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- PDB-7oih: Glycosylation in the crystal structure of neutrophil myeloperoxidase -

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Basic information

Entry
Database: PDB / ID: 7oih
TitleGlycosylation in the crystal structure of neutrophil myeloperoxidase
ComponentsMyeloperoxidase
KeywordsANTIMICROBIAL PROTEIN / Peroxidase / microbicidal / hypochlorous acid / glycosylation / paucimannose / hydrid N-glycan / polymorphonuclear leukocytes / dimer
Function / homology
Function and homology information


myeloperoxidase / hypochlorous acid biosynthetic process / Events associated with phagocytolytic activity of PMN cells / phagocytic vesicle lumen / response to gold nanoparticle / response to yeast / respiratory burst involved in defense response / low-density lipoprotein particle remodeling / azurophil granule / response to food ...myeloperoxidase / hypochlorous acid biosynthetic process / Events associated with phagocytolytic activity of PMN cells / phagocytic vesicle lumen / response to gold nanoparticle / response to yeast / respiratory burst involved in defense response / low-density lipoprotein particle remodeling / azurophil granule / response to food / defense response to fungus / response to mechanical stimulus / removal of superoxide radicals / secretory granule / hydrogen peroxide catabolic process / peroxidase activity / defense response / azurophil granule lumen / heparin binding / response to oxidative stress / response to lipopolysaccharide / lysosome / defense response to bacterium / intracellular membrane-bounded organelle / heme binding / Neutrophil degranulation / chromatin binding / negative regulation of apoptotic process / extracellular space / extracellular exosome / extracellular region / nucleoplasm / metal ion binding / nucleus
Similarity search - Function
Haem peroxidase, animal-type / Haem peroxidase domain superfamily, animal type / Animal haem peroxidase / Animal heme peroxidase superfamily profile. / Peroxidases proximal heme-ligand signature. / Haem peroxidase superfamily
Similarity search - Domain/homology
Paroxetine / PROTOPORPHYRIN IX CONTAINING FE / PHOSPHATE ION / THIOCYANATE ION / Myeloperoxidase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.603 Å
AuthorsKrawczyk, L. / Semwal, S. / Bouckaert, J.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
H2020 Marie Curie Actions of the European Commission847568European Union
Citation
Journal: Acta Crystallogr D Struct Biol / Year: 2022
Title: Native glycosylation and binding of the antidepressant paroxetine in a low-resolution crystal structure of human myeloperoxidase.
Authors: Krawczyk, L. / Semwal, S. / Soubhye, J. / Lemri Ouadriri, S. / Prevost, M. / Van Antwerpen, P. / Roos, G. / Bouckaert, J.
#1: Journal: J.Biol.Chem. / Year: 2010
Title: Glycosylation pattern of mature dimeric leukocyte and recombinant monomeric myeloperoxidase: glycosylation is required for optimal enzymatic activity
Authors: Van Antwerpen, P. / Slomianny, M.-C. / Zouaoui Boudjeltia, K. / Delporte, C. / Faid, V. / Calay, D. / Rousseau, A. / Moguilevsky, N. / Raes, M. / Vanhamme, L. / Furtmuller, P.G. / Obinger, C. ...Authors: Van Antwerpen, P. / Slomianny, M.-C. / Zouaoui Boudjeltia, K. / Delporte, C. / Faid, V. / Calay, D. / Rousseau, A. / Moguilevsky, N. / Raes, M. / Vanhamme, L. / Furtmuller, P.G. / Obinger, C. / Vanhaeverbeek, M. / Neve, J. / Michalski, J.-C.
History
DepositionMay 11, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 24, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 14, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Myeloperoxidase
B: Myeloperoxidase
C: Myeloperoxidase
D: Myeloperoxidase
E: Myeloperoxidase
F: Myeloperoxidase
G: Myeloperoxidase
H: Myeloperoxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)558,964118
Polymers528,0928
Non-polymers30,872110
Water43,7402428
1
A: Myeloperoxidase
B: Myeloperoxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,74731
Polymers132,0232
Non-polymers7,72429
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Myeloperoxidase
D: Myeloperoxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,20832
Polymers132,0232
Non-polymers8,18530
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Myeloperoxidase
F: Myeloperoxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,91326
Polymers132,0232
Non-polymers6,89024
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: Myeloperoxidase
H: Myeloperoxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,09629
Polymers132,0232
Non-polymers8,07327
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)155.910, 144.634, 236.454
Angle α, β, γ (deg.)90.000, 91.526, 90.000
Int Tables number5
Space group name H-MC121
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11C-1145-

HOH

21E-1163-

HOH

31H-1165-

HOH

41H-1180-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 167 through 178 or resid 180...
d_2ens_1(chain "B" and (resid 167 through 178 or resid 180...
d_3ens_1(chain "C" and (resid 167 through 178 or resid 180...
d_4ens_1(chain "D" and (resid 167 through 178 or resid 180...
d_5ens_1(chain "E" and (resid 167 through 178 or resid 180...
d_6ens_1(chain "F" and (resid 167 through 178 or resid 180...
d_7ens_1(chain "G" and (resid 167 through 178 or resid 180...
d_8ens_1(chain "H" and (resid 167 through 178 or resid 180...

