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Basic information

Entry
Database: PDB / ID: 4aue
TitleCrystal structure, recombinant expression and mutagenesis studies of the bifunctional catalase-phenol oxidase from Scytalidium thermophilum
ComponentsCATALASE-PHENOL OXIDASE
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


catalase / catalase activity / hydrogen peroxide catabolic process / response to oxidative stress / heme binding / metal ion binding / cytosol
Similarity search - Function
Catalase, four-helical domain / Large catalase, C-terminal domain / C-terminal domain found in long catalases / Catalase, mono-functional, haem-containing, clade 2 / Catalase, mono-functional, haem-containing, clade 2, helical domain / Hemocyanin, N-terminal domain / Catalase HpII, Chain A, domain 1 / Catalase core domain / Catalase haem-binding site / Catalase proximal heme-ligand signature. ...Catalase, four-helical domain / Large catalase, C-terminal domain / C-terminal domain found in long catalases / Catalase, mono-functional, haem-containing, clade 2 / Catalase, mono-functional, haem-containing, clade 2, helical domain / Hemocyanin, N-terminal domain / Catalase HpII, Chain A, domain 1 / Catalase core domain / Catalase haem-binding site / Catalase proximal heme-ligand signature. / Catalase / Catalase active site / Catalase proximal active site signature. / Catalase immune-responsive domain / Catalase-related immune-responsive / Catalase core domain / Catalase, mono-functional, haem-containing / Catalase / catalase family profile. / Catalase superfamily / Class I glutamine amidotransferase (GATase) domain / Class I glutamine amidotransferase-like / Up-down Bundle / Beta Barrel / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
CIS-HEME D HYDROXYCHLORIN GAMMA-SPIROLACTONE / Catalase
Similarity search - Component
Biological speciesSCYTALIDIUM THERMOPHILUM (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsYuzugullu, Y. / Trinh, C.H. / Smith, M.A. / Pearson, A.R. / Phillips, S.E.V. / Sutay Kocabas, D. / Bakir, U. / Ogel, Z.B. / McPherson, M.J.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2013
Title: Structure, Recombinant Expression and Mutagenesis Studies of the Catalase with Oxidase Activity from Scytalidium Thermophilum
Authors: Yuzugullu, Y. / Trinh, C.H. / Smith, M.A. / Pearson, A.R. / Phillips, S.E.V. / Sutay Kocabas, D. / Bakir, U. / Ogel, Z.B. / McPherson, M.J.
History
DepositionMay 17, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 27, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2013Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / 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 / 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.occupancy / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _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_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_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _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_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_sheet
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.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_sheet.number_strands
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "CB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "DA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CATALASE-PHENOL OXIDASE
B: CATALASE-PHENOL OXIDASE
C: CATALASE-PHENOL OXIDASE
D: CATALASE-PHENOL OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)322,32220
Polymers315,2864
Non-polymers7,03516
Water5,693316
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area58820 Å2
ΔGint-225 kcal/mol
Surface area75900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)185.447, 216.342, 68.607
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: ASP / End label comp-ID: ASP / Refine code: 2 / Auth seq-ID: 27 - 697 / Label seq-ID: 46 - 716

Dom-IDAuth asym-IDLabel asym-ID
1AA
2B - CB - C
3C - BC - B
4DD

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.992423, 0.122857, -0.001464), (0.122568, 0.989118, -0.081377), (-0.00855, -0.08094, -0.996682)130.04922, -6.01984, 48.78191
3given(0.852044, -0.132502, -0.506423), (-0.132744, -0.990503, 0.03582), (-0.50636, 0.036705, -0.861541)28.16237, 110.73186, 73.77698
4given(-0.858822, 0.013962, 0.512083), (0.010453, -0.998943, 0.044769), (0.512167, 0.043801, 0.857768)115.19448, 101.19923, -34.15478

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
CATALASE-PHENOL OXIDASE


Mass: 78821.617 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) SCYTALIDIUM THERMOPHILUM (fungus) / References: UniProt: M4GGR5*PLUS, catalase

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Sugars , 2 types, 11 molecules

#2: 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.: 10
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
#4: 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.: 1
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 , 3 types, 321 molecules

#3: Chemical
ChemComp-HDD / CIS-HEME D HYDROXYCHLORIN GAMMA-SPIROLACTONE / HEME


Mass: 632.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O5
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 316 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsGENBANK ACCESSION: I52101

