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- PDB-6py9: Crystal structure of red kidney bean purple acid phosphatase in c... -

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Basic information

Entry
Database: PDB / ID: 6py9
TitleCrystal structure of red kidney bean purple acid phosphatase in complex with adenosine diphosphate metavanadate
ComponentsFe(3+)-Zn(2+) purple acid phosphatase
KeywordsMETAL BINDING PROTEIN / Hydrolase / Purple acid phosphatase / metallohydrolases / catalysis / phytase / ATPase / agricultural biotechnology
Function / homology
Function and homology information


acid phosphatase / acid phosphatase activity / ferric iron binding / zinc ion binding / extracellular region
Similarity search - Function
Purple acid phosphatase-like, N-terminal / Purple acid phosphatase-like / Purple acid phosphatase, N-terminal / Iron/zinc purple acid phosphatase-like C-terminal domain / Purple acid phosphatase, metallophosphatase domain / Iron/zinc purple acid phosphatase-like protein C / Purple acid Phosphatase, N-terminal domain / Purple acid phosphatase-like, N-terminal / Metallo-dependent phosphatases / Purple Acid Phosphatase; chain A, domain 2 ...Purple acid phosphatase-like, N-terminal / Purple acid phosphatase-like / Purple acid phosphatase, N-terminal / Iron/zinc purple acid phosphatase-like C-terminal domain / Purple acid phosphatase, metallophosphatase domain / Iron/zinc purple acid phosphatase-like protein C / Purple acid Phosphatase, N-terminal domain / Purple acid phosphatase-like, N-terminal / Metallo-dependent phosphatases / Purple Acid Phosphatase; chain A, domain 2 / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like / 4-Layer Sandwich / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ADP METAVANADATE / : / CITRATE ANION / Chem-P4J / TRIETHYLENE GLYCOL / Fe(3+)-Zn(2+) purple acid phosphatase
Similarity search - Component
Biological speciesPhaseolus vulgaris (French bean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsFeder, D. / Schenk, G. / Guddat, L.W. / McGeary, R.P. / Mitic, N. / Furtado, A. / Schulz, B.L. / Henry, R.J. / Schmidt, S.
Funding support Australia, 2items
OrganizationGrant numberCountry
Australian Research Council (ARC)DP0986292 Australia
Australian Research Council (ARC)150104358 Australia
CitationJournal: Plant Sci. / Year: 2020
Title: Structural elements that modulate the substrate specificity of plant purple acid phosphatases: Avenues for improved phosphorus acquisition in crops.
Authors: Feder, D. / McGeary, R.P. / Mitic, N. / Lonhienne, T. / Furtado, A. / Schulz, B.L. / Henry, R.J. / Schmidt, S. / Guddat, L.W. / Schenk, G.
History
DepositionJul 29, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 29, 2020Provider: repository / Type: Initial release
Revision 2.0May 27, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Refinement description / Structure summary
Category: atom_site / atom_type ...atom_site / atom_type / chem_comp / entity / pdbx_distant_solvent_atoms / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_struct_special_symmetry / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / pdbx_validate_rmsd_angle / pdbx_validate_symm_contact / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / struct / struct_asym / struct_conf / struct_conn / struct_mon_prot_cis / struct_sheet / struct_sheet_order / struct_sheet_range / struct_site / struct_site_gen
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_rmsd_angle.angle_deviation / _pdbx_validate_rmsd_angle.angle_value / _pdbx_validate_rmsd_angle.auth_asym_id_1 / _pdbx_validate_rmsd_angle.auth_asym_id_2 / _pdbx_validate_rmsd_angle.auth_asym_id_3 / _pdbx_validate_rmsd_angle.auth_seq_id_1 / _pdbx_validate_rmsd_angle.auth_seq_id_2 / _pdbx_validate_rmsd_angle.auth_seq_id_3 / _pdbx_validate_symm_contact.auth_asym_id_1 / _pdbx_validate_symm_contact.auth_asym_id_2 / _pdbx_validate_symm_contact.auth_seq_id_1 / _pdbx_validate_symm_contact.auth_seq_id_2 / _pdbx_validate_symm_contact.dist / _pdbx_validate_symm_contact.site_symmetry_2 / _pdbx_validate_torsion.auth_asym_id / _pdbx_validate_torsion.auth_comp_id / _pdbx_validate_torsion.auth_seq_id / _pdbx_validate_torsion.phi / _pdbx_validate_torsion.psi / _refine.B_iso_mean / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_number_reflns_R_work / _refine.overall_SU_ML / _refine.pdbx_overall_phase_error / _refine.pdbx_stereochemistry_target_values / _refine.solvent_model_details / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_ligand / _refine_ls_restr.dev_ideal / _refine_ls_restr.number / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work / _struct.title / _struct_conf.end_auth_comp_id / _struct_conf.end_auth_seq_id / _struct_conf.end_label_comp_id / _struct_conf.end_label_seq_id / _struct_conf.pdbx_PDB_helix_class / _struct_conf.pdbx_PDB_helix_length / _struct_mon_prot_cis.pdbx_omega_angle / _struct_sheet.number_strands
Description: Model orientation/position
Details: This was an older refinement with the wrong ligand position, and thus was changed to that which corresponds to the publication.
Provider: author / Type: Coordinate replacement
Revision 3.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / 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_unobs_or_zero_occ_atoms / 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 / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.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_alt_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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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_alt_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_unobs_or_zero_occ_atoms.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_ptnr1_label_alt_id / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.1Oct 11, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fe(3+)-Zn(2+) purple acid phosphatase
B: Fe(3+)-Zn(2+) purple acid phosphatase
D: Fe(3+)-Zn(2+) purple acid phosphatase
C: Fe(3+)-Zn(2+) purple acid phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)224,07596
Polymers211,7064
Non-polymers12,36992
Water23,4381301
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)126.052, 126.052, 295.149
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z

