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- PDB-2x8j: Intracellular subtilisin precursor from B. clausii -

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Basic information

Entry
Database: PDB / ID: 2x8j
TitleIntracellular subtilisin precursor from B. clausii
Components(INTRACELLULAR SUBTILISIN ...) x 2
KeywordsHYDROLASE / SERINE PROTEASE / INTRACELLULAR PROTEINASE REGULATION
Function / homology
Function and homology information


serine-type endopeptidase activity / proteolysis / metal ion binding / identical protein 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 / Subtilase family / Peptidase S8/S53 domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Intracellular subtilisin protease
Similarity search - Component
Biological speciesBACILLUS CLAUSII (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.56 Å
AuthorsVedodova, J. / Gamble, M. / Ariza, A. / Dodson, E. / Jones, D.D. / Wilson, K.S.
CitationJournal: Structure / Year: 2010
Title: Crystal structure of an intracellular subtilisin reveals novel structural features unique to this subtilisin family.
Authors: Vevodova, J. / Gamble, M. / Kunze, G. / Ariza, A. / Dodson, E. / Jones, D.D. / Wilson, K.S.
History
DepositionMar 9, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 11, 2010Provider: repository / Type: Initial release
Revision 1.1Sep 21, 2011Group: Atomic model / Non-polymer description ...Atomic model / Non-polymer description / Refinement description / Version format compliance
Revision 1.2Feb 28, 2018Group: Advisory / Database references / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_polymer_linkage
Item: _citation.journal_id_ISSN / _citation.page_last ..._citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_scientific_name / _pdbx_validate_polymer_linkage.dist / _pdbx_validate_polymer_linkage.label_alt_id_1
Revision 1.3Sep 25, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_status ...exptl_crystal_grow / pdbx_database_status / reflns / struct_conn
Item: _exptl_crystal_grow.method / _pdbx_database_status.status_code_sf ..._exptl_crystal_grow.method / _pdbx_database_status.status_code_sf / _reflns.pdbx_Rmerge_I_obs / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Dec 20, 2023Group: Advisory / Data collection ...Advisory / 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 / 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_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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: INTRACELLULAR SUBTILISIN PROTEASE
B: INTRACELLULAR SUBTILISIN PROTEASE
C: INTRACELLULAR SUBTILISIN PROTEASE
D: INTRACELLULAR SUBTILISIN PROTEASE
E: INTRACELLULAR SUBTILISIN PROTEASE
F: INTRACELLULAR SUBTILISIN PROTEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)210,07420
Polymers208,3226
Non-polymers1,75214
Water27,0411501
1
C: INTRACELLULAR SUBTILISIN PROTEASE
D: INTRACELLULAR SUBTILISIN PROTEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,1428
Polymers69,4352
Non-polymers7076
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4900 Å2
ΔGint-38 kcal/mol
Surface area20560 Å2
MethodPISA
2
E: INTRACELLULAR SUBTILISIN PROTEASE
F: INTRACELLULAR SUBTILISIN PROTEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,9586
Polymers69,4352
Non-polymers5234
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4330 Å2
ΔGint-36.4 kcal/mol
Surface area20850 Å2
MethodPISA
3
A: INTRACELLULAR SUBTILISIN PROTEASE
B: INTRACELLULAR SUBTILISIN PROTEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,9746
Polymers69,4512
Non-polymers5234
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4390 Å2
ΔGint-36 kcal/mol
Surface area20740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.659, 125.659, 106.141
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.65661, 0.75401, -0.01814), (0.75237, -0.65649, -0.05433), (-0.05287, 0.02202, -0.99836)64.41478, -34.20237, 35.93203
2given(0.85946, -0.51118, 0.00382), (0.51041, 0.8577, -0.06193), (0.02838, 0.05517, 0.99807)-63.18617, 38.62783, -8.8003

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Components

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INTRACELLULAR SUBTILISIN ... , 2 types, 6 molecules ACDEFB

#1: Protein
INTRACELLULAR SUBTILISIN PROTEASE / INTRACELLULAR SUBTILISIN


Mass: 34717.746 Da / Num. of mol.: 5 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: THESE CHAINS CONTAIN 1 OXIDISED CYS / 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
#2: Protein INTRACELLULAR SUBTILISIN PROTEASE / INTRACELLULAR SUBTILISIN


Mass: 34733.746 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: THIS CHAIN CONTAINS 2 OXIDISED CYS / 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 , 4 types, 1515 molecules

#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1501 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsENGINEERED RESIDUE IN CHAIN A, SER 250 TO ALA ENGINEERED RESIDUE IN CHAIN B, SER 250 TO ALA ...ENGINEERED RESIDUE IN CHAIN A, SER 250 TO ALA ENGINEERED RESIDUE IN CHAIN B, SER 250 TO ALA ENGINEERED RESIDUE IN CHAIN C, SER 250 TO ALA ENGINEERED RESIDUE IN CHAIN D, SER 250 TO ALA ENGINEERED RESIDUE IN CHAIN E, SER 250 TO ALA ENGINEERED RESIDUE IN CHAIN F, SER 250 TO ALA

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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: 2.49 Å3/Da / Density % sol: 48.5 % / Description: BASED ON PREVIOUSLY DETERMINED STRUCTURE
Crystal growMethod: vapor diffusion, hanging drop / pH: 5.9
Details: PEG 4K GLYCEROL 0.1M SODIUM CACODYLATE PH 5.9 0.2M SODIUM ACETATE.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9805
DetectorType: ADSC CCD / Detector: CCD / Date: Jan 25, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9805 Å / Relative weight: 1
ReflectionResolution: 1.56→108.4 Å / Num. obs: 269002 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Biso Wilson estimate: 21.9 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 13.4
Reflection shellResolution: 1.56→1.64 Å / Redundancy: 5.5 % / Rmerge(I) obs: 1.08 / Mean I/σ(I) obs: 1.6 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WWT

2wwt


Resolution: 1.56→75.98 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.952 / SU B: 1.958 / SU ML: 0.07 / Cross valid method: THROUGHOUT / ESU R: 0.085 / ESU R Free: 0.09 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.22973 16568 6.2 %RANDOM
Rwork0.18697 ---
obs0.18961 252387 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.843 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å2-0.02 Å20 Å2
2---0.04 Å20 Å2
3---0.06 Å2
Refinement stepCycle: LAST / Resolution: 1.56→75.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13583 0 78 1501 15162
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.02214261
X-RAY DIFFRACTIONr_bond_other_d0.0020.029325
X-RAY DIFFRACTIONr_angle_refined_deg2.2151.95919347
X-RAY DIFFRACTIONr_angle_other_deg1.5263.00322623
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.52651898
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.0224.624599
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.136152203
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0291581
X-RAY DIFFRACTIONr_chiral_restr0.160.22204
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0216387
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022812
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_it1.3941.59282
X-RAY DIFFRACTIONr_mcbond_other0.4411.53924
X-RAY DIFFRACTIONr_mcangle_it2.178214829
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.19234979
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.8684.54518
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: 1.556→1.596 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.382 1269 -
Rwork0.339 18653 -
obs--99.89 %

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