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- PDB-3aj9: X-ray analysis of Crystal of Proteinase K Obtained from D2O Solut... -

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Basic information

Entry
Database: PDB / ID: 3aj9
TitleX-ray analysis of Crystal of Proteinase K Obtained from D2O Solution Using PEG 8000
ComponentsProteinase K
KeywordsHYDROLASE / PROTEINASE K / POLYETHYLENE GLYCOL / DEUTERATION
Function / homology
Function and homology information


peptidase K / serine-type endopeptidase activity / proteolysis / extracellular region / 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 speciesTritirachium album (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å
AuthorsChatake, T. / Ishikawa, T. / Morimoto, Y.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2011
Title: High-resolution X-ray study of the effects of deuteration on crystal growth and the crystal structure of proteinase K
Authors: Chatake, T. / Ishikawa, T. / Yanagisawa, Y. / Yamada, T. / Tanaka, I. / Fujiwara, S. / Morimoro, Y.
History
DepositionMay 27, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 22, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 16, 2011Group: Database references
Revision 1.3May 2, 2012Group: Database references
Revision 1.4Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.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 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Proteinase K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1314
Polymers28,9591
Non-polymers1723
Water7,170398
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)68.100, 68.100, 102.464
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-441-

HOH

21A-579-

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) Tritirachium album (fungus) / References: UniProt: P06873, peptidase K
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 398 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsACCORDING TO THE ELECTRON DENSITY MAPS, RESIDUE 207 SHOULD BE AN ASP. THIS IS CONSISTENT WITH THE ...ACCORDING TO THE ELECTRON DENSITY MAPS, RESIDUE 207 SHOULD BE AN ASP. THIS IS CONSISTENT WITH THE OBSERVATIONS FOUND IN PDB ENTRY 1IC6.

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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: 2.05 Å3/Da / Density % sol: 40.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.7
Details: 4.5% PEG 8000, 0.05M calcium acetate, 0.05M cacodylate, pH 6.7, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 0.97802 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 20, 2007
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97802 Å / Relative weight: 1
ReflectionResolution: 1.1→25 Å / Num. obs: 97788 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14 % / Biso Wilson estimate: 5.69 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 23.6
Reflection shellResolution: 1.1→1.16 Å / Redundancy: 9.1 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 7.2 / Num. unique all: 13812 / % possible all: 98.1

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
AMoREphasing
PHENIX(phenix.refine: 1.5_2)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1IC6

1ic6


Resolution: 1.1→23.976 Å / Occupancy max: 1 / Occupancy min: 0.16 / FOM work R set: 0.9365 / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 0.04 / Phase error: 12.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1615 4751 5 %RANDOM
Rwork0.1472 90346 --
obs0.1479 95097 97.03 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 33.718 Å2 / ksol: 0.342 e/Å3
Displacement parametersBiso max: 31.54 Å2 / Biso mean: 8.4661 Å2 / Biso min: 3.14 Å2
Baniso -1Baniso -2Baniso -3
1--0.9864 Å2-0 Å20 Å2
2---0.9864 Å20 Å2
3---0.488 Å2
Refinement stepCycle: LAST / Resolution: 1.1→23.976 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2032 0 8 398 2438
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082119
X-RAY DIFFRACTIONf_angle_d1.3012880
X-RAY DIFFRACTIONf_dihedral_angle_d16.959726
X-RAY DIFFRACTIONf_chiral_restr0.092326
X-RAY DIFFRACTIONf_plane_restr0.007376
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1-1.11250.17621340.14142778X-RAY DIFFRACTION91
1.1125-1.12560.19531620.19542688X-RAY DIFFRACTION88
1.1256-1.13930.14781570.13712727X-RAY DIFFRACTION89
1.1393-1.15370.15031560.10972989X-RAY DIFFRACTION97
1.1537-1.16890.13121440.10952959X-RAY DIFFRACTION97
1.1689-1.18490.13251630.1082999X-RAY DIFFRACTION98
1.1849-1.20190.14621620.10733012X-RAY DIFFRACTION98
1.2019-1.21980.14631430.11862880X-RAY DIFFRACTION94
1.2198-1.23890.19821620.18032885X-RAY DIFFRACTION94
1.2389-1.25920.16091480.13082911X-RAY DIFFRACTION95
1.2592-1.28090.17011540.14812963X-RAY DIFFRACTION96
1.2809-1.30420.21761270.19412886X-RAY DIFFRACTION93
1.3042-1.32920.14941490.11492953X-RAY DIFFRACTION96
1.3292-1.35640.14241630.10843031X-RAY DIFFRACTION99
1.3564-1.38590.17031840.12052983X-RAY DIFFRACTION98
1.3859-1.41810.13581730.1053061X-RAY DIFFRACTION99
1.4181-1.45360.13241630.11732994X-RAY DIFFRACTION98
1.4536-1.49290.14351570.12842985X-RAY DIFFRACTION97
1.4929-1.53680.14341740.11432990X-RAY DIFFRACTION97
1.5368-1.58640.11821700.10253081X-RAY DIFFRACTION99
1.5864-1.64310.13241610.1063082X-RAY DIFFRACTION100
1.6431-1.70880.12751470.1113135X-RAY DIFFRACTION100
1.7088-1.78660.1411610.12113110X-RAY DIFFRACTION100
1.7866-1.88070.14471630.133103X-RAY DIFFRACTION99
1.8807-1.99850.2021590.17853087X-RAY DIFFRACTION99
1.9985-2.15270.15391640.14223118X-RAY DIFFRACTION99
2.1527-2.36920.18641730.18053141X-RAY DIFFRACTION99
2.3692-2.71160.1591550.14783193X-RAY DIFFRACTION100
2.7116-3.41480.14461550.14893245X-RAY DIFFRACTION100
3.4148-23.98150.15671680.16043377X-RAY DIFFRACTION99

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