regulation of interleukin-2 production / ephrin receptor binding / actin filament polymerization / phosphotyrosine residue binding / positive regulation of endothelial cell migration / response to endoplasmic reticulum stress / positive regulation of mitotic cell cycle / substrate adhesion-dependent cell spreading / SH2 domain binding / positive regulation of release of sequestered calcium ion into cytosol / post-embryonic development / thymus development / regulation of autophagy / neural tube closure / establishment of localization in cell / integrin-mediated signaling pathway / regulation of actin cytoskeleton organization / protein kinase C binding
Similarity search - Function
F-actin binding / F-actin binding / F-actin binding domain (FABD) / Tyrosine-protein kinase ABL, SH2 domain / SH2 domain / SHC Adaptor Protein / : / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. ...F-actin binding / F-actin binding / F-actin binding domain (FABD) / Tyrosine-protein kinase ABL, SH2 domain / SH2 domain / SHC Adaptor Protein / : / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / Src homology 3 domains / SH2 domain superfamily / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Immunoglobulins / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Tyrosine-protein kinase ABL1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.75 Å
AuthorsWojcik, J.B. / Duguid, E.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2010
Title: A potent and highly specific FN3 monobody inhibitor of the Abl SH2 domain.
Authors: Wojcik, J. / Hantschel, O. / Grebien, F. / Kaupe, I. / Bennett, K.L. / Barkinge, J. / Jones, R.B. / Koide, A. / Superti-Furga, G. / Koide, S.
History
DepositionSep 30, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 31, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Proto-oncogene tyrosine-protein kinase ABL1
B: Proto-oncogene tyrosine-protein kinase ABL1
C: Monobody HA4
D: Monobody HA4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,0166
Polymers46,8264
Non-polymers1902
Water5,152286
1
A: Proto-oncogene tyrosine-protein kinase ABL1
D: Monobody HA4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,5083
Polymers23,4132
Non-polymers951
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1550 Å2
ΔGint-11 kcal/mol
Surface area10360 Å2
MethodPISA
2
B: Proto-oncogene tyrosine-protein kinase ABL1
C: Monobody HA4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,5083
Polymers23,4132
Non-polymers951
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1490 Å2
ΔGint-10 kcal/mol
Surface area10570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.625, 88.181, 131.081
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11C
21D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: SER / End label comp-ID: SER / Refine code: 4 / Auth seq-ID: 5 - 95 / Label seq-ID: 5 - 95

Dom-IDAuth asym-IDLabel asym-ID
1CC
2DD

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Components

#1: Protein Proto-oncogene tyrosine-protein kinase ABL1 / Abelson murine leukemia viral oncogene homolog 1 / c-ABL / p150


Mass: 12584.924 Da / Num. of mol.: 2 / Fragment: SH2 Domain (UNP residues 121-232)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ABL, ABL1, JTK7 / Plasmid: pHFT2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P00519, non-specific protein-tyrosine kinase
#2: Protein Monobody HA4


Mass: 10827.933 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: Synthetic / Plasmid details: PROTEIN SELECTED BY PHAGE DISPLAY / Plasmid: pHFT2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 286 / 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: 2.2 Å3/Da / Density % sol: 44.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 30% PEG 4000, 0.2M sodium acetate trihydrate, 0.1M Tris hydrochloride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97872 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Oct 24, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.751→50 Å / Num. obs: 38402 / % possible obs: 95.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 6.1 % / Rsym value: 0.046
Reflection shellResolution: 1.751→1.81 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 1.9 / Rsym value: 0.438 / % possible all: 65

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.2.0019refinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OPK: 154-235, 1FNF: loops omitted

