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- PDB-5ggp: Crystal structure of N-terminal domain of human protein O-mannose... -

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Basic information

Entry
Database: PDB / ID: 5ggp
TitleCrystal structure of N-terminal domain of human protein O-mannose beta-1,2-N-acetylglucosaminyltransferase in complex with GlcNAc-beta1,2-Man-peptide
Components
  • 10-mer Peptide from Dystroglycan
  • Protein O-linked-mannose beta-1,2-N-acetylglucosaminyltransferase 1
KeywordsSUGAR BINDING PROTEIN / glycosyltransferease / O-mannosylation / alpha-dystroglycan
Function / homology
Function and homology information


Defective POMT2 causes MDDGA2, MDDGB2 and MDDGC2 / Defective POMT1 causes MDDGA1, MDDGB1 and MDDGC1 / beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,3-N-acetylglucosaminyltransferase activity / muscle attachment / dystroglycan complex / nerve maturation / Defective POMGNT1 causes MDDGA3, MDDGB3 and MDDGC3 / retrograde trans-synaptic signaling by trans-synaptic protein complex / O-linked glycosylation / contractile ring ...Defective POMT2 causes MDDGA2, MDDGB2 and MDDGC2 / Defective POMT1 causes MDDGA1, MDDGB1 and MDDGC1 / beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,3-N-acetylglucosaminyltransferase activity / muscle attachment / dystroglycan complex / nerve maturation / Defective POMGNT1 causes MDDGA3, MDDGB3 and MDDGC3 / retrograde trans-synaptic signaling by trans-synaptic protein complex / O-linked glycosylation / contractile ring / calcium-dependent cell-matrix adhesion / morphogenesis of an epithelial sheet / localization of cell / microtubule anchoring / dystrophin-associated glycoprotein complex / protein O-linked glycosylation via N-acetyl-galactosamine / protein O-linked glycosylation via mannose / reactive gliosis / laminin-1 binding / response to denervation involved in regulation of muscle adaptation / acetylglucosaminyltransferase activity / photoreceptor ribbon synapse / nerve development / basement membrane organization / dystroglycan binding / positive regulation of myelination / cellular response to cholesterol / vinculin binding / dentate gyrus development / EGR2 and SOX10-mediated initiation of Schwann cell myelination / branching involved in salivary gland morphogenesis / skeletal muscle tissue regeneration / Formation of the dystrophin-glycoprotein complex (DGC) / costamere / commissural neuron axon guidance / protein O-linked glycosylation / myelination in peripheral nervous system / node of Ranvier / angiogenesis involved in wound healing / axon regeneration / structural constituent of muscle / Transferases; Glycosyltransferases; Hexosyltransferases / positive regulation of cell-matrix adhesion / response to muscle activity / regulation of synapse organization / epithelial tube branching involved in lung morphogenesis / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / alpha-actinin binding / membrane protein ectodomain proteolysis / positive regulation of oligodendrocyte differentiation / basement membrane / Non-integrin membrane-ECM interactions / plasma membrane raft / ECM proteoglycans / postsynaptic cytosol / heart morphogenesis / laminin binding / negative regulation of MAPK cascade / extracellular matrix organization / myelination / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / tubulin binding / SH2 domain binding / nuclear periphery / axon guidance / negative regulation of cell migration / morphogenesis of an epithelium / adherens junction / filopodium / sensory perception of sound / cellular response to mechanical stimulus / response to peptide hormone / sarcolemma / GABA-ergic synapse / regulation of synaptic plasticity / Golgi lumen / Regulation of expression of SLITs and ROBOs / protein transport / lamellipodium / manganese ion binding / : / virus receptor activity / actin binding / carbohydrate binding / basolateral plasma membrane / gene expression / postsynaptic membrane / cytoskeleton / endoplasmic reticulum lumen / Golgi membrane / external side of plasma membrane / serine-type endopeptidase activity / focal adhesion / intracellular membrane-bounded organelle / calcium ion binding / endoplasmic reticulum membrane / protein-containing complex binding / glutamatergic synapse / extracellular space / extracellular exosome
