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- PDB-1gci: THE 0.78 ANGSTROMS STRUCTURE OF A SERINE PROTEASE-BACILLUS LENTUS... -

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Basic information

Entry
Database: PDB / ID: 1gci
TitleTHE 0.78 ANGSTROMS STRUCTURE OF A SERINE PROTEASE-BACILLUS LENTUS SUBTILISIN
ComponentsSUBTILISIN
KeywordsSERINE PROTEASE / SUBTILISIN / BACILLUS LENTUS / HYDROLASE
Function / homology
Function and homology information


subtilisin / sporulation resulting in formation of a cellular spore / serine-type endopeptidase activity / proteolysis / extracellular region / 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 / Serine proteases, subtilase domain profile. ...: / 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 / Serine proteases, subtilase domain profile. / Peptidase S8, subtilisin-related / Peptidase S8/S53 domain superfamily / Subtilase family / Peptidase S8/S53 domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesBacillus lentus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.78 Å
AuthorsBott, R. / Kuhn, P.
CitationJournal: Biochemistry / Year: 1998
Title: The 0.78 A structure of a serine protease: Bacillus lentus subtilisin.
Authors: Kuhn, P. / Knapp, M. / Soltis, S.M. / Ganshaw, G. / Thoene, M. / Bott, R.
History
DepositionSep 2, 1998Processing site: BNL
Revision 1.0Oct 21, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...database_2 / 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_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.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
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SUBTILISIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,9875
Polymers26,7181
Non-polymers2684
Water6,918384
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.650, 61.250, 74.750
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein SUBTILISIN


Mass: 26718.381 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus lentus (bacteria) / Production host: Bacillus subtilis (bacteria) / References: UniProt: P29600, subtilisin
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 384 / Source method: isolated from a natural source / Formula: H2O

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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: 2.31 Å3/Da / Density % sol: 47 %
Crystal growpH: 5.9 / Details: FREE TEXT GOES HERE., pH 5.9
Crystal grow
*PLUS
Temperature: 37 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
125 mg/mlprotein1drop
250 mMsodium acetate1drop
310 mM1dropCaCl2
530-33 %satammonium sulfate1reservoir
4inhibitor1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.77
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jun 10, 1997 / Details: MIRROR
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.77 Å / Relative weight: 1
ReflectionResolution: 0.78→35 Å / Num. obs: 257583 / % possible obs: 97.3 % / Observed criterion σ(I): 1 / Redundancy: 3.8 % / Rmerge(I) obs: 0.036 / Rsym value: 0.041 / Net I/σ(I): 5.8
Reflection shellResolution: 0.78→0.82 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 2.6 / Rsym value: 0.29 / % possible all: 92.7
Reflection
*PLUS
Num. measured all: 795681
Reflection shell
*PLUS
% possible obs: 92.7 %

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Processing

Software
NameVersionClassification
SHELXLrefinement
PROLSQrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JEA

1jea


Resolution: 0.78→35 Å / Cross valid method: FREE R / σ(F): 0
Details: AMIDE HYDROGEN BOND LENGTHS IN THE PRESENT MODEL CLUSTER ABOUT 0.86 ANGSTROMS AND AROMATIC CARBON HYDROGEN DISTANCES CLUSTER ABOUT 0.96 ANGSTROMS. THESE DISTANCES SHOULD BE REGARDED AS ...Details: AMIDE HYDROGEN BOND LENGTHS IN THE PRESENT MODEL CLUSTER ABOUT 0.86 ANGSTROMS AND AROMATIC CARBON HYDROGEN DISTANCES CLUSTER ABOUT 0.96 ANGSTROMS. THESE DISTANCES SHOULD BE REGARDED AS PRELIMINARY RESULTS, PENDING FURTHER ANALYSIS. RESIDUE PRO 168 IS A CIS PROLINE. RESIDUE CA 276 CA IS A CALCIUM ++ ION RESIDUE CA 277 CA REFINED AS CALCIUM ++ ION HAS LOW OCCUPANCY AND IS PROBABLY ANOTHER CATION, POSSIBLY POTASSIUM RESIDUE SO4 278 IS A SULFATE ION. RESIDUE GOL 301 IS A GLYCEROL MOLECULE. A SPECIAL HYDROGEN BOND EXISTS BETWEEN ASP 32 OD2 AND HIS 64 ND1. THIS HYDROGEN ATOM IS SHARED BETWEEN THESE RESIDUES. THE POSITION IS ESTIMATED FROM THE PEAK FOR THIS ATOM IN A FO-FC DIFFERENCE ELECTRON DENSITY MAP. THIS HYDROGEN ATOM HAS BEEN DESIGNATED AS HD1 OF HIS 64 TO CONFORM TO THE PDB NOMENCLATURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.1026 12879 5 %SHELXL -20
all0.1014 257583 --
obs0.0993 -97.3 %-
Refine analyzeNum. disordered residues: 16
Refinement stepCycle: LAST / Resolution: 0.78→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1880 0 13 384 2277
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.012
X-RAY DIFFRACTIONs_angle_d
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes
X-RAY DIFFRACTIONs_zero_chiral_vol
X-RAY DIFFRACTIONs_non_zero_chiral_vol
X-RAY DIFFRACTIONs_anti_bump_dis_restr
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt
X-RAY DIFFRACTIONs_approx_iso_adps

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