[English] 日本語
Yorodumi
- PDB-1b5f: NATIVE CARDOSIN A FROM CYNARA CARDUNCULUS L. -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1b5f
TitleNATIVE CARDOSIN A FROM CYNARA CARDUNCULUS L.
Components(PROTEIN (CARDOSIN ...) x 2
KeywordsHYDROLASE / ASPARTIC PROTEINASE
Function / homology
Function and homology information


protein storage vacuole / cell wall / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / organelle membrane / lipid metabolic process / aspartic-type endopeptidase activity / endoplasmic reticulum / extracellular region
Similarity search - Function
Saposin-like type B, region 1 / Saposin-like type B, region 1 / Saposin B type, region 2 / Saposin-like type B, region 2 / Saposin B type domain / Saposin-like / Saposin B type domain profile. / Eukaryotic aspartyl protease / Aspartic peptidase A1 family / Peptidase family A1 domain ...Saposin-like type B, region 1 / Saposin-like type B, region 1 / Saposin B type, region 2 / Saposin-like type B, region 2 / Saposin B type domain / Saposin-like / Saposin B type domain profile. / Eukaryotic aspartyl protease / Aspartic peptidase A1 family / Peptidase family A1 domain / Peptidase family A1 domain profile. / Cathepsin D, subunit A; domain 1 / Acid Proteases / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesCynara cardunculus (cardoon)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 Å
AuthorsFrazao, C. / Bento, I. / Carrondo, M.A.
Citation
Journal: J.Biol.Chem. / Year: 1999
Title: Crystal structure of cardosin A, a glycosylated and Arg-Gly-Asp-containing aspartic proteinase from the flowers of Cynara cardunculus L.
Authors: Frazao, C. / Bento, I. / Costa, J. / Soares, C.M. / Verissimo, P. / Faro, C. / Pires, E. / Cooper, J. / Carrondo, M.A.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1999
Title: Crystallization and Preliminary X-Ray Crystallographic Studies of the Plant Aspartic Proteinase Cardosin A
Authors: Bento, I. / Frazao, C. / Coelho, R. / Wilson, K. / Dauter, Z. / Carrondo, M.A.
#2: Journal: Adv.Exp.Med.Biol. / Year: 1998
Title: Crystallization, Structure Solution, and Initial Refinement of Plant Cardosin-A
Authors: Bento, I. / Coelho, R. / Frazao, C. / Costa, J. / Faro, C. / Verissimo, P. / Pires, E. / Cooper, J. / Dauter, Z. / Wilson, K. / Carrondo, M.A.
History
DepositionJan 6, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Jan 13, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
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 / diffrn_source / 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_special_symmetry / 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_alt_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _diffrn_source.pdbx_synchrotron_site / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_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_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.0Sep 23, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_special_symmetry / pdbx_validate_chiral / struct_asym / struct_conn
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_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _chem_comp.pdbx_synonyms / _pdbx_branch_scheme.entity_id / _pdbx_branch_scheme.mon_id / _pdbx_branch_scheme.pdb_mon_id / _pdbx_entity_nonpoly.entity_id / _pdbx_nonpoly_scheme.asym_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.entity_id / _pdbx_nonpoly_scheme.ndb_seq_num / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_nonpoly_scheme.pdb_strand_id / _pdbx_struct_special_symmetry.auth_asym_id / _pdbx_struct_special_symmetry.auth_seq_id / _pdbx_struct_special_symmetry.label_asym_id / _struct_asym.entity_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_label_comp_id
Revision 3.1Aug 9, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PROTEIN (CARDOSIN A)
B: PROTEIN (CARDOSIN A)
C: PROTEIN (CARDOSIN A)
D: PROTEIN (CARDOSIN A)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,3868
Polymers70,9694
Non-polymers3,4174
Water9,512528
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: PROTEIN (CARDOSIN A)
B: PROTEIN (CARDOSIN A)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1124
Polymers35,4852
Non-polymers1,6282
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8360 Å2
ΔGint-16 kcal/mol
Surface area14300 Å2
MethodPISA
3
C: PROTEIN (CARDOSIN A)
D: PROTEIN (CARDOSIN A)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2744
Polymers35,4852
Non-polymers1,7902
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8730 Å2
ΔGint-9 kcal/mol
Surface area14450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.964, 87.186, 81.303
Angle α, β, γ (deg.)90.00, 104.43, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11D-465-

HOH

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.88365, -0.13686, 0.44769), (0.17004, -0.98483, 0.03456), (0.43617, 0.10666, 0.89352)
Vector: 11.5136, 29.8693, -9.2541)

-
Components

-
PROTEIN (CARDOSIN ... , 2 types, 4 molecules ACBD

#1: Protein PROTEIN (CARDOSIN A)


