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- PDB-3wqb: Crystal structure of aeromonas sobria serine protease (ASP) and t... -

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Basic information

Entry
Database: PDB / ID: 3wqb
TitleCrystal structure of aeromonas sobria serine protease (ASP) and the chaperone (ORF2) complex
Components
  • Extracellular serine protease
  • Open reading frame 2
KeywordsHYDROLASE/CHAPERONE / ASP / serine protease / ORF2 / chaperone / Calcium Binding / extracellular space / HYDROLASE-CHAPERONE complex
Function / homology
Function and homology information


Lys-Lys/Arg-Xaa endopeptidase / periplasmic space / serine-type endopeptidase activity / proteolysis / extracellular region / metal ion binding
Similarity search - Function
: / Open reading frame 2 N-terminal domain / Kexin/furin catalytic domain / P domain / Proprotein convertase P-domain / P/Homo B domain profile. / Peptidase S8/S53 domain / Peptidase S8, subtilisin, His-active site / Serine proteases, subtilase family, histidine active site. / Serine proteases, subtilase family, aspartic acid active site. ...: / Open reading frame 2 N-terminal domain / Kexin/furin catalytic domain / P domain / Proprotein convertase P-domain / P/Homo B domain profile. / Peptidase S8/S53 domain / 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 / Galactose-binding domain-like / Peptidase S8, subtilisin-related / Serine proteases, subtilase domain profile. / Peptidase S8/S53 domain superfamily / Subtilase family / Peptidase S8/S53 domain / Galactose-binding-like domain superfamily / Jelly Rolls / Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Aeromonas extracellular serine protease / ASP external chaperone
Similarity search - Component
Biological speciesAeromonas sobria (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.41 Å
AuthorsKobayashi, H. / Yoshida, T. / Miyakawa, T. / Kato, R. / Tashiro, M. / Yamanaka, H. / Tanokura, M. / Tsuge, H.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Structural Basis for Action of the External Chaperone for a Propeptide-deficient Serine Protease from Aeromonas sobria.
Authors: Kobayashi, H. / Yoshida, T. / Miyakawa, T. / Tashiro, M. / Okamoto, K. / Yamanaka, H. / Tanokura, M. / Tsuge, H.
History
DepositionJan 24, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 25, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software
Revision 1.2Dec 25, 2019Group: Database references / Category: citation / struct_ref_seq_dif
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _struct_ref_seq_dif.details
Revision 1.3Nov 8, 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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Extracellular serine protease
B: Open reading frame 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,1115
Polymers79,9912
Non-polymers1203
Water7,062392
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3000 Å2
ΔGint-12 kcal/mol
Surface area25090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)152.062, 152.062, 51.625
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Extracellular serine protease


Mass: 64254.121 Da / Num. of mol.: 1 / Mutation: S336A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aeromonas sobria (bacteria) / Plasmid: pSA19 / Production host: Escherichia coli (E. coli) / Strain (production host): HB101 / References: UniProt: Q9L5A4
#2: Protein Open reading frame 2 / ORF2


Mass: 15736.529 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aeromonas sobria (bacteria) / Plasmid: pSA19 / Production host: Escherichia coli (E. coli) / Strain (production host): HB101 / References: UniProt: W5JXD7*PLUS
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 392 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE SEQUENCE OF ORF2 (ENTITY 2) WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) ...THE SEQUENCE OF ORF2 (ENTITY 2) WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT THE TIME OF DEPOSITION.

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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: 2.15 Å3/Da / Density % sol: 42.9 % / Mosaicity: 0.475 ° / Mosaicity esd: 0.003 °
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 7.5% PEG 3000, 0.05M HEPES, 0.05M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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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 210r / Detector: CCD / Date: Apr 24, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.41→50 Å / Num. obs: 130476 / % possible obs: 99.2 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.088 / Χ2: 6.126 / Net I/σ(I): 21
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.41-1.432.50.38164392.09797.9
1.43-1.462.50.32563632.36498.2
1.46-1.492.60.30263972.77797.7
1.49-1.522.60.27664513.09498.1
1.52-1.552.70.24264173.32298.8
1.55-1.592.80.21564833.199.2
1.59-1.636.40.23165603.48599.9
1.63-1.677.40.21165793.895100
1.67-1.727.60.1965484.157100
1.72-1.787.70.17265314.449100
1.78-1.847.90.15365914.956100
1.84-1.9180.13765565.821100
1.91-28.20.12165486.699100
2-2.118.30.1165857.212100
2.11-2.248.40.09966067.336100
2.24-2.418.40.09265547.556100
2.41-2.658.40.08566027.665100
2.65-3.048.40.07766458.354100
3.04-3.8380.06866319.03699.5
3.83-5070.06563908.61793.9

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3 Å28.74 Å
Translation3 Å28.74 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.5.0109refinement
PDB_EXTRACT3.14data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HJR

3hjr


Resolution: 1.41→28.74 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.947 / WRfactor Rfree: 0.2087 / WRfactor Rwork: 0.1874 / FOM work R set: 0.8837 / SU B: 1.903 / SU ML: 0.035 / SU R Cruickshank DPI: 0.0743 / SU Rfree: 0.0633 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.074 / ESU R Free: 0.063 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2069 6544 5 %RANDOM
Rwork0.1867 ---
obs0.1877 130244 98.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 45.91 Å2 / Biso mean: 16.733 Å2 / Biso min: 7.9 Å2
Baniso -1Baniso -2Baniso -3
1--0.58 Å2-0.29 Å20 Å2
2---0.58 Å20 Å2
3---0.87 Å2
Refinement stepCycle: LAST / Resolution: 1.41→28.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5208 0 3 392 5603
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0215297
X-RAY DIFFRACTIONr_angle_refined_deg1.1481.9597203
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0885693
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.40224.873236
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.53715852
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5711537
X-RAY DIFFRACTIONr_chiral_restr0.0750.2820
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214065
X-RAY DIFFRACTIONr_mcbond_it0.7911.53443
X-RAY DIFFRACTIONr_mcangle_it1.3325508
X-RAY DIFFRACTIONr_scbond_it2.10931854
X-RAY DIFFRACTIONr_scangle_it3.1614.51695
X-RAY DIFFRACTIONr_rigid_bond_restr0.86635297
LS refinement shellResolution: 1.408→1.445 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.255 466 -
Rwork0.214 8791 -
all-9257 -
obs--95.76 %

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