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Basic information

Entry
Database: PDB / ID: 2ixt
TitleSPHERICASE
Components36KDA PROTEASE
KeywordsHYDROLASE / SERINE PROTEASE / SUBTILISIN LIKE PROTEASE
Function / homology
Function and homology information


serine-type endopeptidase activity / proteolysis / 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
Putative 36kDa protease
Similarity search - Component
Biological speciesBACILLUS SPHAERICUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.8 Å
AuthorsAlmog, O. / Gonzalez, A. / Godin, N.
Citation
Journal: 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.
#1: Journal: J.Mol.Biol. / Year: 2003
Title: The 0.93A Crystal Structure of Sphericase: A Calcium-Loaded Serine Protease from Bacillus Sphaericus
Authors: Almog, O. / Gonzalez, A. / Klein, D. / Braun, S. / Shohamm, G.
History
DepositionJul 11, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 21, 2007Provider: repository / Type: Initial release
Revision 1.1Oct 10, 2012Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Other / Structure summary / Version format compliance
Revision 1.2Jul 24, 2019Group: Advisory / Data collection / Category: diffrn_source / pdbx_validate_polymer_linkage
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_validate_polymer_linkage.dist ..._diffrn_source.pdbx_synchrotron_site / _pdbx_validate_polymer_linkage.dist / _pdbx_validate_polymer_linkage.label_alt_id_1 / _pdbx_validate_polymer_linkage.label_alt_id_2
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...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 / 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_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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_alt_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_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.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_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_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
Revision 1.4Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 36KDA PROTEASE
B: 36KDA PROTEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,13012
Polymers63,7292
Non-polymers40110
Water18,2311012
1
A: 36KDA PROTEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,0656
Polymers31,8651
Non-polymers2005
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: 36KDA PROTEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,0656
Polymers31,8651
Non-polymers2005
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.088, 62.668, 84.874
Angle α, β, γ (deg.)90.00, 95.47, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1116A1 - 315
2116B1 - 315

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Components

#1: Protein 36KDA PROTEASE


Mass: 31864.654 Da / Num. of mol.: 2 / Fragment: RESIDUES 122-431 / Source method: isolated from a natural source / Source: (natural) BACILLUS SPHAERICUS (bacteria) / References: UniProt: Q9S3L6
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1012 / 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: 1.39 Å3/Da / Density % sol: 10.83 % / Description: NONE
Crystal growpH: 7.5 / Details: pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8423
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 18, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8423 Å / Relative weight: 1
ReflectionResolution: 0.8→84.5 Å / Num. obs: 411650 / % possible obs: 81 % / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Rmerge(I) obs: 0.05 / Rsym value: 0.044 / Net I/σ(I): 6.5
Reflection shellMean I/σ(I) obs: 1.8 / Rsym value: 0.23

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EA7

1ea7


Resolution: 0.8→84.52 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.976 / SU B: 0.313 / SU ML: 0.01 / Cross valid method: THROUGHOUT / ESU R: 0.016 / ESU R Free: 0.017 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.154 20621 5 %RANDOM
Rwork0.137 ---
obs0.138 411650 81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 4.98 Å2
Baniso -1Baniso -2Baniso -3
1--0.31 Å20 Å20.04 Å2
2--0.33 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 0.8→84.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4478 0 10 1012 5500
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0215408
X-RAY DIFFRACTIONr_bond_other_d0.0020.023386
X-RAY DIFFRACTIONr_angle_refined_deg1.6131.9317466
X-RAY DIFFRACTIONr_angle_other_deg1.4923.0018393
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2135779
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.37625.284229
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.40915798
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.4311522
X-RAY DIFFRACTIONr_chiral_restr0.1040.2829
X-RAY DIFFRACTIONr_gen_planes_refined0.010.026569
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021077
X-RAY DIFFRACTIONr_nbd_refined0.3440.21386
X-RAY DIFFRACTIONr_nbd_other0.2190.23959
X-RAY DIFFRACTIONr_nbtor_refined0.190.22743
X-RAY DIFFRACTIONr_nbtor_other0.0930.22721
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2140.2841
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2640.223
X-RAY DIFFRACTIONr_symmetry_vdw_other0.230.276
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2170.2143
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2491.53654
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.72625792
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.44632008
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.1174.51653
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
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 3498 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
loose positional0.285
loose thermal0.7810
LS refinement shellResolution: 0.8→0.83 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.375 1320
Rwork0.358 24208

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