1opk

1fnf


Resolution: 1.75→39 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.941 / Occupancy max: 1 / Occupancy min: 1 / SU B: 4.725 / SU ML: 0.079 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2 / ESU R: 0.125 / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.221 1922 5 %RANDOM
Rwork0.18 ---
all0.183 40297 --
obs0.182 38402 95.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 63.32 Å2 / Biso mean: 27.667 Å2 / Biso min: 11.64 Å2
Baniso -1Baniso -2Baniso -3
1--0.76 Å20 Å20 Å2
2---0.18 Å20 Å2
3---0.94 Å2
Refinement stepCycle: LAST / Resolution: 1.75→39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3089 0 10 286 3385
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0213183
X-RAY DIFFRACTIONr_angle_refined_deg1.51.9484343
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9555395
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.39622.248129
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.70615470
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7421519
X-RAY DIFFRACTIONr_chiral_restr0.1010.2478
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022427
X-RAY DIFFRACTIONr_nbd_refined0.2010.21396
X-RAY DIFFRACTIONr_nbtor_refined0.3030.22193
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.2263
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2320.260
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1960.222
X-RAY DIFFRACTIONr_mcbond_it0.9341.52031
X-RAY DIFFRACTIONr_mcangle_it1.48223214
X-RAY DIFFRACTIONr_scbond_it2.2731356
X-RAY DIFFRACTIONr_scangle_it2.9354.51129
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: C / Ens-ID: 1 / Number: 686 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
MEDIUM POSITIONAL0.740.5
MEDIUM THERMAL1.312
LS refinement shellResolution: 1.751→1.796 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.336 94 -
Rwork0.277 1613 -
all-1707 -
obs-1613 58.84 %
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)
112.0497.9655-3.750429.19811.710318.91970.4581-0.01370.8129-0.1082-0.1296-0.8233-1.07720.6438-0.3285-0.0566-0.0350.06780.0593-0.0296-0.02864.9997-10.09331.4813
23.45330.77580.76270.72580.05641.74460.01570.36910.0481-0.01170.0370.1804-0.03160.0868-0.0526-0.0770.01420.0102-0.0242-0.0233-0.0731-6.8368-17.78472.0237
325.3291-0.8893-7.83729.0639-4.27114.71310.2717-0.48712.29290.14450.24710.33340.03121.0599-0.51880.22340.0925-0.06350.0828-0.00590.2031-12.6043-5.5044.7632
44.22120.62690.19597.21922.42273.53410.04270.05620.0662-0.0939-0.07430.11860.057-0.04640.0316-0.06510.01230.0028-0.0232-0.0073-0.0469-9.8397-17.73299.6372
56.0801-2.1663-2.161917.16250.92225.0487-0.1561-0.31540.33390.59460.2770.082-0.15580.1708-0.1209-0.0606-0.01440.0223-0.0411-0.0528-0.0638-3.6065-6.35419.7572
64.73680.2481-0.0051.40030.37222.12530.0781-0.1249-0.07390.1020.0104-0.11090.04430.3278-0.0885-0.09420.01960.01090.0188-0.0379-0.05920.7593-16.019915.7017
73.51692.4098-2.781417.0058-10.091614.1352-0.2480.57150.0073-0.852-0.12610.06920.6378-0.04390.3741-0.12780.00550.01330.0519-0.0772-0.1075-0.9007-20.7408-0.9043
837.201-15.05590.563620.7433-2.888512.7058-0.9225-0.4787-0.75052.3791-0.2833-1.8217-0.22610.49421.20580.084-0.3585-0.15760.1742-0.1087-0.0646-0.2712-8.81867.0921
98.56690.42121.05364.3630.18554.84710.2219-1.67260.20681.00640.01810.141-0.5744-0.3249-0.240.1407-0.13160.03460.3465-0.0379-0.1992-14.205-11.834667.6872
107.3798-3.51680.978813.25441.02543.28260.0679-1.25570.0980.8140.15110.4582-0.13710.095-0.2190.0774-0.07170.01670.221-0.1075-0.1177-12.6265-10.260363.1326
