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- PDB-1sh7: Crystal structure of a cold adapted subtilisin-like serine proteinase -

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Basic information

Entry
Database: PDB / ID: 1sh7
TitleCrystal structure of a cold adapted subtilisin-like serine proteinase
Componentsextracellular subtilisin-like serine proteinase
KeywordsHYDROLASE / cold adaptation / psychrotrophic / subtilisin-like proteinase / calcium depentent
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / serine-type endopeptidase activity / proteolysis / extracellular space / metal ion binding
Similarity search - Function
Peptidase, C-terminal, archaeal/bacterial / Bacterial pre-peptidase C-terminal domain / Proteinase K-like catalytic domain / Peptidase S8 propeptide/proteinase inhibitor I9 / Peptidase inhibitor I9 / Peptidase S8 propeptide/proteinase inhibitor I9 superfamily / Peptidase S8/S53 domain / : / Peptidase S8, subtilisin, His-active site / Serine proteases, subtilase family, histidine active site. ...Peptidase, C-terminal, archaeal/bacterial / Bacterial pre-peptidase C-terminal domain / Proteinase K-like catalytic domain / Peptidase S8 propeptide/proteinase inhibitor I9 / Peptidase inhibitor I9 / Peptidase S8 propeptide/proteinase inhibitor I9 superfamily / 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 / Peptidase S8, subtilisin-related / Serine proteases, subtilase domain profile. / Peptidase S8/S53 domain superfamily / Subtilase family / Peptidase S8/S53 domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
phenylmethanesulfonic acid / Extracellular subtilisin-like serine proteinase
Similarity search - Component
Biological speciesVibrio sp. PA-44 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å
AuthorsArnorsdottir, J. / Kristjansson, M.M. / Ficner, R.
CitationJournal: Febs J. / Year: 2005
Title: Crystal structure of a subtilisin-like serine proteinase from a psychrotrophic Vibrio species reveals structural aspects of cold adaptation.
Authors: Arnorsdottir, J. / Kristjansson, M.M. / Ficner, R.
History
DepositionFeb 25, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_entry_details / pdbx_modification_feature / 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 / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.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_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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_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_asym_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_conn.ptnr2_label_seq_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: extracellular subtilisin-like serine proteinase
B: extracellular subtilisin-like serine proteinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,59010
Polymers58,0052
Non-polymers5858
Water10,683593
1
A: extracellular subtilisin-like serine proteinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2955
Polymers29,0021
Non-polymers2924
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: extracellular subtilisin-like serine proteinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2955
Polymers29,0021
Non-polymers2924
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.212, 36.881, 140.488
Angle α, β, γ (deg.)90.00, 97.80, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein extracellular subtilisin-like serine proteinase


Mass: 29002.395 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio sp. PA-44 (bacteria) / Plasmid: pBAD TOPO / Production host: Escherichia coli (E. coli) / Strain (production host): Top10
References: UniProt: Q8GB52, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-PMS / phenylmethanesulfonic acid


Mass: 172.202 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H8O3S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 593 / 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: 1.96 Å3/Da / Density % sol: 36.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: PEC 4000, isopropanol, HEPES, pH 8, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 1.0092 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jan 21, 2004
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0092 Å / Relative weight: 1
ReflectionResolution: 1.81→40 Å / Num. all: 37883 / Num. obs: 37883 / Redundancy: 3.6 % / Rsym value: 0.067 / Net I/σ(I): 12
Reflection shellResolution: 1.81→1.87 Å / Num. unique all: 2031 / Rsym value: 0.496 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.84→30 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.937 / SU B: 2.917 / SU ML: 0.087 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.147 / ESU R Free: 0.139 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19659 3767 9.9 %RANDOM
Rwork0.14082 ---
all0.16 ---
obs0.14632 34113 97.18 %-
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: 11.925 Å2
Baniso -1Baniso -2Baniso -3
1-0.73 Å20 Å20.56 Å2
2---0.1 Å20 Å2
3----0.48 Å2
Refinement stepCycle: LAST / Resolution: 1.84→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3990 0 26 593 4609
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0214110
X-RAY DIFFRACTIONr_bond_other_d0.0020.023460
X-RAY DIFFRACTIONr_angle_refined_deg1.5211.9335592
X-RAY DIFFRACTIONr_angle_other_deg1.29438075
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8595555
X-RAY DIFFRACTIONr_chiral_restr0.1050.2632
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024803
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02785
X-RAY DIFFRACTIONr_nbd_refined0.2160.2939
X-RAY DIFFRACTIONr_nbd_other0.2520.24363
X-RAY DIFFRACTIONr_nbtor_other0.0870.22321
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1580.2340
X-RAY DIFFRACTIONr_metal_ion_refined0.0820.226
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1610.229
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2220.281
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1910.258
X-RAY DIFFRACTIONr_mcbond_it0.7611.52728
X-RAY DIFFRACTIONr_mcangle_it1.2724345
X-RAY DIFFRACTIONr_scbond_it2.23531381
X-RAY DIFFRACTIONr_scangle_it3.3464.51247
LS refinement shellResolution: 1.84→1.883 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.298 250
Rwork0.226 2236
Refinement TLS params.Method: refined / Origin x: 1.622 Å / Origin y: 2.9087 Å / Origin z: 86.8946 Å
111213212223313233
T0.0028 Å2-0.001 Å2-0.0018 Å2-0.0032 Å2-0.0029 Å2--0.0068 Å2
L0.0024 °20.014 °20.0643 °2--0.013 °20.0189 °2--0.3414 °2
S0.0053 Å °-0.0003 Å °-0.0047 Å °0.0046 Å °-0.0017 Å °0.0005 Å °0.0188 Å °0.0082 Å °-0.0036 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 2701 - 270
2X-RAY DIFFRACTION1BB1 - 2701 - 270

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