[English] 日本語
Yorodumi
- PDB-4ay1: Human YKL-39 is a pseudo-chitinase with retained chitooligosaccha... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4ay1
TitleHuman YKL-39 is a pseudo-chitinase with retained chitooligosaccharide binding properties
ComponentsCHITINASE-3-LIKE PROTEIN 2
KeywordsHYDROLASE / CHILECTIN / LECTIN / CHITOOLIGOSACCHARIDE / PSEUDOCHITINASE
Function / homology
Function and homology information


chitin catabolic process / chitin binding / carbohydrate binding / carbohydrate metabolic process / hydrolase activity / extracellular space / extracellular region
Similarity search - Function
Chitinase A; domain 3 - #10 / : / Chitinase insertion domain superfamily / Chitinase II / Glyco_18 / Glycosyl hydrolases family 18 (GH18) domain profile. / Glycosyl hydrolases family 18 / Glycoside hydrolase family 18, catalytic domain / Chitinase A; domain 3 / Glycosidases ...Chitinase A; domain 3 - #10 / : / Chitinase insertion domain superfamily / Chitinase II / Glyco_18 / Glycosyl hydrolases family 18 (GH18) domain profile. / Glycosyl hydrolases family 18 / Glycoside hydrolase family 18, catalytic domain / Chitinase A; domain 3 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Roll / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Chitinase-3-like protein 2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.95 Å
AuthorsSchimpl, M. / Rush, C.L. / Betou, M. / Eggleston, I.M. / Penman, G.A. / Recklies, A.D. / van Aalten, D.M.F.
CitationJournal: Biochem.J. / Year: 2012
Title: Human Ykl-39 is a Pseudo-Chitinase with Retained Chitooligosaccharide-Binding Properties.
Authors: Schimpl, M. / Rush, C.L. / Betou, M. / Eggleston, I.M. / Recklies, A.D. / Van Aalten, D.M.F.
History
DepositionJun 17, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 8, 2012Provider: repository / Type: Initial release
Revision 2.0Apr 11, 2018Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations
Category: atom_site / pdbx_nonpoly_scheme ...atom_site / pdbx_nonpoly_scheme / pdbx_struct_sheet_hbond / pdbx_validate_close_contact / pdbx_validate_symm_contact / struct_conf / struct_conn / struct_sheet / struct_sheet_order / struct_sheet_range / 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_seq_id / _atom_site.label_asym_id / _pdbx_nonpoly_scheme.asym_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.ndb_seq_num / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_nonpoly_scheme.pdb_strand_id / _struct_conf.pdbx_PDB_helix_id / _struct_conn.pdbx_leaving_atom_flag / _struct_site.details / _struct_site.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id / _struct_site.pdbx_num_residues
Revision 3.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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 / 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_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _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_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.1Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" 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 "CA" 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. THE SHEETS PRESENTED AS "EA" 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 "FA" 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 "GA" 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 "HA" 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 "IA" 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 "JA" 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 "KA" 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 "LA" 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.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CHITINASE-3-LIKE PROTEIN 2
B: CHITINASE-3-LIKE PROTEIN 2
C: CHITINASE-3-LIKE PROTEIN 2
D: CHITINASE-3-LIKE PROTEIN 2
E: CHITINASE-3-LIKE PROTEIN 2
F: CHITINASE-3-LIKE PROTEIN 2
G: CHITINASE-3-LIKE PROTEIN 2
H: CHITINASE-3-LIKE PROTEIN 2
I: CHITINASE-3-LIKE PROTEIN 2
J: CHITINASE-3-LIKE PROTEIN 2
K: CHITINASE-3-LIKE PROTEIN 2
L: CHITINASE-3-LIKE PROTEIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)501,82024
Polymers491,85012
Non-polymers9,96912
Water34,1021893
1
A: CHITINASE-3-LIKE PROTEIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,8182
Polymers40,9881
Non-polymers8311
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: CHITINASE-3-LIKE PROTEIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,8182
Polymers40,9881
Non-polymers8311
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: CHITINASE-3-LIKE PROTEIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,8182
Polymers40,9881
Non-polymers8311
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: CHITINASE-3-LIKE PROTEIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,8182
Polymers40,9881
Non-polymers8311
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: CHITINASE-3-LIKE PROTEIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,8182
Polymers40,9881
Non-polymers8311
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: CHITINASE-3-LIKE PROTEIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,8182
Polymers40,9881
Non-polymers8311
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: CHITINASE-3-LIKE PROTEIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,8182
Polymers40,9881
Non-polymers8311
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
H: CHITINASE-3-LIKE PROTEIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,8182
Polymers40,9881
Non-polymers8311
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
9
I: CHITINASE-3-LIKE PROTEIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,8182
Polymers40,9881
Non-polymers8311
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
10
J: CHITINASE-3-LIKE PROTEIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,8182
Polymers40,9881
Non-polymers8311
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
11
K: CHITINASE-3-LIKE PROTEIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,8182
Polymers40,9881
Non-polymers8311
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
12
L: CHITINASE-3-LIKE PROTEIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,8182
Polymers40,9881
Non-polymers8311
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)255.686, 152.543, 138.186
Angle α, β, γ (deg.)90.00, 94.62, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H
91I
101J
111K
121L