Mass: 26042.812 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: RESIDUE NAMES ACCORDING TO PEPSIN NUMBERING AFTER A.R.SIELECKI, A.A.FEDOROV, A.BOODHOO, N.S.ANDREEVA, AND M.N.G.JAMES (1990).J.MOL.BIOL. 214, 143-170. NATIVE CARDOSIN A SEQUENCE DIFFERS FROM ...Details: RESIDUE NAMES ACCORDING TO PEPSIN NUMBERING AFTER A.R.SIELECKI, A.A.FEDOROV, A.BOODHOO, N.S.ANDREEVA, AND M.N.G.JAMES (1990).J.MOL.BIOL. 214, 143-170. NATIVE CARDOSIN A SEQUENCE DIFFERS FROM THAT DEDUCED FROM CDNA THROUGH EXCISION OF THE PSI DOMAIN. MATURE CARDOSIN A IS FOUND IN A TWO CHAIN FORM DUE TO A POST-TRANSLATIONAL CLEAVAGE EVENT. A FIRST, 35 KD CHAIN COMPRISES RESIDUES 0/1 - 238 AND THE SECOND 15 KD CHAIN COMPRISES RESIDUES 243 - 326. THE ASYMMETRIC UNIT CONTAINS TWO CARDOSIN A MOLECULES. MOLECULE 1 HAS BEEN ASSIGNED CHAIN INDICATORS *A* AND *B*, AND MOLECULE 2 HAVE BEEN ASSIGNED CHAIN INDICATORS *C* AND *D*. MOLECULE 1 COMPOSED BY CHAINS A(0-238) AND B (243-326). MOLECULE 2 COMPOSED BY CHAINS C(1-238) AND D (243-326). N-LINKED CARBOHYDRATES (RESIDUES 401-405 A AND 401-406 C) ATTACHED TO ASN 67. N-LINKED CARBOHYDRATES (RESIDUES 501-504 B AND 501-504 D) ATTACHED TO ASN 257.
Source: (natural) Cynara cardunculus (cardoon) / Organ: FLOWER;PISTIL / Organelle: STORAGE VACUOLES / Tissue: PAPILLAR EPIDERMIS OF THE STIGMA
References: EMBL: CAB4134, UniProt: Q9XFX3*PLUS, Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases
#2: Protein PROTEIN (CARDOSIN A)


Mass: 9441.812 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: RESIDUE NAMES ACCORDING TO PEPSIN NUMBERING AFTER A.R.SIELECKI, A.A.FEDOROV, A.BOODHOO, N.S.ANDREEVA, AND M.N.G.JAMES (1990).J.MOL.BIOL. 214, 143-170. NATIVE CARDOSIN A SEQUENCE DIFFERS FROM ...Details: RESIDUE NAMES ACCORDING TO PEPSIN NUMBERING AFTER A.R.SIELECKI, A.A.FEDOROV, A.BOODHOO, N.S.ANDREEVA, AND M.N.G.JAMES (1990).J.MOL.BIOL. 214, 143-170. NATIVE CARDOSIN A SEQUENCE DIFFERS FROM THAT DEDUCED FROM CDNA THROUGH EXCISION OF THE PSI DOMAIN. MATURE CARDOSIN A IS FOUND IN A TWO CHAIN FORM DUE TO A POST-TRANSLATIONAL CLEAVAGE EVENT. A FIRST, 35 KD CHAIN COMPRISES RESIDUES 0/1 - 238 AND THE SECOND 15 KD CHAIN COMPRISES RESIDUES 243 - 326. THE ASYMMETRIC UNIT CONTAINS TWO CARDOSIN A MOLECULES. MOLECULE 1 HAS BEEN ASSIGNED CHAIN INDICATORS *A* AND *B*, AND MOLECULE 2 HAVE BEEN ASSIGNED CHAIN INDICATORS *C* AND *D*. MOLECULE 1 COMPOSED BY CHAINS A(0-238) AND B (243-326). MOLECULE 2 COMPOSED BY CHAINS C(1-238) AND D (243-326). N-LINKED CARBOHYDRATES (RESIDUES 401-405 A AND 401-406 C) ATTACHED TO ASN 67. N-LINKED CARBOHYDRATES (RESIDUES 501-504 B AND 501-504 D) ATTACHED TO ASN 257.
Source: (natural) Cynara cardunculus (cardoon) / Organ: FLOWER;PISTIL / Organelle: STORAGE VACUOLES / Tissue: PAPILLAR EPIDERMIS OF THE STIGMA
References: EMBL: CAB4134, UniProt: Q9XFX3*PLUS, Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases

-
Sugars , 3 types, 4 molecules

#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)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 894.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4[LFucpa1-3]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/4,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5][a1122h-1b_1-5][a1122h-1a_1-5]/1-2-1-3-4/a3-b1_a4-c1_c4-d1_d3-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#4: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 732.682 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4[LFucpa1-3]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5][a1122h-1b_1-5]/1-2-1-3/a3-b1_a4-c1_c4-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#5: 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-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1056.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4[LFucpa1-3]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/4,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5][a1122h-1b_1-5][a1122h-1a_1-5]/1-2-1-3-4-4/a3-b1_a4-c1_c4-d1_d3-e1_d6-f1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE

-
Non-polymers , 1 types, 528 molecules

#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 528 / Source method: isolated from a natural source / Formula: H2O

