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- PDB-5yl7: Proteases from Pseudoalteromonas arctica PAMC 21717 (Pro21717) -

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Basic information

Entry
Database: PDB / ID: 5yl7
TitleProteases from Pseudoalteromonas arctica PAMC 21717 (Pro21717)
Components
  • Copurified unknown peptide
  • Pseudoalteromonas arctica PAMC 21717
KeywordsHYDROLASE / Serine protease / psychrophilic bacterium / Pseudoalteromonas arctica
Function / homology
Function and homology information


serine-type endopeptidase activity
Similarity search - Function
Peptidase MprA-like catalytic domain / Peptidase, C-terminal, archaeal/bacterial / Bacterial pre-peptidase C-terminal domain / Peptidase S8/S53 domain / Peptidase S8, subtilisin, His-active site / Serine proteases, subtilase family, histidine active site. / Serine proteases, subtilase family, serine active site. / Peptidase S8, subtilisin, Ser-active site / Peptidase S8, subtilisin-related / Peptidase S8/S53 domain superfamily ...Peptidase MprA-like catalytic domain / Peptidase, C-terminal, archaeal/bacterial / Bacterial pre-peptidase C-terminal domain / Peptidase S8/S53 domain / Peptidase S8, subtilisin, His-active site / Serine proteases, subtilase family, histidine active site. / Serine proteases, subtilase family, serine active site. / Peptidase S8, subtilisin, Ser-active site / 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 speciesPseudoalteromonas arctica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsLee, J.H. / Lee, C.W.
CitationJournal: PLoS ONE / Year: 2018
Title: Crystal structure of a cold-active protease (Pro21717) from the psychrophilic bacterium, Pseudoalteromonas arctica PAMC 21717, at 1.4 angstrom resolution: Structural adaptations to cold and ...Title: Crystal structure of a cold-active protease (Pro21717) from the psychrophilic bacterium, Pseudoalteromonas arctica PAMC 21717, at 1.4 angstrom resolution: Structural adaptations to cold and functional analysis of a laundry detergent enzyme
Authors: Park, H.J. / Lee, C.W. / Kim, D. / Do, H. / Han, S.J. / Kim, J.E. / Koo, B.H. / Lee, J.H. / Yim, J.H.
History
DepositionOct 17, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 31, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 12, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pseudoalteromonas arctica PAMC 21717
B: Copurified unknown peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2576
Polymers35,0972
Non-polymers1604
Water10,719595
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area720 Å2
ΔGint-38 kcal/mol
Surface area11700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.948, 74.562, 83.012
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Pseudoalteromonas arctica PAMC 21717


Mass: 34823.406 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Catalytic domain of protease from the psychrophilic bacterium
Source: (gene. exp.) Pseudoalteromonas arctica (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A290S6P3*PLUS
#2: Protein/peptide Copurified unknown peptide


Mass: 273.330 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudoalteromonas arctica (bacteria)
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 595 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE AUTHORS DO NOT KNOW THE SEQUENCE OF THE CHAIN B. THESE THREE ALANINE RESIDUES ARE A CO-PURIFIED ...THE AUTHORS DO NOT KNOW THE SEQUENCE OF THE CHAIN B. THESE THREE ALANINE RESIDUES ARE A CO-PURIFIED (SEQUENCE UNKNOWN) PEPTIDE LOCATED IN SUBSTRATE BINDING POCKET OF OUR PRO21717 PROTEASE.

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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: 2.11 Å3/Da / Density % sol: 41.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.16M magnesium chloride, 0.08M Tris-HCl buffer pH 8.5, 24% PEG4000, 20% glycerol

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: May 22, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.4→30 Å / Num. obs: 58245 / % possible obs: 98 % / Redundancy: 13.8 % / Net I/σ(I): 69

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data processing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→30 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.958 / SU B: 0.587 / SU ML: 0.025 / Cross valid method: THROUGHOUT / ESU R: 0.049 / ESU R Free: 0.052 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.15529 2939 5.1 %RANDOM
Rwork0.12999 ---
obs0.13128 55253 97.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 10.619 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2---0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: 1 / Resolution: 1.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2386 0 4 595 2985
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.0192431
X-RAY DIFFRACTIONr_bond_other_d0.0020.022070
X-RAY DIFFRACTIONr_angle_refined_deg2.3711.9243328
X-RAY DIFFRACTIONr_angle_other_deg1.1634818
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3495340
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.18325.8100
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.09415309
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.009159
X-RAY DIFFRACTIONr_chiral_restr0.1420.2377
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0212892
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02458
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_it1.0750.7711366
X-RAY DIFFRACTIONr_mcbond_other1.0720.771365
X-RAY DIFFRACTIONr_mcangle_it1.5161.1591704
X-RAY DIFFRACTIONr_mcangle_other1.5161.161705
X-RAY DIFFRACTIONr_scbond_it2.1940.8991065
X-RAY DIFFRACTIONr_scbond_other2.1930.91066
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.011.2971625
X-RAY DIFFRACTIONr_long_range_B_refined16.79614.1463169
X-RAY DIFFRACTIONr_long_range_B_other13.40411.4152885
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.399→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.161 207 -
Rwork0.137 4008 -
obs--97.16 %

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