NCS oper:
IDCodeMatrixVector
1given(0.00872777109745, -0.951491347737, 0.307551688653), (-0.949924487894, -0.103962589595, -0.294678209686), (0.31235763687, -0.289578996383, -0.904752292919)173.170799527, 217.419921059, 102.55723389
2given(0.00721500337813, -0.95306114251, 0.302691926493), (0.9477373577, 0.103071965275, 0.301943820594), (-0.318969974366, 0.284693920926, 0.903995313506)176.703083163, -199.903126801, 17.0434195142
3given(0.999966238407, -0.00804838248507, -0.00165698066091), (-0.00806352972175, -0.999923800928, -0.00934728974736), (-0.00158162383743, 0.00936033528078, -0.99995494028)2.8540833553, 20.0740317764, 118.504680332
4given(0.946253859679, 0.0455639323344, 0.320199252206), (0.0402032970055, 0.965777358006, -0.256237760046), (-0.320916387791, 0.255339035076, 0.912038732299)-54.7216189503, 51.9012514577, 75.435762091
5given(0.0595718465289, -0.998210929097, -0.00511235102982), (-0.997668453119, -0.0593670659152, -0.0336631717954), (0.0332994407136, 0.00710580864759, -0.999420159258)152.516401148, 241.900068134, 170.16562399
6given(0.944593504603, 0.0407831956784, 0.325699005236), (-0.0480438772088, -0.964387017389, 0.260095110594), (0.324707402017, -0.261331995061, -0.908994329704)-51.8860693445, -33.159372852, 41.5303603333
7given(0.0596130312882, -0.998111458641, -0.0148257421301), (0.997744229941, 0.0591187030932, 0.0318029961394), (-0.0308664562187, -0.0166881716689, 0.999384193795)156.294284356, -224.26586022, -52.6217181244

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Components

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Protein , 1 types, 8 molecules ABCDEFGH

#1: Protein
Myeloperoxidase / MPO


Mass: 66011.492 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P05164, myeloperoxidase

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Sugars , 9 types, 30 molecules

#2: Polysaccharide
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1260.157 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-2DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/4,7,6/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-3-3-1-4/a4-b1_a6-g1_b4-c1_c3-d1_c6-e1_e2-f1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{}}}}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#4: Polysaccharide alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D- ...alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1072.964 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3/a4-b1_b4-c1_c3-d1_c6-e1_e3-f1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#5: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#6: Polysaccharide
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1056.964 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/4,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-3-3-4/a4-b1_a6-f1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#7: 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)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#8: Polysaccharide alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c6-d1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#9: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1072.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3/a4-b1_b4-c1_c3-d1_c6-f1_d2-e1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}[(6+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#16: 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.: 5
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
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 , 7 types, 2508 molecules

#10: Chemical...
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 36
Source method: isolated from a genetically manipulated source
Formula: Cl
#11: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Formula: Ca
#12: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#13: Chemical
ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Formula: CNS
#14: Chemical
ChemComp-8PR / Paroxetine / (3S,4R)-3-[(1,3-benzodioxol-5-yloxy)methyl]-4-(4-fluorophenyl)piperidine


Mass: 329.365 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C19H20FNO3 / Feature type: SUBJECT OF INVESTIGATION
#15: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: PO4
#17: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2428 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.55 Å3/Da / Density % sol: 51.85 % / Description: Bipyramidal tetrahedral
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M Potassium thiocyanate 0.1 M Sodium cacodylate 8% w/v PGA L/M

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 5, 2018
RadiationMonochromator: Si(111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.6→40 Å / Num. obs: 158296 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 54.98 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.164 / Rrim(I) all: 0.195 / Net I/σ(I): 7.47
Reflection shellResolution: 2.6→2.76 Å / Redundancy: 3.45 % / Rmerge(I) obs: 1.25 / Mean I/σ(I) obs: 1.02 / Num. unique obs: 24289 / CC1/2: 0.409 / Rrim(I) all: 1.47 / % possible all: 95.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0349refinement
PHENIX1.19.2_4158refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6BMT

6bmt


Resolution: 2.603→38.994 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.937 / WRfactor Rfree: 0.194 / WRfactor Rwork: 0.156 / SU B: 0.001 / SU ML: 0 / Average fsc free: 0.9541 / Average fsc work: 0.9679 / Cross valid method: FREE R-VALUE / ESU R: 0.241 / ESU R Free: 0.295 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.2195 1994 1.26 %
Rwork0.1788 156302 -
all0.179 --
obs-158296 98.701 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 59.008 Å2
Baniso -1Baniso -2Baniso -3
1-1.984 Å2-0 Å20.068 Å2
2---1.946 Å20 Å2
3----0.041 Å2
Refinement stepCycle: LAST / Resolution: 2.603→38.994 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms36597 0 1993 2428 41018
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.603-2.670.3531310.326102450.327117580.9150.92588.24630.323
2.67-2.7430.3431320.306113510.306114920.9160.93799.92170.299
2.743-2.8220.331490.295109480.295111090.9320.94499.8920.283
2.822-2.9090.3051410.277106810.277108590.9310.95299.65930.26
2.909-3.0030.3381210.257103670.258105090.9360.95999.80020.235
3.003-3.1080.281320.234100370.235102040.9430.96599.6570.208
3.108-3.2250.2661270.22596910.22698610.9540.96799.56390.2
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