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- PDB-6lf3: 3D domain-swapped dimer of the maltose-binding protein fused to a... -

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Basic information

Entry
Database: PDB / ID: 6lf3
Title3D domain-swapped dimer of the maltose-binding protein fused to a fragment of the protein-tyrosine kinase 2-beta
ComponentsMaltose/maltodextrin-binding periplasmic protein,Protein-tyrosine kinase 2-beta
KeywordsSUGAR BINDING PROTEIN / maltose binding protein / domain-swapping / arm exchange / folding / passenger protein / surface entropy reduction / fixed-arm carrier / dimer / PYK2 / apo-protein
Function / homology
Function and homology information


regulation of macrophage chemotaxis / response to cation stress / positive regulation of B cell chemotaxis / marginal zone B cell differentiation / 3-phosphoinositide-dependent protein kinase binding / regulation of ubiquitin-dependent protein catabolic process / endothelin receptor signaling pathway / negative regulation of myeloid cell differentiation / regulation of postsynaptic density assembly / blood vessel endothelial cell migration ...regulation of macrophage chemotaxis / response to cation stress / positive regulation of B cell chemotaxis / marginal zone B cell differentiation / 3-phosphoinositide-dependent protein kinase binding / regulation of ubiquitin-dependent protein catabolic process / endothelin receptor signaling pathway / negative regulation of myeloid cell differentiation / regulation of postsynaptic density assembly / blood vessel endothelial cell migration / negative regulation of muscle cell apoptotic process / negative regulation of bone mineralization / cortical cytoskeleton organization / apical dendrite / positive regulation of ubiquitin-dependent protein catabolic process / regulation of release of sequestered calcium ion into cytosol / activation of Janus kinase activity / cellular response to fluid shear stress / focal adhesion assembly / signal complex assembly / chemokine-mediated signaling pathway / NMDA glutamate receptor activity / NMDA selective glutamate receptor complex / Interleukin-2 signaling / sprouting angiogenesis / oocyte maturation / long-term synaptic depression / regulation of NMDA receptor activity / calmodulin-dependent protein kinase activity / Signal regulatory protein family interactions / positive regulation of cell-matrix adhesion / positive regulation of DNA biosynthetic process / postsynaptic modulation of chemical synaptic transmission / detection of maltose stimulus / positive regulation of actin filament polymerization / maltose transport complex / stress fiber assembly / maltose binding / maltose transport / maltodextrin transmembrane transport / negative regulation of potassium ion transport / positive regulation of excitatory postsynaptic potential / RHOU GTPase cycle / carbohydrate transport / carbohydrate transmembrane transporter activity / response to immobilization stress / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / positive regulation of protein kinase activity / postsynaptic density, intracellular component / glial cell proliferation / cellular defense response / regulation of cell adhesion / vascular endothelial growth factor receptor signaling pathway / response to glucose / response to mechanical stimulus / cellular response to retinoic acid / peptidyl-tyrosine autophosphorylation / bone resorption / response to cAMP / tumor necrosis factor-mediated signaling pathway / ionotropic glutamate receptor signaling pathway / positive regulation of endothelial cell migration / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / positive regulation of synaptic transmission, glutamatergic / response to cocaine / response to hormone / positive regulation of translation / integrin-mediated signaling pathway / response to ischemia / long-term synaptic potentiation / regulation of actin cytoskeleton organization / positive regulation of JNK cascade / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / Schaffer collateral - CA1 synapse / regulation of synaptic plasticity / response to hydrogen peroxide / epidermal growth factor receptor signaling pathway / VEGFA-VEGFR2 Pathway / positive regulation of neuron projection development / response to calcium ion / peptidyl-tyrosine phosphorylation / positive regulation of angiogenesis / positive regulation of reactive oxygen species metabolic process / : / neuron projection development / positive regulation of nitric oxide biosynthetic process / MAPK cascade / positive regulation of peptidyl-tyrosine phosphorylation / presynapse / lamellipodium / cell cortex / cell body / regulation of cell shape / outer membrane-bounded periplasmic space / positive regulation of cytosolic calcium ion concentration / growth cone / positive regulation of cell growth / protein-containing complex assembly