1110.9387-2.08460.792711.39610.32956.47680.117-0.79370.05160.2265-0.07770.1727-0.36660.0033-0.0394-0.0316-0.07890.0379-0.01-0.0629-0.1524-14.3427-11.134857.903
1216.4809-2.3324-2.27047.63530.79134.66420.39380.175-0.0117-0.5963-0.2269-0.2421-0.07490.1176-0.1669-0.0903-0.03790.042-0.0055-0.0396-0.1259-1.0336-17.083350.286
136.8913-1.6283-1.77145.59440.85055.13620.2083-0.6851.0907-0.26280.1704-0.7546-0.73360.7197-0.3787-0.1226-0.15810.0569-0.1346-0.2034-0.068-5.5514-4.698255.2977
1410.1013-19.95172.604948.9834-5.29490.6741-0.1215-0.4797-0.25380.54810.30350.5895-0.1267-0.0503-0.1821-0.00660.00550.0115-0.0789-0.0023-0.0277-16.8207-22.029540.2718
154.75336.713-3.377621.0041-10.222710.8471-0.26890.06780.3152-0.20680.46990.934-0.0424-0.3347-0.201-0.0507-0.0126-0.0108-0.1231-0.00870.0594-22.0502-8.80931.4289
164.24653.2034-0.63593.7805-0.70091.71150.0606-0.19510.22080.16370.03420.3409-0.0837-0.0205-0.0947-0.00350.00830.0135-0.1129-0.02290.0989-20.66290.459231.6027
171.20940.98060.32652.2658-1.41772.84610.0913-0.24540.0010.2978-0.11260.0074-0.04110.06370.0214-0.0054-0.00960.0327-0.0562-0.0697-0.0234-17.5029-7.808641.1449
183.5647-3.01281.56786.13348.991630.36080.3781-0.14850.31320.4435-0.0554-1.0970.18663.3914-0.32260.0033-0.0375-0.04970.3683-0.02880.2463-3.0821-0.830636.9707
191.10070.3469-0.00712.2013-1.27731.39110.0447-0.21090.18390.1904-0.01860.1817-0.16980.0972-0.02610.0049-0.02430.0245-0.0693-0.06750.0103-15.8774-1.911637.7515
201.90511.2263-1.39992.322-2.5955.6396-0.0026-0.16750.01640.0506-0.01510.05240.2282-0.00410.0176-0.0421-0.00080.0051-0.0905-0.0315-0.037-15.6123-11.1939.5534
212.0491-2.0481.13214.0458-1.67411.33350.0257-0.0466-0.1290.06190.0036-0.01170.04640.0531-0.0293-0.0060.02130.0064-0.09320.01480.0003-13.1364-26.627534.1464
227.0957-9.37410.590312.3837-13.990615.80590.14980.0429-0.2973-0.4240.10470.61990.5744-0.6577-0.25450.0464-0.0161-0.10860.15710.04450.1459-24.3814-23.524725.3425
234.31790.80722.08781.27730.1214.68410.05660.13170.1453-0.0598-0.0797-0.1222-0.04080.18130.0231-0.08440.00980.0188-0.0898-0.0111-0.0428-7.7393-22.308127.5954
2411.97418.92249.199420.764614.861118.16960.18520.4581-0.23650.26930.2521-0.80280.05470.8732-0.4373-0.11810.02140.0251-0.07180.0332-0.0375-0.3467-23.680728.4387
252.3996-0.43050.37682.1509-1.07361.4628-0.05230.0305-0.227-0.02540.078-0.10730.12520.1641-0.0257-0.04720.0446-0.0041-0.0831-0.0162-0.0192-6.959-29.149331.791
261.321-1.34982.0451.385-1.94027.10120.04010.0764-0.10050.07380.02070.1494-0.0514-0.1653-0.0608-0.07220.00920.0031-0.0596-0.0078-0.0486-15.5712-16.346220.309
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A140 - 145
2X-RAY DIFFRACTION2A146 - 171
3X-RAY DIFFRACTION3A172 - 177
4X-RAY DIFFRACTION4A178 - 195
5X-RAY DIFFRACTION5A196 - 209
6X-RAY DIFFRACTION6A210 - 233
7X-RAY DIFFRACTION7A234 - 239
8X-RAY DIFFRACTION8B142 - 146
9X-RAY DIFFRACTION9B147 - 160
10X-RAY DIFFRACTION10B161 - 176
11X-RAY DIFFRACTION11B177 - 194
12X-RAY DIFFRACTION12B195 - 213
13X-RAY DIFFRACTION13B214 - 237
14X-RAY DIFFRACTION14C1 - 7
15X-RAY DIFFRACTION15C8 - 12
16X-RAY DIFFRACTION16C13 - 28
17X-RAY DIFFRACTION17C29 - 44
18X-RAY DIFFRACTION18C45 - 52
19X-RAY DIFFRACTION19C53 - 82
20X-RAY DIFFRACTION20C83 - 100
21X-RAY DIFFRACTION21D2 - 25
22X-RAY DIFFRACTION22D26 - 32
23X-RAY DIFFRACTION23D33 - 47
24X-RAY DIFFRACTION24D48 - 53
25X-RAY DIFFRACTION25D54 - 77
26X-RAY DIFFRACTION26D78 - 94

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  • 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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