-
Details

Compound detailsMATURE CARDOSIN A IS FOUND IN A TWO CHAIN FORM DUE TO A POST-TRANSLATIONAL CLEAVAGE EVENT. A FIRST, ...MATURE CARDOSIN A IS FOUND IN A TWO CHAIN FORM DUE TO A POST-TRANSLATIONAL CLEAVAGE EVENT. A FIRST, 35 KD CHAIN COMPRISES RESIDUES 0/1 - 238 AND THE SECOND 15 KD CHAIN COMPRISES RESIDUES 243 - 326. THE ASYMMETRIC UNIT CONTAINS TWO CARDOSIN A MOLECULES. MOLECULE 1 HAS BEEN ASSIGNED CHAIN INDICATORS *A* AND *B*, AND MOLECULE 2 HAVE BEEN ASSIGNED CHAIN INDICATORS *C* AND *D*.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 46 %
Crystal growpH: 5.5
Details: LYOPHILIZED PROTEIN DISSOLVED IN WATER TO 12 MG/ML, SITTING DROPS OF PROTEIN SOLUTION AN ALIQUOTA OF PRECIPITANT SOLUTION, COMPOSED OF PEG 4 K 40%, SODIUM CITRATE BUFFER 0.1 M AND AMMONIUM ACETATE 0.2 M, pH 5.5
Crystal
*PLUS
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop / Details: Bento, I., (1998) Acta Cryst., D54, 991.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
112 mg/mlprotein1drop
240 %PEG40001reservoir
30.1 Msodium citrate1reservoirpH5.5
40.2 Mammonium acetate1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.9091
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 5, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9091 Å / Relative weight: 1
ReflectionResolution: 1.72→34.78 Å / Num. obs: 84399 / % possible obs: 96.9 % / Redundancy: 11.3 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 15.9
Reflection shellResolution: 1.72→1.75 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.413 / Mean I/σ(I) obs: 2.5 / % possible all: 99.3
Reflection shell
*PLUS
% possible obs: 99.3 %

-
Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
SHELXL-97refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: HUMAN CATHEPSIN D (PDB ENTRY 1LYB))

1lyb


Resolution: 1.72→34.8 Å / Num. parameters: 23395 / Num. restraintsaints: 27500 / Cross valid method: FREE R / σ(F): 0
StereochEM target val spec case: FUCOSE STEREOCHEMICAL TARGET PARAMETERS DERIVED FROM 1.6 A RESOLUTION STRUCTURE PDB ENTRY 2MYR; MANNOSE STEREOCHEMICAL TARGET PARAMETERS DERIVED FROM 1.25 A ...StereochEM target val spec case: FUCOSE STEREOCHEMICAL TARGET PARAMETERS DERIVED FROM 1.6 A RESOLUTION STRUCTURE PDB ENTRY 2MYR; MANNOSE STEREOCHEMICAL TARGET PARAMETERS DERIVED FROM 1.25 A RESOLUTION STRUCTURE PDB ENTRY 2WEA; N- ACETYL-GLUCOSAMINE STEREOCHEMICAL TARGET PARAMETERS DERIVED FROM 1.5 A STRUCTURE PDB ENTRY 1LZB
Stereochemistry target values: ENGH AND HUBER
Details: ANISOTROPIC SCALING APPLIED BY THE METHOD OF PARKIN, MOEZZI & HOPE, J.APPL.CRYST.28 (1995)53-56. DISORDERED REGIONS THAT WERE MODELED STEREOCHEMICALLY: 75-78 CHAIN A AND 75-79 CHAIN C (FLAP); ...Details: ANISOTROPIC SCALING APPLIED BY THE METHOD OF PARKIN, MOEZZI & HOPE, J.APPL.CRYST.28 (1995)53-56. DISORDERED REGIONS THAT WERE MODELED STEREOCHEMICALLY: 75-78 CHAIN A AND 75-79 CHAIN C (FLAP); 46-46 CHAIN A AND 46-47 CHAIN C; 159-160 AND 160B CHAIN A. DISORDERED REGIONS THAT WERE MODELED STEREOCHEMICALLY: 75-78 CHAIN A AND 75-79 CHAIN C (FLAP); 46-46 CHAIN A AND 46-47 CHAIN C; 159-160 AND 160B CHAIN A.
RfactorNum. reflection% reflectionSelection details
Rfree0.256 3994 4.8 %RANDOM
all0.206 83681 --
obs0.205 -99.8 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-2
Refine analyzeNum. disordered residues: 18 / Occupancy sum hydrogen: 4964 / Occupancy sum non hydrogen: 5754.5
Refinement stepCycle: LAST / Resolution: 1.72→34.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5000 0 229 528 5757
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.007
X-RAY DIFFRACTIONs_angle_d0.025
X-RAY DIFFRACTIONs_similar_dist0.04
X-RAY DIFFRACTIONs_from_restr_planes0.03
X-RAY DIFFRACTIONs_zero_chiral_vol0.038
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.045
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.021
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.069
X-RAY DIFFRACTIONs_approx_iso_adps0
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 4.8 % / Rfactor Rwork: 0.205
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: s_plane_restr / Dev ideal: 0.03

+
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