Similarity search - Function
Protein O-linked-mannose beta-1,2-N-acetylglucosaminyltransferase 1, PANDER-like domain / : / Dystroglycan-type cadherin-like / Dystroglycan, C-terminal / Alpha-dystroglycan domain 2 / DG-type SEA domain / Alpha-dystroglycan N-terminal domain 2 / Dystroglycan (Dystrophin-associated glycoprotein 1) / Alpha-Dystroglycan N-terminal domain 2 / DG-type SEA domain profile. ...Protein O-linked-mannose beta-1,2-N-acetylglucosaminyltransferase 1, PANDER-like domain / : / Dystroglycan-type cadherin-like / Dystroglycan, C-terminal / Alpha-dystroglycan domain 2 / DG-type SEA domain / Alpha-dystroglycan N-terminal domain 2 / Dystroglycan (Dystrophin-associated glycoprotein 1) / Alpha-Dystroglycan N-terminal domain 2 / DG-type SEA domain profile. / Dystroglycan-type cadherin-like domains. / Glycosyl transferase, family 13 / ILEI/PANDER domain / GNT-I family / Interleukin-like EMT inducer / GG-type lectin domain profile. / Putative Ig domain / Cadherin-like superfamily / Nucleotide-diphospho-sugar transferases / Immunoglobulin-like fold
Similarity search - Domain/homology
Dystroglycan 1 / Protein O-linked-mannose beta-1,2-N-acetylglucosaminyltransferase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.599 Å
AuthorsKuwabara, N. / Senda, T. / Kato, R.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Carbohydrate-binding domain of the POMGnT1 stem region modulates O-mannosylation sites of alpha-dystroglycan
Authors: Kuwabara, N. / Manya, H. / Yamada, T. / Tateno, H. / Kanagawa, M. / Kobayashi, K. / Akasaka-Manya, K. / Hirose, Y. / Mizuno, M. / Ikeguchi, M. / Toda, T. / Hirabayashi, J. / Senda, T. / Endo, T. / Kato, R.
History
DepositionJun 16, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 10, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 31, 2016Group: Database references
Revision 1.2Feb 26, 2020Group: Data collection / Database references / Derived calculations
Category: chem_comp / citation ...chem_comp / citation / diffrn_source / pdbx_struct_oper_list
Item: _chem_comp.type / _citation.journal_id_CSD ..._chem_comp.type / _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / 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_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_asym / struct_conn / struct_conn_type / 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_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_special_symmetry.label_asym_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 2.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein O-linked-mannose beta-1,2-N-acetylglucosaminyltransferase 1
B: Protein O-linked-mannose beta-1,2-N-acetylglucosaminyltransferase 1
C: 10-mer Peptide from Dystroglycan
D: 10-mer Peptide from Dystroglycan
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,98211
Polymers37,1004
Non-polymers8827
Water5,008278
1
A: Protein O-linked-mannose beta-1,2-N-acetylglucosaminyltransferase 1
C: 10-mer Peptide from Dystroglycan
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9795
Polymers18,5502
Non-polymers4293
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Protein O-linked-mannose beta-1,2-N-acetylglucosaminyltransferase 1
D: 10-mer Peptide from Dystroglycan
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,0026
Polymers18,5502
Non-polymers4524
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)111.113, 49.743, 61.716
Angle α, β, γ (deg.)90.00, 105.89, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-521-