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A21 - 384
2114B21 - 384
3114C21 - 384
4114D21 - 384
5114E21 - 384
6114F21 - 384
7114G21 - 384
8114H21 - 384
9114I21 - 384
10114J21 - 384
11114K21 - 384
12114L21 - 384

-
Components

#1: Protein
CHITINASE-3-LIKE PROTEIN 2 / CHONDROCYTE PROTEIN 39 / YKL-39


Mass: 40987.535 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: KOMAGATAELLA PASTORIS (fungus) / Strain (production host): GS115 / References: UniProt: Q15782
#2: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 830.786 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,4,3/[a2122h-1b_1-5_2*NCC/3=O]/1-1-1-1/a4-b1_b4-c1_c4-d1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1893 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsMATURE PROTEIN 26-END

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.8 Å3/Da / Density % sol: 56 % / Description: NONE
Crystal growpH: 6 / Details: 23% PEG 3000, 0.1 M SODIUM CITRATE PH 6

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.873
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 1.95→20 Å / Num. obs: 383206 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 17.2

-
Processing

SoftwareName: REFMAC / Version: 5.4.0073 / Classification: refinement
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 1.95→137.36 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.929 / SU B: 6.734 / SU ML: 0.098 / Cross valid method: THROUGHOUT / ESU R: 0.15 / ESU R Free: 0.146 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.23899 1898 0.5 %RANDOM
Rwork0.19128 ---
obs0.19151 379115 99.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.271 Å2
Baniso -1Baniso -2Baniso -3
1-1.26 Å20 Å2-0.07 Å2
2---0.88 Å20 Å2
3----0.39 Å2
Refinement stepCycle: LAST / Resolution: 1.95→137.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms34527 0 684 1893 37104
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02236180
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3561.98149094
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.83554356
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.10724.7131566
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.696156005
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9471596
X-RAY DIFFRACTIONr_chiral_restr0.0970.25398
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02127092
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_it0.5381.521680
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.99234970
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.693314500
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.7134.514124
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 / Number: 2830 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Amedium positional0.330.5
2Bmedium positional0.360.5
3Cmedium positional0.380.5
4Dmedium positional0.470.5
5Emedium positional0.410.5
6Fmedium positional0.390.5
7Gmedium positional0.370.5