Similarity search - Function
Focal adhesion kinase, targeting (FAT) domain / Focal adhesion kinase, targeting (FAT) domain superfamily / Focal adhesion kinase, N-terminal / FAK1/PYK2, FERM domain C-lobe / Focal adhesion targeting region / FERM N-terminal domain / : / FAK1/PYK2, FERM domain C-lobe / FERM central domain / FERM/acyl-CoA-binding protein superfamily ...Focal adhesion kinase, targeting (FAT) domain / Focal adhesion kinase, targeting (FAT) domain superfamily / Focal adhesion kinase, N-terminal / FAK1/PYK2, FERM domain C-lobe / Focal adhesion targeting region / FERM N-terminal domain / : / FAK1/PYK2, FERM domain C-lobe / FERM central domain / FERM/acyl-CoA-binding protein superfamily / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / FERM central domain / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / FERM superfamily, second domain / FERM domain / FERM domain profile. / Band 4.1 domain / Band 4.1 homologues / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / PH-like domain superfamily / Tyrosine-protein kinase, active site / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Ubiquitin-like domain superfamily / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
alpha-maltose / Maltose/maltodextrin-binding periplasmic protein / Protein-tyrosine kinase 2-beta
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsMomin, A.A. / Shahul Hameed, U.F. / Arold, S.T.
Funding support Saudi Arabia, 1items
OrganizationGrant numberCountry
Other governmentKAUST - URF/1/2602-01-01 Saudi Arabia
CitationJournal: Sci Rep / Year: 2019
Title: Passenger sequences can promote interlaced dimers in a common variant of the maltose-binding protein.
Authors: Momin, A.A. / Hameed, U.F.S. / Arold, S.T.
History
DepositionNov 28, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 11, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 29, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_validate_close_contact / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_atom_id_2 / _pdbx_validate_close_contact.auth_comp_id_2 / _pdbx_validate_close_contact.auth_seq_id_2
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Maltose/maltodextrin-binding periplasmic protein,Protein-tyrosine kinase 2-beta
B: Maltose/maltodextrin-binding periplasmic protein,Protein-tyrosine kinase 2-beta
C: Maltose/maltodextrin-binding periplasmic protein,Protein-tyrosine kinase 2-beta
D: Maltose/maltodextrin-binding periplasmic protein,Protein-tyrosine kinase 2-beta
E: Maltose/maltodextrin-binding periplasmic protein,Protein-tyrosine kinase 2-beta
F: Maltose/maltodextrin-binding periplasmic protein,Protein-tyrosine kinase 2-beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)280,43912
Polymers278,3856
Non-polymers2,0546
Water0
1
A: Maltose/maltodextrin-binding periplasmic protein,Protein-tyrosine kinase 2-beta
B: Maltose/maltodextrin-binding periplasmic protein,Protein-tyrosine kinase 2-beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,4804
Polymers92,7952
Non-polymers6852
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24340 Å2
ΔGint-162 kcal/mol
Surface area28680 Å2
MethodPISA
2
C: Maltose/maltodextrin-binding periplasmic protein,Protein-tyrosine kinase 2-beta
D: Maltose/maltodextrin-binding periplasmic protein,Protein-tyrosine kinase 2-beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,4804
Polymers92,7952
Non-polymers6852
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24190 Å2
ΔGint-166 kcal/mol
Surface area28510 Å2
MethodPISA
3
E: Maltose/maltodextrin-binding periplasmic protein,Protein-tyrosine kinase 2-beta
F: Maltose/maltodextrin-binding periplasmic protein,Protein-tyrosine kinase 2-beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,4804
Polymers92,7952
Non-polymers6852
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24260 Å2
ΔGint-164 kcal/mol
Surface area28640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.780, 92.740, 93.610
Angle α, β, γ (deg.)112.460, 101.660, 94.930
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16B
26C
17B
27D
18B
28E
19B
29F
110C
210D
111C
211E
112C
212F
113D
213E
114D
214F
115E
215F

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A3 - 371
2010B3 - 371
1020A3 - 369
2020C3 - 369
1030A3 - 369
2030D3 - 369
1040A3 - 369
2040E3 - 369
1050A3 - 371
2050F3 - 371
1060B3 - 369
2060C3 - 369
1070B3 - 369
2070D3 - 369
1080B3 - 369
2080E3 - 369
1090B3 - 371
2090F3 - 371
10100C3 - 370
20100D3 - 370
10110C3 - 370
20110E3 - 370
10120C3 - 369
20120F3 - 369
10130D3 - 370
20130E3 - 370
10140D3 - 369
20140F3 - 369
10150E3 - 369
20150F3 - 369

