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- PDB-4gdi: A subtype N10 neuraminidase-like protein of A/little yellow-shoul... -

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Basic information

Entry
Database: PDB / ID: 4gdi
TitleA subtype N10 neuraminidase-like protein of A/little yellow-shouldered bat/Guatemala/164/2009
ComponentsNeuraminidase
KeywordsVIRAL PROTEIN / INFLUENZA VIRUS / NEURAMINIDASE-LIKE / N10 / BETA-PROPELLER / ECTODOMAIN
Function / homology
Function and homology information


exo-alpha-sialidase / exo-alpha-sialidase activity / carbohydrate metabolic process / host cell plasma membrane / virion membrane / metal ion binding / identical protein binding / membrane
Similarity search - Function
Glycoside hydrolase, family 34 / Neuraminidase / Neuraminidase - #10 / Sialidase superfamily / 6 Propeller / Neuraminidase / Mainly Beta
Similarity search - Domain/homology
NITRATE ION / Neuraminidase
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsZhu, X. / Wilson, I.A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Crystal structures of two subtype N10 neuraminidase-like proteins from bat influenza A viruses reveal a diverged putative active site.
Authors: Zhu, X. / Yang, H. / Guo, Z. / Yu, W. / Carney, P.J. / Li, Y. / Chen, L.M. / Paulson, J.C. / Donis, R.O. / Tong, S. / Stevens, J. / Wilson, I.A.
History
DepositionJul 31, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 26, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 10, 2012Group: Database references
Revision 1.2Nov 28, 2012Group: Database references
Revision 1.3Dec 17, 2014Group: Data collection
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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_ref_seq_dif / 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 / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 13, 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
Revision 2.2Oct 16, 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: Neuraminidase
B: Neuraminidase
C: Neuraminidase
D: Neuraminidase
E: Neuraminidase
F: Neuraminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)260,59866
Polymers249,5456
Non-polymers11,05260
Water25,3651408
1
A: Neuraminidase
B: Neuraminidase
C: Neuraminidase
D: Neuraminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,16942
Polymers166,3644
Non-polymers6,80538
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23720 Å2
ΔGint-38 kcal/mol
Surface area49980 Å2
MethodPISA
2
E: Neuraminidase
hetero molecules

E: Neuraminidase
hetero molecules

E: Neuraminidase
hetero molecules

E: Neuraminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,89540
Polymers166,3644
Non-polymers7,53236
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area21620 Å2
ΔGint-34 kcal/mol
Surface area50510 Å2
MethodPISA
3
F: Neuraminidase
hetero molecules

F: Neuraminidase
hetero molecules

F: Neuraminidase
hetero molecules

F: Neuraminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,82056
Polymers166,3644
Non-polymers9,45752
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation4_565y,-x+1,z1
Buried area26040 Å2
ΔGint-36 kcal/mol
Surface area51960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)176.324, 176.324, 193.313
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4
Components on special symmetry positions
IDModelComponents
11E-765-

HOH

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Components

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
Neuraminidase


Mass: 41590.883 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus
Strain: A/little yellow-shouldered bat/Guatemala/164/2009(H17N10))
Gene: NA / Plasmid: pFastbacHT-A / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): Hi5 / References: UniProt: H6QM85

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Sugars , 7 types, 21 molecules

#2: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-3) ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-3)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 878.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4[LFucpb1-3][LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/4,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1b_1-5][a1122h-1b_1-5][a1221m-1a_1-5]/1-2-1-3-4/a3-b1_a4-c1_a6-e1_c4-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(3+1)][b-L-Fucp]{}[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#3: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-3)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1040.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4[LFucpb1-3][LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/5,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1b_1-5][a1122h-1b_1-5][a1122h-1a_1-5][a1221m-1a_1-5]/1-2-1-3-4-5/a3-b1_a4-c1_a6-f1_c4-d1_d3-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(3+1)][b-L-Fucp]{}[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#4: Polysaccharide beta-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)][alpha-L-fucopyranose-(1- ...beta-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 716.682 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpb1-3[DGlcpNAcb1-4][LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1b_1-5][a1221m-1a_1-5]/1-2-1-3/a3-b1_a4-c1_a6-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(3+1)][b-L-Fucp]{}[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#5: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#6: Polysaccharide alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-6DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#7: Polysaccharide beta-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta- ...beta-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpb1-3[DGlcpNAcb1-4]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1b_1-5]/1-2-1/a3-b1_a4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(3+1)][b-L-Fucp]{}[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#8: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 13
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 1447 molecules