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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: 2.18 Å3/Da / Density % sol: 43.74 % / Description: NONE
Crystal growpH: 6.8
Details: PROTEIN CRYSTAL WAS OBTAINED IN 22% PEG-2000 AT PH 6.8 100MM BIS-TRIS BUFFER WITH 0.1M BARIUM CHLORIDE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 19, 2009
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.7→45.93 Å / Num. obs: 76826 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 6.5 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 13.3
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 4 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2IUF

2iuf


Resolution: 2.7→141.42 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.909 / SU B: 13.562 / SU ML: 0.276 / Cross valid method: THROUGHOUT / ESU R Free: 0.377 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. U VALUES REFINED INDIVIDUALLY. ALL FOLLOWING RESIDUE NUMBERS WERE DECREASED BY 19 FOR ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. U VALUES REFINED INDIVIDUALLY. ALL FOLLOWING RESIDUE NUMBERS WERE DECREASED BY 19 FOR DEPOSITION. DISORDERED REGION BETWEEN RESIDUE 637 AND 640 IN CHAIN A WAS NOT MODELED DUE TO WEAK DENSITY. C- TERMINAL RESIDUE SER717 IN CHAIN A WAS NOT MODELED DUE TO WEAK DENSITY. DISORDERED REGION BETWEEN RESIDUE 637 AND 639 IN CHAIN B WAS NOT MODELED DUE TO WEAK DENSITY. DISORDERED REGION BETWEEN RESIDUE 637 AND 639 IN CHAIN C WAS NOT MODELED DUE TO WEAK DENSITY. C-TERMINAL RESIDUE SER717 IN CHAIN C WAS NOT MODELED DUE TO WEAK DENSITY. DISORDERED REGION BETWEEN RESIDUE 637 AND 641 IN CHAIN D WAS NOT MODELED DUE TO WEAK DENSITY. WATER MOLECULES F251, F252, F253, F254, F255 AND F268 WERE PLACED SO THAT THE COMPLEXES FORMED WERE SIX COORDINATE FOR CA1. RESIDUES ARG197, GLU510, GLU579, ASP584, GLU609, GLY669, SER672, GLU673, ASP676, ASP679, GLU682, GLU691, SER692, ASP694, MET695 AND GLU698 IN CHAIN A WITH B FACTOR VALUES GREATER THAN 100 PRESENT ON THE SURFACE WERE MODELED FROM POOR DENSITY MAP. RESIDUES GLU510, GLU511, ASN550, GLU579, SER580, SER581, GLN588, GLU609, LYS670- ASP683 AND GLU690-GLU698 IN CHAIN C WITH B FACTOR VALUES GREATER THAN 100 PRESENT ON THE SURFACE WERE MODELED FROM POOR DENSITY MAP. RESIDUES ARG269, ASP315, GLN318, GLU335, TYR337, GLU511, VAL558, GLU579, ASP584, GLN585, ARG608, GLU609, ASP630, GLY668- ASP679, SER 689-GLU698 AND SER717 IN CHAIN B WITH B FACTOR VALUES GREATER THAN 100 PRESENT ON THE SURFACE WERE MODELED FROM POOR DENSITY MAP. RESIDUES GLU510-GLU511, SER578-ASP584, GLU609, GLU673, ASP676, ASP679, GLU682-ASP683, GLU691-SER692, ASP694 AND GLU 698 IN CHAIN D WITH B FACTOR VALUES GREATER THAN 100 PRESENT ON THE SURFACE WERE MODELED FROM POOR DENSITY MAP. LYS651 IN CHAINS A, B AND D HAVE TRUNCATED SIDECHAINS DUE TO WEAK SIDECHAIN DENSITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.25118 3852 5 %RANDOM
Rwork0.19228 ---
obs0.19522 72876 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 49.111 Å2
Baniso -1Baniso -2Baniso -3
1-1 Å20 Å20 Å2
2---2.52 Å20 Å2
3---1.52 Å2
Refinement stepCycle: LAST / Resolution: 2.7→141.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20887 0 471 316 21674
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222059
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.621.96230107
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.99152701
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.43623.8661089
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.802153286
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.80715158
X-RAY DIFFRACTIONr_chiral_restr0.0910.23257
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02117410
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

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

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A2701medium positional0.050.5
2B2701medium positional0.060.5
3C2701medium positional0.050.5
4D2701medium positional0.050.5
1A2852tight thermal6.660.5
2B2852tight thermal4.640.5
3C2852tight thermal9.240.5
4D2852tight thermal5.570.5
1A2701medium thermal7.272
2B2701medium thermal5.962
3C2701medium thermal10.152
4D2701medium thermal6.322
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 283 -
Rwork0.283 4984 -
obs--99.96 %

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