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

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Components

#1: Protein
Maltose/maltodextrin-binding periplasmic protein,Protein-tyrosine kinase 2-beta / MMBP / Maltodextrin-binding protein / Maltose-binding protein / MBP / Calcium-dependent tyrosine ...MMBP / Maltodextrin-binding protein / Maltose-binding protein / MBP / Calcium-dependent tyrosine kinase / CADTK / Calcium-regulated non-receptor proline-rich tyrosine kinase / Cell adhesion kinase beta / CAKB / Focal adhesion kinase 2 / FADK 2 / Proline-rich tyrosine kinase 2 / Related adhesion focal tyrosine kinase / RAFTK


Mass: 46397.578 Da / Num. of mol.: 6
Mutation: surface entropy reduction mutant, D83A,K84A,E173A,N174A,K240A,E360A,K363A,D364A
Source method: isolated from a genetically manipulated source
Details: maltose-binding protein fused to a fragment of the protein-tyrosine kinase 2-beta
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria), (gene. exp.) Homo sapiens (human)
Gene: malE, b4034, JW3994, PTK2B, FAK2, PYK2, RAFTK / Plasmid: pJEx411c / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P0AEX9, UniProt: Q14289, non-specific protein-tyrosine kinase
#2: Polysaccharide
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
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: 2.19 Å3/Da / Density % sol: 43.76 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 10.5 / Details: 30% (v/v) PEG 400, 0.1M CAPS/Sodium hydroxide

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 21, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.2→47.9 Å / Num. obs: 37579 / % possible obs: 96.78 % / Redundancy: 3.8 % / Biso Wilson estimate: 92.5 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.1046 / Rpim(I) all: 0.06884 / Rrim(I) all: 0.1257 / Χ2: 0.87 / Net I/σ(I): 3.1
Reflection shellResolution: 3.2→3.3 Å / Rmerge(I) obs: 0.8408 / Mean I/σ(I) obs: 1.03 / Num. unique obs: 3539 / CC1/2: 0.56 / Rpim(I) all: 0.5674 / Rrim(I) all: 1 / Χ2: 0.55 / % possible all: 90.43