#9: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Ca
#10: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C3H8O3
#11: Chemical
ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: NO3
#12: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1408 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.01 Å3/Da / Density % sol: 59.14 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.2 M Mg nitrate, 14% polyethylene glycol 3350, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 1.033
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 22, 2011
RadiationMonochromator: SIDE SCATTERING BENT CUBE-ROOT I -BEAM SINGLE CRYSTAL, ASYMMETRIC CUT 4.965 DEGS
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 210731 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 2.6 % / Biso Wilson estimate: 41.7 Å2 / Rsym value: 0.059 / Net I/σ(I): 23.1
Reflection shellResolution: 1.95→1.98 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 1.5 / Rsym value: 0.889 / % possible all: 99.5

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.7.2_869) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3BEQ

3beq


Resolution: 1.95→40.11 Å / SU ML: 0.62 / σ(F): 1.34 / Phase error: 24.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.223 10561 5.02 %
Rwork0.18 --
obs0.182 210561 98.6 %
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 61.13 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.5582 Å2-0 Å20 Å2
2---1.5582 Å20 Å2
3---3.1163 Å2
Refinement stepCycle: LAST / Resolution: 1.95→40.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17256 0 706 1408 19370
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00918821
X-RAY DIFFRACTIONf_angle_d1.16125581
X-RAY DIFFRACTIONf_dihedral_angle_d24.8577127
X-RAY DIFFRACTIONf_chiral_restr0.0682900
X-RAY DIFFRACTIONf_plane_restr0.0053168
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-1.97280.46053450.45956521X-RAY DIFFRACTION96
1.9728-1.9960.40093450.38946747X-RAY DIFFRACTION100
1.996-2.02030.40533540.35996702X-RAY DIFFRACTION100
2.0203-2.04590.35213350.30856706X-RAY DIFFRACTION100
2.0459-2.07280.36583270.31786420X-RAY DIFFRACTION94
2.0728-2.10120.31793440.28696648X-RAY DIFFRACTION99
2.1012-2.13120.3123540.25876758X-RAY DIFFRACTION100
2.1312-2.16310.35063670.26056673X-RAY DIFFRACTION99
2.1631-2.19680.31013770.24746665X-RAY DIFFRACTION99
2.1968-2.23290.30553610.24396695X-RAY DIFFRACTION99
2.2329-2.27140.34373500.28216391X-RAY DIFFRACTION95
2.2714-2.31270.28763320.21296738X-RAY DIFFRACTION99
2.3127-2.35710.26623470.19246743X-RAY DIFFRACTION99
2.3571-2.40520.25253250.18266670X-RAY DIFFRACTION99
2.4052-2.45750.2243550.17766755X-RAY DIFFRACTION100
2.4575-2.51470.2393580.16476779X-RAY DIFFRACTION100
2.5147-2.57760.21863710.16246688X-RAY DIFFRACTION100
2.5776-2.64730.22843600.16426736X-RAY DIFFRACTION100
2.6473-2.72510.21853550.16826646X-RAY DIFFRACTION99
2.7251-2.81310.21943610.14846767X-RAY DIFFRACTION100
2.8131-2.91360.20873690.15326693X-RAY DIFFRACTION100
2.9136-3.03020.2173570.15386732X-RAY DIFFRACTION100
3.0302-3.16810.1973440.15496762X-RAY DIFFRACTION99
3.1681-3.3350.18043500.14496669X-RAY DIFFRACTION99
3.335-3.54380.20473460.15476692X-RAY DIFFRACTION98
3.5438-3.81730.19753450.14926637X-RAY DIFFRACTION98
3.8173-4.2010.17023400.13416693X-RAY DIFFRACTION98
4.201-4.80810.13993740.11786620X-RAY DIFFRACTION98
4.8081-6.05430.1793510.14676615X-RAY DIFFRACTION97
6.0543-40.11540.21973620.2056439X-RAY DIFFRACTION94
Refinement TLS params.Method: refined / Origin x: 18.7921 Å / Origin y: 52.5581 Å / Origin z: 54.0801 Å
111213212223313233
T0.1732 Å20.0072 Å2-0.0019 Å2-0.165 Å20.0051 Å2--0.1949 Å2
L0.0784 °20.0252 °2-0.0215 °2-0.0564 °20.0088 °2--0.1216 °2
S-0.0026 Å °0.0113 Å °-0.0072 Å °-0.0043 Å °-0.0247 Å °0.0018 Å °-0.0132 Å °-0.0421 Å °0.025 Å °
Refinement TLS groupSelection details: ALL

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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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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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