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- PDB-2gko: S41 Psychrophilic Protease -

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Basic information

Entry
Database: PDB / ID: 2gko
TitleS41 Psychrophilic Protease
Componentsmicrobial serine proteinases; subtilisin
KeywordsHYDROLASE / s41 protease TA41 psychrophilic
Function / homology
Function and homology information


3.4.21.14 / serine-type endopeptidase activity / metal ion binding
Similarity search - Function
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 / Peptidase S8/S53 domain superfamily / Subtilase family ...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 / 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 / : / Microbial serine proteinases
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsWalter, R.L. / Mekel, M.J. / Grayling, R.A. / Arnold, F.H. / Wintrode, P.L. / Almog, O.
CitationJournal: Proteins / Year: 2009
Title: The crystal structures of the psychrophilic subtilisin S41 and the mesophilic subtilisin Sph reveal the same calcium-loaded state.
Authors: Almog, O. / Gonzalez, A. / Godin, N. / de Leeuw, M. / Mekel, M.J. / Klein, D. / Braun, S. / Shoham, G. / Walter, R.L.
History
DepositionApr 3, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Aug 30, 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_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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_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: microbial serine proteinases; subtilisin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6047
Polymers31,2491
Non-polymers3566
Water9,656536
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.000, 61.000, 174.770
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein microbial serine proteinases; subtilisin


Mass: 31248.986 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: TA41 / Gene: s41 / Production host: Escherichia coli (E. coli)
References: GenBank: 40199, UniProt: Q45681*PLUS, subtilisin
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-PMS / phenylmethanesulfonic acid


Mass: 172.202 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H8O3S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 536 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 52.7 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 20-35% (w/v) PEG-8000 100mM HEPES (pH 7.0-7.2) 2ul protein @ 8.0mg/ml + 2ul reservoir solution, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: BRUKER / Detector: CCD / Date: Mar 1, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→57.7 Å / Num. all: 46272 / Num. obs: 43299 / % possible obs: 83.6 % / Observed criterion σ(I): 1.2 / Redundancy: 4.38 % / Rsym value: 0.046 / Net I/σ(I): 1555.4
Reflection shellResolution: 1.4→1.46 Å / Redundancy: 4.38 % / Num. unique all: 43299 / Rsym value: 0.437 / % possible all: 66.25

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Phasing

Phasing MR
Highest resolutionLowest resolution
Rotation2.5 Å8 Å
Translation2.5 Å8 Å

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Processing

Software
NameVersionClassificationNB
SAINTV5.I07data scaling
AMoREphasing
REFMACrefinement
PDB_EXTRACT1.701data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YJA

1yja


Resolution: 1.4→57.7 Å / σ(F): 1.2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.1977 2187 -Random 5%
all0.1603 ---
obs0.1603 43171 85.3 %-
Displacement parametersBiso mean: 18.588 Å2
Refinement stepCycle: LAST / Resolution: 1.4→57.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2204 0 15 536 2755
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.011
X-RAY DIFFRACTIONp_angle_d1.36
LS refinement shell
Resolution (Å)Refine-IDNum. reflection obs% reflection obs (%)
1.4-1.46X-RAY DIFFRACTION4329966.3
1.46-1.51X-RAY DIFFRACTION4283672.7
1.51-1.58X-RAY DIFFRACTION4155979.1
1.58-1.67X-RAY DIFFRACTION3955785.8
1.67-1.77X-RAY DIFFRACTION3966592.2
1.77-1.9X-RAY DIFFRACTION3322596.5
1.9-2.1X-RAY DIFFRACTION2672299.1
2.1-2.4X-RAY DIFFRACTION20327100
2.4-3X-RAY DIFFRACTION13924100
3-57X-RAY DIFFRACTION7143100

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