HOH

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Components

#1: Protein Protein O-linked-mannose beta-1,2-N-acetylglucosaminyltransferase 1 / POMGnT1 / UDP-GlcNAc:alpha-D-mannoside beta-1 / 2-N-acetylglucosaminyltransferase I.2 / GnT I.2


Mass: 17623.020 Da / Num. of mol.: 2 / Fragment: UNP residues 92-250
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POMGNT1, MGAT1.2, UNQ746/PRO1475 / Production host: Escherichia coli (E. coli)
References: UniProt: Q8WZA1, Transferases; Glycosyltransferases; Hexosyltransferases
#2: Protein/peptide 10-mer Peptide from Dystroglycan / Dystrophin-associated glycoprotein 1


Mass: 927.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q14118
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose


Type: oligosaccharide / Mass: 383.349 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-2DManpa1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a1122h-1a_1-5][a2122h-1b_1-5_2*NCC/3=O]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[]{[(3+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 278 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 44.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: MES-NaOH, LiCl2, Na acetate, PEG-6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 21, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.599→46.6 Å / Num. obs: 78168 / % possible obs: 98 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.103 / Net I/σ(I): 8.7
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.729 / Mean I/σ(I) obs: 1.5 / % possible all: 95.8

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5GGG

5ggg


Resolution: 1.599→46.554 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.77
Details: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS IN I_PLUS/MINUS COLUMNS
RfactorNum. reflection% reflection
Rfree0.2464 3727 4.77 %
Rwork0.2161 --
obs0.2176 78168 93.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.599→46.554 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2370 0 55 278 2703
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072476
X-RAY DIFFRACTIONf_angle_d1.1213371
X-RAY DIFFRACTIONf_dihedral_angle_d12.712893
X-RAY DIFFRACTIONf_chiral_restr0.043401
X-RAY DIFFRACTIONf_plane_restr0.005420
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5994-1.61970.33551200.31482367X-RAY DIFFRACTION81
1.6197-1.6410.35931420.29552751X-RAY DIFFRACTION92
1.641-1.66340.29761300.3032686X-RAY DIFFRACTION90
1.6634-1.68720.31641380.29972717X-RAY DIFFRACTION93
1.6872-1.71240.35661370.28532799X-RAY DIFFRACTION93
1.7124-1.73920.39031340.29212719X-RAY DIFFRACTION93
1.7392-1.76770.31311400.27222808X-RAY DIFFRACTION94
1.7677-1.79810.28181420.25172764X-RAY DIFFRACTION93
1.7981-1.83080.26261350.24652728X-RAY DIFFRACTION93
1.8308-1.86610.25851370.23852796X-RAY DIFFRACTION94
1.8661-1.90420.27251340.22752794X-RAY DIFFRACTION94
1.9042-1.94560.25981350.21942713X-RAY DIFFRACTION93
1.9456-1.99080.25381380.21212766X-RAY DIFFRACTION92
1.9908-2.04060.24151390.19582750X-RAY DIFFRACTION94
2.0406-2.09580.23821430.20622837X-RAY DIFFRACTION95
2.0958-2.15740.26261430.19782773X-RAY DIFFRACTION94
2.1574-2.22710.23591390.19742765X-RAY DIFFRACTION94
2.2271-2.30670.26341450.20572864X-RAY DIFFRACTION95
2.3067-2.3990.21261440.19842795X-RAY DIFFRACTION95
2.399-2.50820.26641440.20362762X-RAY DIFFRACTION93
2.5082-2.64040.27581430.20742784X-RAY DIFFRACTION95
2.6404-2.80580.23541390.20672815X-RAY DIFFRACTION95
2.8058-3.02240.22861390.21292812X-RAY DIFFRACTION95
3.0224-3.32650.23811340.20492808X-RAY DIFFRACTION94
3.3265-3.80770.18741420.19122712X-RAY DIFFRACTION92
3.8077-4.79650.21531320.19212754X-RAY DIFFRACTION93
4.7965-46.57410.21621390.22042802X-RAY DIFFRACTION94
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)
