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- PDB-3wy8: Crystal Structure of Protease Anisep from Arthrobacter Nicotinovorans -

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Basic information

Entry
Database: PDB / ID: 3wy8
TitleCrystal Structure of Protease Anisep from Arthrobacter Nicotinovorans
ComponentsSerine protease
KeywordsHYDROLASE / TRYPSIN-LIKE
Function / homology
Function and homology information


peptidase activity / proteolysis
Similarity search - Function
: / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesArthrobacter nicotinovorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsSone, T. / Haraguchi, Y. / Kuwahara, A. / Ose, T. / Takano, M. / Abe, A. / Tanaka, M. / Tanaka, I. / Asano, K.
CitationJournal: Protein Pept.Lett. / Year: 2015
Title: Structural characterization reveals the keratinolytic activity of an arthrobacter nicotinovorans protease.
Authors: Sone, T. / Haraguchi, Y. / Kuwahara, A. / Ose, T. / Takano, M. / Abe, A. / Tanaka, M. / Tanaka, I. / Asano, K.
History
DepositionAug 20, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 26, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2019Group: Data collection / Database references / Category: citation / Item: _citation.pdbx_database_id_DOI / _citation.title
Revision 1.2Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine protease


Theoretical massNumber of molelcules
Total (without water)22,7821
Polymers22,7821
Non-polymers00
Water5,188288
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)103.017, 103.017, 103.017
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23
Components on special symmetry positions
IDModelComponents
11A-528-

HOH

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Components

#1: Protein Serine protease


Mass: 22781.861 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arthrobacter nicotinovorans (bacteria) / Strain: 23-0-11 / Gene: Spr / Plasmid: pDEST14 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-AI / References: UniProt: K7ZK39, chymotrypsin
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 288 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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 Å3/Da / Density % sol: 38.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPES, 4.3M sodium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 22, 2009 / Details: mirrors
RadiationMonochromator: silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. all: 20158 / Num. obs: 20158 / % possible obs: 100 % / Redundancy: 22.2 % / Biso Wilson estimate: 20.68 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 44.9
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 22 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 7.2 / Num. unique all: 1001 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3CP7

3cp7


Resolution: 1.7→29.74 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.962 / SU B: 1.858 / SU ML: 0.062 / Cross valid method: THROUGHOUT / ESU R: 0.108 / ESU R Free: 0.099 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.18103 1036 5.1 %RANDOM
Rwork0.15361 ---
obs0.15502 19120 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.719 Å2
Refinement stepCycle: LAST / Resolution: 1.7→29.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1606 0 0 288 1894
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0221654
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9991.9182259
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7395218
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.02925.14768
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.25215215
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.119151
X-RAY DIFFRACTIONr_chiral_restr0.0730.2235
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211315
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_it0.3451.51079
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.66821715
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.0373575
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.5944.5544
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
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.229 64 -
Rwork0.201 1426 -
obs--99.93 %

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