[English] 日本語
Yorodumi
- PDB-1zpu: Crystal Structure of Fet3p, a Multicopper Oxidase that Functions ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1zpu
TitleCrystal Structure of Fet3p, a Multicopper Oxidase that Functions in Iron Import
ComponentsIron transport multicopper oxidase FET3
KeywordsOXIDOREDUCTASE / multicopper oxidase / ferroxidase / iron transport
Function / homology
Function and homology information


high-affinity iron permease complex / iron ion import across cell outer membrane / arsenate ion transmembrane transport / reductive iron assimilation / oxidoreductase activity, acting on metal ions, oxygen as acceptor / cuproxidase / cellular response to iron ion starvation / iron ion transmembrane transport / fungal-type vacuole / response to copper ion ...high-affinity iron permease complex / iron ion import across cell outer membrane / arsenate ion transmembrane transport / reductive iron assimilation / oxidoreductase activity, acting on metal ions, oxygen as acceptor / cuproxidase / cellular response to iron ion starvation / iron ion transmembrane transport / fungal-type vacuole / response to copper ion / ferroxidase / ferroxidase activity / intracellular copper ion homeostasis / intracellular iron ion homeostasis / copper ion binding / endoplasmic reticulum / plasma membrane
Similarity search - Function
Iron transport multicopper oxidase Fet3-like, the second Cupredoxin domain / Multicopper oxidases, conserved site / Multicopper oxidases signature 1. / Multicopper oxidase, copper-binding site / Multicopper oxidases signature 2. / Multicopper oxidase, C-terminal / Multicopper oxidase / Multicopper oxidase, type 1 / Multicopper oxidase / Multicopper oxidase ...Iron transport multicopper oxidase Fet3-like, the second Cupredoxin domain / Multicopper oxidases, conserved site / Multicopper oxidases signature 1. / Multicopper oxidase, copper-binding site / Multicopper oxidases signature 2. / Multicopper oxidase, C-terminal / Multicopper oxidase / Multicopper oxidase, type 1 / Multicopper oxidase / Multicopper oxidase / Multicopper oxidase, N-terminal / Multicopper oxidase / Cupredoxins - blue copper proteins / Cupredoxin / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
COPPER (I) ION / Iron transport multicopper oxidase FET3
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.8 Å
AuthorsTaylor, A.B. / Stoj, C.S. / Ziegler, L. / Kosman, D.J. / Hart, P.J.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2005
Title: The copper-iron connection in biology: Structure of the metallo-oxidase Fet3p.
Authors: Taylor, A.B. / Stoj, C.S. / Ziegler, L. / Kosman, D.J. / Hart, P.J.
History
DepositionMay 17, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 4, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
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 / database_PDB_caveat / 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_validate_chiral / struct_asym / 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_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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 / _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.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 13, 2024Group: 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_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Iron transport multicopper oxidase FET3
B: Iron transport multicopper oxidase FET3
C: Iron transport multicopper oxidase FET3
D: Iron transport multicopper oxidase FET3
E: Iron transport multicopper oxidase FET3
F: Iron transport multicopper oxidase FET3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)398,63093
Polymers365,1556
Non-polymers33,47587
Water00
1
A: Iron transport multicopper oxidase FET3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,71116
Polymers60,8591
Non-polymers5,85215
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Iron transport multicopper oxidase FET3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,71116
Polymers60,8591
Non-polymers5,85215
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Iron transport multicopper oxidase FET3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,87416
Polymers60,8591
Non-polymers6,01415
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Iron transport multicopper oxidase FET3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,12515
Polymers60,8591
Non-polymers5,26614
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Iron transport multicopper oxidase FET3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,28715
Polymers60,8591
Non-polymers5,42814
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Iron transport multicopper oxidase FET3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,92215
Polymers60,8591
Non-polymers5,06314
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)168.534, 168.534, 174.605
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: 2 / Auth seq-ID: 22 - 550 / Label seq-ID: 1 - 529

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD
5EE
6FF

-
Components

-
Protein / Non-polymers , 2 types, 30 molecules ABCDEF

#1: Protein
Iron transport multicopper oxidase FET3


Mass: 60859.156 Da / Num. of mol.: 6 / Fragment: Fet3p ectodomain (residues 22-555)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: FET3 / Plasmid: pDY148 / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): M2* / References: UniProt: P38993, Oxidoreductases
#9: Chemical...
ChemComp-CU1 / COPPER (I) ION


Mass: 63.546 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: Cu

-
Sugars , 7 types, 63 molecules

#2: 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)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#3: 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.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam 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
[]{[(4+1)][a-D-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
#4: 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-Glycam 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
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#5: 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.: 7
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam 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
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#6: 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-Glycam 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
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#7: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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: 1235.105 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,7,6/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-e1_e3-f1_e6-g1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-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]{}[(6+1)][a-D-Manp]{}}}}}}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.: 31
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

