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- PDB-2xrm: Processed Intracellular subtilisin from B. clausii -

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Basic information

Entry
Database: PDB / ID: 2xrm
TitleProcessed Intracellular subtilisin from B. clausii
ComponentsINTRACELLULAR SUBTILISIN PROTEASE
KeywordsHYDROLASE / ACTIVATED FORM / POST-TRANSLATIONAL MODIFICATION
Function / homology
Function and homology information


serine-type endopeptidase activity / proteolysis / identical protein binding / metal ion binding
Similarity search - Function
: / Subtilisin Carlsberg-like catalytic domain / 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 ...: / Subtilisin Carlsberg-like catalytic domain / 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 / Peptidase S8/S53 domain / Subtilase family / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
STRONTIUM ION / Intracellular subtilisin protease
Similarity search - Component
Biological speciesBACILLUS CLAUSII (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsGamble, M. / Kunze, G. / Dodson, E.J. / Jones, D.D. / Wilson, K.S.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Regulation of an Intracellular Subtilisin Protease Activity by a Short Propeptide Sequence Through an Original Combined Dual Mechanism.
Authors: Gamble, M. / Kunze, G. / Dodson, E.J. / Wilson, K.S. / Jones, D.D.
History
DepositionSep 20, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 16, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2013Group: Source and taxonomy / Version format compliance
Revision 1.2Jan 24, 2018Group: Advisory / Source and taxonomy / Category: entity_src_gen / pdbx_unobs_or_zero_occ_atoms
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 1.3Dec 20, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.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: INTRACELLULAR SUBTILISIN PROTEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1535
Polymers32,7641
Non-polymers3894
Water46826
1
A: INTRACELLULAR SUBTILISIN PROTEASE
hetero molecules

A: INTRACELLULAR SUBTILISIN PROTEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,30710
Polymers65,5292
Non-polymers7788
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_545x,-y-1,-z1
Buried area4380 Å2
ΔGint-112.9 kcal/mol
Surface area21550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.982, 132.982, 132.982
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-2006-

HOH

21A-2008-

HOH

31A-2009-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein INTRACELLULAR SUBTILISIN PROTEASE


Mass: 32764.332 Da / Num. of mol.: 1 / Fragment: PROCESSED PROTEIN, RESIDUES 19-321 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: N TERMINAL 18 RESIDUES DELETED / Source: (gene. exp.) BACILLUS CLAUSII (bacteria)
Description: ISOLATED FROM A NOVOZYMES STRAIN B. CLAUSII STRAIN -STRAIN NUMBER AVAILABLE ON REQUEST.
Plasmid: PET22B / Production host: ESCHERICHIA COLI BL21 (bacteria) / References: UniProt: D0AB41, subtilisin

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Non-polymers , 5 types, 30 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-SR / STRONTIUM ION


Mass: 87.620 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Sr
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsENGINEERED RESIDUE IN CHAIN A, SER 250 TO ALA
Nonpolymer detailsSODIUM ION (NA): NA OCCUPIES THE HIGH AFFINITY CALCIUM SITE FOUND IN OTHER SUBTILISINS

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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: 2.86 Å3/Da / Density % sol: 57 %
Description: ONE CHAIN OF THE ENTRY 2X8J WAS USED AS A MODEL
Crystal growpH: 6.7 / Details: pH 6.7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.98
DetectorType: ADSC CCD / Detector: CCD / Date: Mar 10, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.6→108.4 Å / Num. obs: 12244 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 19.6 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 13.4
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 11 % / Rmerge(I) obs: 1.41 / Mean I/σ(I) obs: 0.5 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.6.0081refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2X8J

2x8j


Resolution: 2.6→66.49 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.929 / SU B: 11.922 / SU ML: 0.254 / Cross valid method: THROUGHOUT / ESU R: 0.479 / ESU R Free: 0.326 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. U VALUES REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.28084 599 4.9 %RANDOM
Rwork0.19799 ---
obs0.20175 11642 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 69.629 Å2
Refinement stepCycle: LAST / Resolution: 2.6→66.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2209 0 16 26 2251
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222264
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8241.9563055
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4125300
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.70625.36197
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.55715336
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.4231510
X-RAY DIFFRACTIONr_chiral_restr0.1320.2349
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211725
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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: 2.599→2.666 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.445 51 -
Rwork0.309 849 -
obs--100 %

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