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- PDB-3dyb: proteinase K- digalacturonic acid complex -

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Basic information

Entry
Database: PDB / ID: 3dyb
Titleproteinase K- digalacturonic acid complex
ComponentsProteinase K
KeywordsHYDROLASE / proteinase K / HEPES / digalacturonic acid / silverbullets / Structural Genomics / PSI-2 / Protein Structure Initiative / Center for High-Throughput Structural Biology / CHTSB / Metal-binding / Protease / Serine protease / Zymogen
Function / homology
Function and homology information


peptidase K / serine-type endopeptidase activity / proteolysis / extracellular space / metal ion binding
Similarity search - Function
Proteinase K-like catalytic domain / Peptidase S8/S53 domain / Peptidase S8 propeptide/proteinase inhibitor I9 / Peptidase inhibitor I9 / Peptidase S8 propeptide/proteinase inhibitor I9 superfamily / Peptidase S8, subtilisin, His-active site / Serine proteases, subtilase family, histidine active site. / Serine proteases, subtilase family, aspartic acid active site. / Peptidase S8, subtilisin, Asp-active site / Serine proteases, subtilase family, serine active site. ...Proteinase K-like catalytic domain / Peptidase S8/S53 domain / Peptidase S8 propeptide/proteinase inhibitor I9 / Peptidase inhibitor I9 / Peptidase S8 propeptide/proteinase inhibitor I9 superfamily / Peptidase S8, subtilisin, His-active site / Serine proteases, subtilase family, histidine active site. / Serine proteases, subtilase family, aspartic acid active site. / Peptidase S8, subtilisin, Asp-active site / Serine proteases, subtilase family, serine active site. / Peptidase S8, subtilisin, Ser-active site / Serine proteases, subtilase domain profile. / Peptidase S8, subtilisin-related / Peptidase S8/S53 domain superfamily / Subtilase family / Peptidase S8/S53 domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesEngyodontium album (fungus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.32 Å
AuthorsLarson, S.B. / Day, J.S. / McPherson, A. / Cudney, R. / Nguyen, C. / Center for High-Throughput Structural Biology (CHTSB)
Citation
Journal: Acta Crystallogr.,Sect.F / Year: 2009
Title: High-resolution structure of proteinase K cocrystallized with digalacturonic acid.
Authors: Larson, S.B. / Day, J.S. / Nguyen, C. / Cudney, R. / McPherson, A.
#1: Journal: CRYST.GROWTH DES. / Year: 2008
Title: Progress in the Development of an Alternative Approach to Macromolecular Crystallization
Authors: Larson, S.B. / Day, J.S. / Nguyen, C. / Cudney, R. / McPherson, A.
History
DepositionJul 25, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Atomic model / Version format compliance
Revision 1.2Oct 25, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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_conn_angle / pdbx_validate_symm_contact / struct_conn / struct_conn_type / 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_atom_id / _atom_site.label_comp_id / _atom_site.occupancy / _atom_site.type_symbol / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.src_method / _entity.type / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.value / _pdbx_validate_symm_contact.auth_asym_id_1 / _pdbx_validate_symm_contact.auth_asym_id_2 / _pdbx_validate_symm_contact.auth_atom_id_1 / _pdbx_validate_symm_contact.auth_atom_id_2 / _pdbx_validate_symm_contact.auth_comp_id_1 / _pdbx_validate_symm_contact.auth_comp_id_2 / _pdbx_validate_symm_contact.auth_seq_id_1 / _pdbx_validate_symm_contact.auth_seq_id_2
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 17, 2021Group: Advisory / Database references / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / pdbx_unobs_or_zero_occ_residues / struct_keywords
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_keywords.text
Revision 2.2Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Proteinase K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6485
Polymers28,9591
Non-polymers6894
Water6,143341
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.720, 67.720, 101.890
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-841-

HOH

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Components

#1: Protein Proteinase K / Tritirachium alkaline proteinase / Endopeptidase K


Mass: 28958.791 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Engyodontium album (fungus) / References: UniProt: P06873, peptidase K
#2: Polysaccharide alpha-D-galactopyranuronic acid-(1-4)-alpha-D-galactopyranuronic acid


Type: oligosaccharide / Mass: 370.263 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpAa1-4DGalpAa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2112A-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-GalpA]{[(4+1)][a-D-GalpA]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 341 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAUTHORS STATE THAT ACCORDING TO THE ELECTRON DENSITY MAPS, RESIDUE 207 SHOULD BE AN ASP. THIS IS ...AUTHORS STATE THAT ACCORDING TO THE ELECTRON DENSITY MAPS, RESIDUE 207 SHOULD BE AN ASP. THIS IS CONSISTENT WITH THE OBSERVATIONS FOUND IN PDB ENTRIES 1IC6, 1P7V AND 2PWA.