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5BMY

5bmy


Resolution: 3.2→47.9 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.908 / SU B: 108.03 / SU ML: 0.784 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.648 / Details: U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2839 1864 5 %RANDOM
Rwork0.2439 ---
obs0.2459 35715 96.97 %-
Solvent computationIon probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1 Å
Displacement parametersBiso max: 302.45 Å2 / Biso mean: 130.844 Å2 / Biso min: 26.36 Å2
Baniso -1Baniso -2Baniso -3
1-2.26 Å27.42 Å2-1.56 Å2
2---3.22 Å22.55 Å2
3----1.22 Å2
Refinement stepCycle: final / Resolution: 3.2→47.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16986 0 138 0 17124
Biso mean--101.6 --
Num. residues----2210
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01217556
X-RAY DIFFRACTIONr_angle_refined_deg1.3481.64423881
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.83952203
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.87225.214771
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.296152841
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.0571530
X-RAY DIFFRACTIONr_chiral_restr0.0930.22348
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213300
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A113650.08
12B113650.08
21A112870.08
22C112870.08
31A112530.08
32D112530.08
41A112730.08
42E112730.08
51A113980.08
52F113980.08
61B112860.08
62C112860.08
71B112830.08
72D112830.08
81B113290.08
82E113290.08
91B113820.08
92F113820.08
101C113520.07
102D113520.07
111C113930.07
112E113930.07
121C113790.06
122F113790.06
131D113730.07
132E113730.07
141D113400.07
142F113400.07
151E113400.07
152F113400.07
LS refinement shellResolution: 3.205→3.288 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.409 124 -
Rwork0.37 2400 -
all-2524 -
obs--88.13 %
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)
13.6915-0.2868-0.22986.02960.44244.54380.45370.96940.3384-0.3915-0.3881-0.1035-0.64020.3685-0.06560.3101-0.33430.15531.4199-0.27090.5492-0.172.521-13.771
23.3057-1.03880.18952.5936-1.2343.1944-0.128-0.17660.10390.52610.01090.2468-0.70720.06450.11710.3658-0.46650.1771.1827-0.50870.6927-0.52-2.44812.521
32.1953-0.371.58635.3226-3.87955.1655-0.8335-0.29930.83061.79210.5222-0.0107-2.331-1.02450.31131.20620.0899-0.09511.1745-0.40880.844838.26418.5754.638
42.07270.2259-0.7541.6083-0.09473.0536-0.13120.75460.7476-0.0765-0.14610.0192-0.4946-0.05870.27730.2424-0.4387-0.04841.41450.15950.712543.0738.742-19.703
51.57840.0091-0.9137.76453.10464.94540.17930.819-0.0028-1.0848-0.0912-0.25830.69340.2578-0.08810.78390.12390.01071.5226-0.26540.356246.49664.631-30.946
62.1651-0.56441.03624.9274-3.25335.31620.80650.8009-0.6518-1.4574-0.44060.14922.33611.212-0.36581.18360.3741-0.23021.4833-0.75910.713251.20949.672-9.385
73.3824-0.2508-3.365.17571.02328.33610.80130.7195-1.1583-1.1024-1.45160.73940.7353-0.07710.65031.06890.4755-0.62532.1005-1.41691.857212.84939.696-24.54
84.6282-1.7690.5785.7541-1.59170.46821.22971.8833-0.8806-1.5884-1.10750.13370.42250.5249-0.12220.72440.4299-0.23462.3718-1.17550.80184.09862.811-33.748
94.5339-4.2126-2.14537.8022-0.21376.4373-2.0996-1.4446-1.37451.9051.22510.91261.06550.58140.87451.07030.31980.65211.65930.28971.08128.8222.562-51.747
104.2661-3.1179-1.88616.24310.80624.4742-1.4291-0.5019-2.48241.02760.5841.89971.38950.10810.84510.8963-0.37270.80741.2394-0.07462.40336.27-16.199-69.336
114.0818-1.3749-1.84373.1992-0.80297.7453-0.2742-0.5522-0.61320.30530.3320.21060.77180.2941-0.05780.2427-0.22590.04280.8268-0.0830.372472.1722.876-55.309
123.4218-0.92130.17853.7759-0.14632.5188-0.2841-0.73950.27030.60430.25750.0313-0.4356-0.03010.02660.3518-0.32840.06411.1-0.38970.427963.50327.98-51.826
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 111
2X-RAY DIFFRACTION1B261 - 314
3X-RAY DIFFRACTION2A112 - 173
4X-RAY DIFFRACTION2B174 - 260
5X-RAY DIFFRACTION2B315 - 371
6X-RAY DIFFRACTION3B3 - 111
7X-RAY DIFFRACTION3A261 - 314
8X-RAY DIFFRACTION4B112 - 173
9X-RAY DIFFRACTION4A174 - 260
10X-RAY DIFFRACTION4A315 - 371
11X-RAY DIFFRACTION5C3 - 111
12X-RAY DIFFRACTION5D261 - 314
13X-RAY DIFFRACTION6C112 - 173
14X-RAY DIFFRACTION6D174 - 260
15X-RAY DIFFRACTION6D315 - 370
16X-RAY DIFFRACTION7D3 - 111
17X-RAY DIFFRACTION7C261 - 314
18X-RAY DIFFRACTION8D112 - 173
19X-RAY DIFFRACTION8C174 - 260
20X-RAY DIFFRACTION8C315 - 370
21X-RAY DIFFRACTION9E3 - 111
22X-RAY DIFFRACTION9F261 - 314
23X-RAY DIFFRACTION10E112 - 173
24X-RAY DIFFRACTION10F174 - 260
25X-RAY DIFFRACTION10F315 - 370
26X-RAY DIFFRACTION11F3 - 111
27X-RAY DIFFRACTION11E261 - 314
28X-RAY DIFFRACTION12F112 - 173
29X-RAY DIFFRACTION12E174 - 260
30X-RAY DIFFRACTION12E315 - 370

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Yorodumi

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  • 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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