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- PDB-1sup: SUBTILISIN BPN' AT 1.6 ANGSTROMS RESOLUTION: ANALYSIS OF DISCRETE... -

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Basic information

Entry
Database: PDB / ID: 1sup
TitleSUBTILISIN BPN' AT 1.6 ANGSTROMS RESOLUTION: ANALYSIS OF DISCRETE DISORDER AND COMPARISON OF CRYSTAL FORMS
ComponentsSUBTILISIN BPN'
KeywordsHYDROLASE (SERINE PROTEASE)
Function / homology
Function and homology information


subtilisin / sporulation resulting in formation of a cellular spore / fibrinolysis / serine-type endopeptidase activity / proteolysis / extracellular region / metal ion binding
Similarity search - Function
: / Fervidolysin N-terminal prodomain / Subtilisin Carlsberg-like catalytic domain / Peptidase S8/S53 domain / : / Peptidase S8 propeptide/proteinase inhibitor I9 superfamily / 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 ...: / Fervidolysin N-terminal prodomain / Subtilisin Carlsberg-like catalytic domain / Peptidase S8/S53 domain / : / Peptidase S8 propeptide/proteinase inhibitor I9 superfamily / 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
phenylmethanesulfonic acid / Subtilisin BPN'
Similarity search - Component
Biological speciesBacillus amyloliquefaciens (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.6 Å
AuthorsGallagher, D.T. / Oliver, J.D. / Betzel, C. / Gilliland, G.L.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 1996
Title: Subtilisin BPN' at 1.6 A resolution: analysis for discrete disorder and comparison of crystal forms.
Authors: Gallagher, T. / Oliver, J. / Bott, R. / Betzel, C. / Gilliland, G.L.
History
DepositionAug 14, 1995Processing site: BNL
Revision 1.0Nov 14, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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.process_site / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_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

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Assembly

Deposited unit
A: SUBTILISIN BPN'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7884
Polymers27,5531
Non-polymers2353
Water3,495194
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.560, 54.150, 62.730
Angle α, β, γ (deg.)90.00, 91.87, 90.00
Int Tables number5
Space group name H-MC121
Atom site foot note1: CIS PROLINE - PRO 168
Components on special symmetry positions
IDModelComponents
11A-472-

HOH

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Components

#1: Protein SUBTILISIN BPN' / SUBTILISIN NOVO


Mass: 27552.525 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus amyloliquefaciens (bacteria) / References: UniProt: P00782, subtilisin
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / 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.: 194 / Source method: isolated from a natural source / Formula: H2O
Compound detailsSER 221 IS COVALENTLY DERIVATIZED WITH PHENYLMETHYLSULFONATE (PMS), HET GROUP 278.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.05 Å3/Da / Density % sol: 39.98 %
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
17.5 mg/mlprotein1drop
220 mMMES1droppH7.0
32 mMPMSF1drop
435-40 %saturatedammonium sulfate1reservoir
50.5 %PEG80001reservoir
61 %beta-octylglucoside1reservoir
72 %MPD1reservoir
850 mMMES1reservoirpH7.0

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Data collection

ReflectionNum. obs: 26328 / % possible obs: 92 %

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementHighest resolution: 1.6 Å / σ(F): 2
Details: PEPTIDE 257 - 258 IS DISCRETELY DISORDERED. THE ZONE 256 - 259 WAS REFINED IN TWO DISTINCT CONFORMATIONS. ATOMS CD, CE, AND NZ OF LYS 256 ARE FURTHER DISORDERED, SO THEIR OCCUPANCIES DO NOT SUM TO 1.0.
RfactorNum. reflection
obs0.168 26220
Displacement parametersBiso mean: 13.5 Å2
Refinement stepCycle: LAST / Highest resolution: 1.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2018 0 12 194 2224
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.020.021
X-RAY DIFFRACTIONp_angle_d0.0340.027
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0460.04
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.1361
X-RAY DIFFRACTIONp_mcangle_it1.7771.5
X-RAY DIFFRACTIONp_scbond_it1.6321
X-RAY DIFFRACTIONp_scangle_it2.5071.5
X-RAY DIFFRACTIONp_plane_restr0.0290.03
X-RAY DIFFRACTIONp_chiral_restr0.2190.25
X-RAY DIFFRACTIONp_singtor_nbd0.4280.2
X-RAY DIFFRACTIONp_multtor_nbd0.3550.2
X-RAY DIFFRACTIONp_xhyhbond_nbd0.1950.2
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor4.73
X-RAY DIFFRACTIONp_staggered_tor15.815
X-RAY DIFFRACTIONp_orthonormal_tor4520
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Lowest resolution: 8 Å / Rfactor obs: 0.17 / Rfactor Rwork: 0.168
Solvent computation
*PLUS
Displacement parameters
*PLUS

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