17.6762-1.13262.75653.1184-0.58873.7357-0.0391-0.33610.18110.0276-0.09180.4247-0.3773-0.30610.04510.15690.02010.00810.1435-0.0130.151720.26229.79315.4791
27.7772-0.57293.03652.2299-0.30922.80290.1071-0.5954-0.13240.17050.00590.2026-0.1068-0.4963-0.07850.1116-0.00930.01820.1676-0.00950.117325.64334.374217.9896
31.51841.4336-1.40181.9414-0.80792.5348-0.0221-0.1182-0.52790.010.08080.0078-0.05510.0479-0.0330.1301-0.02570.0070.12720.01010.15329.2864-1.541616.091
44.8253-0.69921.21081.8349-0.62752.6090.24340.1708-0.3087-0.2966-0.03890.35110.2046-0.387-0.1480.1758-0.0341-0.03240.1428-0.00490.12923.29193.5484.7148
52.5901-0.41280.42131.0043-0.44841.81320.09370.2274-0.0391-0.2939-0.04980.04950.14340.0143-0.0380.16720.0016-0.00520.07270.00240.0735.20186.00873.8541
62.6997-0.20541.11121.1853-0.30493.1138-0.0010.23170.1651-0.11410.02010.0384-0.35840.0535-0.00780.1498-0.01780.00740.10960.01150.104637.517414.9736.515
73.15810.82070.08133.49410.29945.61250.01780.0749-0.0121-0.52610.01590.2745-0.2249-0.3604-0.01210.1506-0.0283-0.00290.1216-0.01960.107227.453413.49569.128
81.42060.1565-0.70811.69290.45010.8660.00450.03290.2717-0.24730.0172-0.0405-0.304-0.126-0.03050.13320.03860.02090.1246-0.00590.149626.434217.12468.7201
93.2863-0.19630.73311.256-0.15421.05460.1796-0.1980.2267-0.0845-0.08660.0922-0.0044-0.1339-0.03270.1275-0.00320.01520.15060.01480.103330.184112.894417.4689
104.173-1.97860.14842.52020.13961.6746-0.035-0.64310.13180.30150.0537-0.36430.08260.10790.00520.12650.0089-0.02940.17830.01220.144620.5807-13.423830.9863
113.71840.52652.65272.3411-0.37264.1746-0.2526-0.32880.22990.22860.20720.0451-0.3904-0.23640.02560.18070.02330.01910.1342-0.0380.162114.3369-4.432228.2547
122.1977-0.072-0.42580.9137-0.22170.1125-0.03320.14660.1245-0.01730.01-0.05420.0433-0.08080.0230.0997-0.0104-0.00110.1176-0.00680.070519.6553-10.734316.0505
132.78770.7253-2.92560.63140.04874.6326-0.22010.0184-0.70260.0143-0.0943-0.25420.27790.38050.35490.17-0.02660.00220.1757-0.01420.24512.66-20.15414.3641
140.9498-0.4953-0.84942.1431-0.87333.24030.0344-0.0624-0.1767-0.2554-0.0958-0.05760.20520.32240.08480.15630.0110.02020.10170.00130.096121.2289-21.65321.68
155.5041-0.81580.62151.2539-0.4790.87380.05320.0899-0.1038-0.0238-0.0354-0.07880.12050.0490.00730.12750.0093-00.12420.01180.07714.0304-19.484227.3962
166.0635-0.4408-0.69728.80281.59052.03160.12380.3026-0.6636-0.1654-0.0593-0.13990.2391-0.0152-0.0040.1656-0.0259-0.01680.2529-0.00350.180851.43912.64612.6006
175.2862-0.66231.26365.59760.17468.6944-0.30920.76170.3988-0.5619-0.226-0.3036-0.43610.43870.33270.1497-0.0333-0.00040.28660.07560.1779-3.9563-9.579110.5845
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 98 through 105 )
2X-RAY DIFFRACTION2chain 'A' and (resid 106 through 116 )
3X-RAY DIFFRACTION3chain 'A' and (resid 117 through 129 )
4X-RAY DIFFRACTION4chain 'A' and (resid 130 through 149 )
5X-RAY DIFFRACTION5chain 'A' and (resid 150 through 186 )
6X-RAY DIFFRACTION6chain 'A' and (resid 187 through 208 )
7X-RAY DIFFRACTION7chain 'A' and (resid 209 through 215 )
8X-RAY DIFFRACTION8chain 'A' and (resid 216 through 226 )
9X-RAY DIFFRACTION9chain 'A' and (resid 227 through 247 )
10X-RAY DIFFRACTION10chain 'B' and (resid 98 through 116 )
11X-RAY DIFFRACTION11chain 'B' and (resid 117 through 129 )
12X-RAY DIFFRACTION12chain 'B' and (resid 130 through 186 )
13X-RAY DIFFRACTION13chain 'B' and (resid 187 through 208 )
14X-RAY DIFFRACTION14chain 'B' and (resid 209 through 226 )
15X-RAY DIFFRACTION15chain 'B' and (resid 227 through 247 )
16X-RAY DIFFRACTION16chain 'C' and (resid 2 through 6 )
17X-RAY DIFFRACTION17chain 'D' and (resid 2 through 10 )

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

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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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