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

CrystalDensity Matthews: 3.2 Å3/Da / Density % sol: 62 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: sodium citrate, HEPES, ethylene glycol, ethanol, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 19-BM11.37837
SYNCHROTRONAPS 19-BM21.37837, 1.37944, 1.34766
Detector
TypeIDDetectorDate
CUSTOM-MADE1CCDAug 20, 2004
CUSTOM-MADE2CCDAug 20, 2004
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
11.378371
21.379441
31.347661
ReflectionResolution: 2.8→50 Å / Num. all: 136782 / Num. obs: 136782 / % possible obs: 99.6 % / Redundancy: 3.7 % / Biso Wilson estimate: 68.6 Å2 / Rsym value: 0.081 / Net I/σ(I): 14.9
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 2.3 / Num. unique all: 20049 / Rsym value: 0.36 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 2.8→50 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.908 / SU B: 35.47 / SU ML: 0.299 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic (NCS-restrained) / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.829 / ESU R Free: 0.344 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25742 6726 5 %RANDOM
Rwork0.22563 ---
all0.22721 127444 --
obs0.22721 127444 98.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 69.824 Å2
Baniso -1Baniso -2Baniso -3
1--4.46 Å2-2.23 Å20 Å2
2---4.46 Å20 Å2
3---6.7 Å2
Refinement stepCycle: LAST / Resolution: 2.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25524 0 2135 0 27659
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02128521
X-RAY DIFFRACTIONr_angle_refined_deg1.4112.01439203
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.87853168
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.03425.3881392
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.709153996
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4431566
X-RAY DIFFRACTIONr_chiral_restr0.0920.24715
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0221032
X-RAY DIFFRACTIONr_nbd_refined0.2020.211921
X-RAY DIFFRACTIONr_nbtor_refined0.3220.219117
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1330.2893
X-RAY DIFFRACTIONr_metal_ion_refined0.040.213
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2550.243
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2490.25
X-RAY DIFFRACTIONr_mcbond_it0.1951.516133
X-RAY DIFFRACTIONr_mcangle_it0.366225878
X-RAY DIFFRACTIONr_scbond_it0.775313747
X-RAY DIFFRACTIONr_scangle_it1.334.513325
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A2116tight positional0.030.05
2B2116tight positional0.030.05
3C2116tight positional0.030.05
4D2116tight positional0.020.05
5E2116tight positional0.020.05
6F2116tight positional0.020.05
1A2138medium positional0.250.5
2B2138medium positional0.240.5
3C2138medium positional0.260.5
4D2138medium positional0.230.5
5E2138medium positional0.270.5
6F2138medium positional0.270.5
1A2116tight thermal0.050.5
2B2116tight thermal0.050.5
3C2116tight thermal0.040.5
4D2116tight thermal0.040.5
5E2116tight thermal0.030.5
6F2116tight thermal0.030.5
1A2138medium thermal0.452
2B2138medium thermal0.42
3C2138medium thermal0.362
4D2138medium thermal0.312
5E2138medium thermal0.292
6F2138medium thermal0.312
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.371 474 -
Rwork0.345 9614 -
obs-9614 99.73 %
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)
13.64960.54240.47362.97750.37361.5999-0.1617-0.21070.51620.010.0504-0.2873-0.2274-0.02910.1113-0.35990.00780.0088-0.3932-0.0033-0.489385.7603108.093383.493
23.0040.1894-0.06614.3162-0.18511.82840.1733-0.1151-0.26930.0992-0.1483-0.0408-0.05430.158-0.025-0.367-0.00350.0094-0.3625-0.0585-0.563951.203466.648656.5513
33.4885-0.6155-0.20063.150.85821.66190-0.028-0.06240.4407-0.24620.8850.3053-0.2630.2462-0.2986-0.07420.1551-0.2739-0.1549-0.204133.4823115.3236111.977
44.18950.82670.58783.2973-0.07612.4461-0.0151-0.46310.012-0.04160.2017-0.2522-0.0993-0.569-0.1866-0.2895-0.06960.2555-0.01870.1303-0.19791.825459.763188.6462
52.8660.2245-0.10032.9662-0.75021.98060.1856-0.4224-1.3221-0.035-0.0556-0.43630.00190.4223-0.13-0.2216-0.05350.1443-0.17660.07820.911552.57568.2173144.5667
67.4528-1.7199-4.09313.12981.52484.95140.39060.64581.84090.79940.4816-0.13590.5177-0.5423-0.8722-0.0340.0649-0.1428-0.12880.29620.514632.218918.5784118.6425
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A22 - 550
2X-RAY DIFFRACTION2B22 - 550
3X-RAY DIFFRACTION3C22 - 550
4X-RAY DIFFRACTION4D22 - 550
5X-RAY DIFFRACTION5E22 - 550
6X-RAY DIFFRACTION6F22 - 550

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

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

-
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

Read more