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Components

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Protein , 1 types, 4 molecules ABDC

#1: Protein
Fe(3+)-Zn(2+) purple acid phosphatase / PAP / Iron(III)-zinc(II) purple acid phosphatase


Mass: 52926.434 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Phaseolus vulgaris (French bean) / References: UniProt: P80366, acid phosphatase

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Sugars , 2 types, 15 molecules

#2: Polysaccharide
alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta- ...alpha-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.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-3[DGlcpNAcb1-4]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2-1/a3-b1_a4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#5: 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.: 11
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 , 12 types, 1378 molecules

#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#6: Chemical ChemComp-AD9 / ADP METAVANADATE


Mass: 527.149 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P2V / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#8: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#9: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 32 / Source method: obtained synthetically / Formula: C2H6O2
#10: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C3H8O3
#11: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O4
#12: Chemical ChemComp-P4J / [(2~{R},3~{R},4~{R},5~{S})-2-(5-azanylimidazol-1-yl)-4-[[bis(oxidanyl)-[tris(oxidanyl)vanadiooxy]vanadio]oxy-bis(oxidanyl)vanadio]oxy-5-[[bis(oxidanyl)-[tris(oxidanyl)vanadiooxy]vanadio]oxymethyl]oxolan-3-yl]oxy-tris(oxidanyl)vanadium


Mass: 790.806 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H9N2O22V6
#13: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#14: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H5O7
#15: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1301 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 3.43 Å3/Da / Density % sol: 64.16 % / Description: Hexagonal
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 2.3 M ammonium sulfate, 0.1 M sodium acetate, pH 4.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Mar 1, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.2→19.9 Å / Num. obs: 112252 / % possible obs: 82 % / Redundancy: 5.4 % / Biso Wilson estimate: 28.2 Å2 / CC1/2: 0.994 / Rpim(I) all: 0.068 / Net I/σ(I): 8.3
Reflection shellResolution: 2.2→2.225 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 1.8 / Num. unique obs: 3858 / CC1/2: 0.585 / Rpim(I) all: 0.45 / % possible all: 84.9

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
Blu-Icedata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DHL

4dhl


Resolution: 2.2→19.9 Å / SU ML: 0.277 / Cross valid method: FREE R-VALUE / σ(F): 0.3 / Phase error: 21.0004 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2268 5649 5.04 %
Rwork0.1621 106410 -
obs0.1654 112059 81.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.91 Å2
Refinement stepCycle: LAST / Resolution: 2.2→19.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13971 0 736 1331 16038
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007415215
X-RAY DIFFRACTIONf_angle_d0.917920666
X-RAY DIFFRACTIONf_chiral_restr0.05542108
X-RAY DIFFRACTIONf_plane_restr0.00532590
X-RAY DIFFRACTIONf_dihedral_angle_d14.79338662
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.230.32071900.23973668X-RAY DIFFRACTION84.38
2.23-2.250.31392130.24553670X-RAY DIFFRACTION84.34
2.25-2.280.33051900.23593570X-RAY DIFFRACTION83.98
2.28-2.310.32391840.23913647X-RAY DIFFRACTION83.74
2.31-2.340.3021840.22263663X-RAY DIFFRACTION83.98
2.34-2.370.291790.22023612X-RAY DIFFRACTION83.96
2.37-2.40.28571890.20493613X-RAY DIFFRACTION83.52
2.4-2.440.27352050.20023576X-RAY DIFFRACTION83.37
2.44-2.480.28221880.20063652X-RAY DIFFRACTION83.59
2.48-2.520.28162040.19323593X-RAY DIFFRACTION83.3
2.52-2.560.23612140.18143550X-RAY DIFFRACTION82.91
2.56-2.610.26261950.17463601X-RAY DIFFRACTION82.49
2.61-2.660.25121890.17963594X-RAY DIFFRACTION82.92
2.66-2.710.25871770.18073596X-RAY DIFFRACTION82.49
2.71-2.770.24411860.17413573X-RAY DIFFRACTION82.24
2.77-2.830.23881940.17183558X-RAY DIFFRACTION81.92
2.83-2.910.25021810.16833552X-RAY DIFFRACTION81.88
2.91-2.980.23591900.16043562X-RAY DIFFRACTION81.25
2.98-3.070.2341930.15633541X-RAY DIFFRACTION81.23
3.07-3.170.20931620.14813526X-RAY DIFFRACTION80.68
3.17-3.280.18861630.14033550X-RAY DIFFRACTION80.59
3.28-3.410.17872010.13693508X-RAY DIFFRACTION80.21
3.41-3.570.20781910.13093477X-RAY DIFFRACTION79.69
3.57-3.760.16352120.12533437X-RAY DIFFRACTION79.29
3.76-3.990.19411590.12973488X-RAY DIFFRACTION78.55
3.99-4.290.16971780.11823449X-RAY DIFFRACTION78.2
4.29-4.720.1651740.1253358X-RAY DIFFRACTION75.44
4.72-5.390.19181790.13133426X-RAY DIFFRACTION76.91
5.39-6.750.231990.17093387X-RAY DIFFRACTION75.75
6.75-19.90.26911860.19193413X-RAY DIFFRACTION73

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