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- PDB-1scd: X-RAY CRYSTAL STRUCTURE OF CROSS-LINKED SUBTILISM CARLSBERG IN WA... -

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Basic information

Entry
Database: PDB / ID: 1scd
TitleX-RAY CRYSTAL STRUCTURE OF CROSS-LINKED SUBTILISM CARLSBERG IN WATER VS. ACETONITRILE
ComponentsSUBTILISIN CARLSBERG
KeywordsSERINE PROTEASE
Function / homology
Function and homology information


subtilisin / serine-type endopeptidase activity / proteolysis / extracellular space / metal ion binding
Similarity search - Function
Subtilisin Carlsberg-like catalytic domain / Peptidase S8 propeptide/proteinase inhibitor I9 / Peptidase inhibitor I9 / Peptidase S8 propeptide/proteinase inhibitor I9 superfamily / 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 ...Subtilisin Carlsberg-like catalytic domain / Peptidase S8 propeptide/proteinase inhibitor I9 / Peptidase inhibitor I9 / Peptidase S8 propeptide/proteinase inhibitor I9 superfamily / 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
Subtilisin Carlsberg
Similarity search - Component
Biological speciesBacillus licheniformis (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.3 Å
AuthorsFitzpatrick, P.A. / Ringe, D. / Klibanov, A.M.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 1994
Title: X-ray crystal structure of cross-linked subtilisin Carlsberg in water vs. acetonitrile.
Authors: Fitzpatrick, P.A. / Ringe, D. / Klibanov, A.M.
History
DepositionAug 23, 1993Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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_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.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_ref_seq_dif.details / _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 CARLSBERG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,3863
Polymers27,3061
Non-polymers802
Water2,054114
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.200, 55.800, 53.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: CIS PROLINE - PRO 168
2: PRO 210 - THR 211 OMEGA =215.36 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION

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Components

#1: Protein SUBTILISIN CARLSBERG


Mass: 27306.199 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus licheniformis (bacteria) / References: UniProt: P00780, subtilisin
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE NUMBERING USED FOR SUBTILISIN IS BASED ON THAT OF SUBTILISIN BPN' WITH A SINGLE ...THE SEQUENCE NUMBERING USED FOR SUBTILISIN IS BASED ON THAT OF SUBTILISIN BPN' WITH A SINGLE DELETION AT RESIDUE 56.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.12 Å3/Da / Density % sol: 41.9 %
Crystal
*PLUS
Density % sol: 42 %
Crystal grow
*PLUS
pH: 5.6 / Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.5 %protein11
217 %aqueous sodium sulfate11

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Data collection

Reflection
*PLUS
Highest resolution: 2.3 Å / Num. obs: 9464 / % possible obs: 86 % / Num. measured all: 39330 / Rmerge(I) obs: 0.095

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 2.3→10 Å /
RfactorNum. reflection
obs0.146 9464
Refinement stepCycle: LAST / Resolution: 2.3→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1920 0 2 114 2036
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.015
X-RAY DIFFRACTIONp_angle_d1.6
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.146
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 14 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal targetDev ideal
X-RAY DIFFRACTIONp_bond_d0.02
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg41.6
X-RAY DIFFRACTIONp_plane_restr0.0250.019

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