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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: 2.02 Å3/Da / Density % sol: 39.02 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 5% PEG 3350, 0.1 M HEPES; reservoir of 25% PEG 3350, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 26, 2006 / Details: Osmic Mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.32→32.14 Å / Num. all: 53100 / Num. obs: 53026 / % possible obs: 94 % / Redundancy: 5.33 % / Biso Wilson estimate: 15.9 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 11.5
Reflection shellResolution: 1.32→1.37 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.482 / Mean I/σ(I) obs: 1.3 / Num. unique all: 2566 / % possible all: 46.2

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Processing

Software
NameVersionClassification
REFMAC5.4.0069refinement
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3PRK

3prk


Resolution: 1.32→30.36 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.964 / SU B: 2.839 / SU ML: 0.049 / Isotropic thermal model: ANISOTROPIC / Cross valid method: THROUGHOUT / ESU R: 0.067 / ESU R Free: 0.064 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS FOR ALL NON-WATER MOLECULES HAVE BEEN ADDED IN THE RIDING POSITION AND ADJUSTED TO AVOID STERIC PROBLEMS. OCCUPANCIES FOR HYDROGENS WERE SET TO THE OCCUPANCY OF THE ATOM TO WHICH ...Details: HYDROGENS FOR ALL NON-WATER MOLECULES HAVE BEEN ADDED IN THE RIDING POSITION AND ADJUSTED TO AVOID STERIC PROBLEMS. OCCUPANCIES FOR HYDROGENS WERE SET TO THE OCCUPANCY OF THE ATOM TO WHICH THE HYDROGEN WAS ATTACHED. THE ATOMS OF AD0 HAVING ZERO OCCUPANCY WERE INCLUDED AS A COMPLETE DESCRIPTION OF THE LIGAND. THERE WAS NO ELECTRON DENSITY TO INDICATE WHERE THIS PYRANOSE RING BELONGED. HOWEVER, THERE WAS DENSITY SUGGESTIVE OF WATER MOLECULES IN THIS REGION AND, THEREFORE, WAS MODELED AS SUCH. HENCE, THERE APPEARS TO BE CLOSE CONTACTS AS SHOWN IN REMARK 500. THERE IS EXCELLENT DENSITY FOR EACH OF THE RESIDUES DESCRIBED IN REMARK 500 AS RAMACHANDRAN OUTLIERS.
RfactorNum. reflection% reflectionSelection details
Rfree0.20669 2646 5.1 %RANDOM
Rwork0.1579 ---
all0.16036 49454 --
obs0.16036 49454 92.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 15.875 Å2
Baniso -1Baniso -2Baniso -3
1--0.45 Å20 Å20 Å2
2---0.45 Å20 Å2
3---0.9 Å2
Refinement stepCycle: LAST / Resolution: 1.32→30.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2032 0 42 341 2415
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0212199
X-RAY DIFFRACTIONr_bond_other_d00.022067
X-RAY DIFFRACTIONr_angle_refined_deg1.2651.9513015
X-RAY DIFFRACTIONr_angle_other_deg0.67434665
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2345311
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.85423.73691
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.81915329
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3211514
X-RAY DIFFRACTIONr_chiral_restr0.0780.2335
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022566
X-RAY DIFFRACTIONr_gen_planes_other00.02537
X-RAY DIFFRACTIONr_mcbond_it2.56821422
X-RAY DIFFRACTIONr_mcbond_other2.2622601
X-RAY DIFFRACTIONr_mcangle_it3.35342281
X-RAY DIFFRACTIONr_scbond_it4.0854777
X-RAY DIFFRACTIONr_scangle_it5.3156717
X-RAY DIFFRACTIONr_rigid_bond_restr2.37732198
X-RAY DIFFRACTIONr_sphericity_free8.4813380
X-RAY DIFFRACTIONr_sphericity_bonded4.87132140
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection obs% reflection obs (%)
1.319-1.3530.475670.45611190.457411428.83
1.353-1.390.4741630.39428760.399399076.16
1.39-1.4310.4251850.37634450.379387493.7
1.431-1.4750.41980.33135890.334381299.34
1.475-1.5230.4061850.29734410.303364499.51
1.523-1.5760.3071520.25533940.257356099.61
1.576-1.6360.3061620.21132540.216342999.62
1.636-1.7020.2661700.17731390.182332399.58
1.702-1.7780.2221720.14830020.152318899.56
1.778-1.8640.2171570.12628690.131304499.41
1.864-1.9640.1781370.11527550.118290599.55
1.964-2.0830.1761320.11326220.116276499.64
2.083-2.2260.1751420.11524550.118261199.46
2.226-2.4030.1451410.11722790.119242599.79
2.403-2.6310.1691130.11821240.12224899.51
2.631-2.9390.1571080.12319470.125206299.66
2.939-3.3880.159970.11817300.12183699.51
3.388-4.1370.145760.11214820.114156399.68
4.137-5.7970.18500.16312030.164125799.68
5.797-30.3590.179390.2247290.22277698.97

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