8Hmedium positional0.360.5
9Imedium positional0.360.5
10Jmedium positional0.370.5
11Kmedium positional0.360.5
12Lmedium positional0.370.5
1Amedium thermal0.842
2Bmedium thermal0.742
3Cmedium thermal0.812
4Dmedium thermal0.722
5Emedium thermal0.782
6Fmedium thermal0.732
7Gmedium thermal0.772
8Hmedium thermal0.752
9Imedium thermal0.712
10Jmedium thermal0.72
11Kmedium thermal0.792
12Lmedium thermal0.712
LS refinement shellResolution: 1.949→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 119 -
Rwork0.244 27123 -
obs--96.09 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.06610.3784-0.29681.6826-0.17151.11970.00860.0302-0.0157-0.05620.0362-0.04560.02240.0263-0.0447-0.18050.0173-0.0231-0.1359-0.0131-0.117887.0777149.029451.0436
20.6504-0.09350.14561.3461-0.64652.434-0.0650.0706-0.009-0.16870.0358-0.2271-0.00750.03260.0292-0.0851-0.02360.0299-0.1224-0.0346-0.027429.2048161.581411.5826
30.8296-0.03460.01830.9221-0.4291.9695-0.01280.0810.0818-0.1131-0.0160.0054-0.18220.10280.0289-0.08340.0148-0.0119-0.1196-0.0165-0.082219.9334119.675768.1183
41.28280.4796-0.25121.75780.01831.1667-0.10950.1401-0.0397-0.07890.0610.11750.1096-0.13570.0486-0.1362-0.00810.0194-0.072-0.0038-0.101765.3413186.268335.1938
51.2699-0.7919-0.17081.67910.12670.91150.0144-0.10040.00320.00130.0354-0.0147-0.07090.0912-0.0498-0.1344-0.03270.0046-0.10270.0091-0.155699.5476188.23928.9633
60.70590.0093-0.16290.93040.52832.3977-0.0197-0.0869-0.03430.09370.03650.0550.0525-0.1169-0.0168-0.15510.0141-0.0059-0.08450.0372-0.1106136.813163.644331.7848
70.7513-0.02580.15721.03990.40631.6354-0.0403-0.1161-0.03680.07840.0278-0.01080.0318-0.07790.0125-0.15090.01810.0226-0.09330.0156-0.060748.3091159.269776.5089
80.7026-0.05440.09211.3426-0.55041.8827-0.01560.01990.0546-0.14930.0116-0.06-0.00580.03180.004-0.11840.02340.0178-0.1365-0.0051-0.0705111.4761119.321622.3358
91.39-0.4183-0.56071.72380.38871.8258-0.04640.0742-0.10730.1349-0.03370.21420.2024-0.25170.0801-0.0802-0.0763-0.0274-0.06410.0134-0.038282.8364147.7043-5.1293
101.2953-0.90180.2932.2509-0.46020.8309-0.0545-0.0760.08250.16950.0152-0.0376-0.1066-0.0150.0393-0.0633-0.0006-0.0548-0.0978-0.0174-0.0917.6764187.091953.9032
110.70690.00880.40891.02890.73392.8471-0.14590.09270.0464-0.07120.082-0.1023-0.42420.41970.0639-0.0038-0.1649-0.06560.04520.0614-0.012461.979116.124224.231
121.5793-0.8334-0.41812.37120.36441.26-0.0537-0.062-0.13470.00140.07450.11040.14330.0099-0.0208-0.06920.0107-0.0176-0.10370.0381-0.098-5.4818149.449341.2411
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A21 - 400
2X-RAY DIFFRACTION2B21 - 400
3X-RAY DIFFRACTION3C21 - 400
4X-RAY DIFFRACTION4D21 - 400
5X-RAY DIFFRACTION5E21 - 400
6X-RAY DIFFRACTION6F21 - 400
7X-RAY DIFFRACTION7G21 - 400
8X-RAY DIFFRACTION8H21 - 400
9X-RAY DIFFRACTION9I21 - 400
10X-RAY DIFFRACTION10J21 - 400
11X-RAY DIFFRACTION11K21 - 400
12X-RAY DIFFRACTION12L21 - 400

+
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