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- PDB-1au9: SUBTILISIN BPN' MUTANT 8324 IN CITRATE -

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Basic information

Entry
Database: PDB / ID: 1au9
TitleSUBTILISIN BPN' MUTANT 8324 IN CITRATE
ComponentsSUBTILISIN BPN'
KeywordsSERINE PROTEASE / HYDROLASE
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 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 ...: / Fervidolysin N-terminal prodomain / Subtilisin Carlsberg-like catalytic domain / 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
ISOPROPYL ALCOHOL / Subtilisin BPN'
Similarity search - Component
Biological speciesBacillus amyloliquefaciens (bacteria)
MethodX-RAY DIFFRACTION / DIFFERENCE MAP / Resolution: 1.8 Å
AuthorsWhitlow, M. / Howard, A.J. / Wood, J.F.
Citation
Journal: Biochemistry / Year: 1989
Title: Large increases in general stability for subtilisin BPN' through incremental changes in the free energy of unfolding.
Authors: Pantoliano, M.W. / Whitlow, M. / Wood, J.F. / Dodd, S.W. / Hardman, K.D. / Rollence, M.L. / Bryan, P.N.
#1: Journal: Biochemistry / Year: 1988
Title: The Engineering of Binding Affinity at Metal Ion Binding Sites for the Stabilization of Proteins: Subtilisin as a Test Case
Authors: Pantoliano, M.W. / Whitlow, M. / Wood, J.F. / Rollence, M.L. / Finzel, B.C. / Gilliland, G.L. / Poulos, T.L. / Bryan, P.N.
#2: Journal: Biochemistry / Year: 1987
Title: Protein Engineering of Subtilisin Bpn': Enhanced Stabilization Through the Introduction of Two Cysteines to Form a Disulfide Bond
Authors: Pantoliano, M.W. / Ladner, R.C. / Bryan, P.N. / Rollence, M.L. / Wood, J.F. / Poulos, T.L.
#3: Journal: Proteins / Year: 1986
Title: Proteases of Enhanced Stability: Characterization of a Thermostable Variant of Subtilisin
Authors: Bryan, P.N. / Rollence, M.L. / Pantoliano, M.W. / Wood, J. / Finzel, B.C. / Gilliland, G.L. / Howard, A.J. / Poulos, T.L.
#4: Journal: Biochem.Biophys.Res.Commun. / Year: 1971
Title: Atomic Coordinates for Subtilisin Bpn' (or Novo)
Authors: Alden, R.A. / Birktoft, J.J. / Kraut, J. / Robertus, J.D. / Wright, C.S.
History
DepositionSep 12, 1997Processing site: BNL
Revision 1.0Dec 31, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...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_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.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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 25, 2024Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature / pdbx_validate_close_contact / struct_conn

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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)27,7157
Polymers27,5151
Non-polymers2006
Water3,585199
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.640, 79.450, 37.260
Angle α, β, γ (deg.)90.00, 114.53, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein SUBTILISIN BPN'


Mass: 27514.631 Da / Num. of mol.: 1 / Mutation: T22C, M50F, S87C, G169A, Q206C, Y217K, N218S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus amyloliquefaciens (bacteria) / Strain: GX8324 / Cellular location: SECRETED / Plasmid: PGX8324 / Production host: Bacillus subtilis (bacteria) / Strain (production host): GX8324 / References: UniProt: P00782, subtilisin
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 2 / Source method: obtained synthetically
#4: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 199 / 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: 2.04 Å3/Da / Density % sol: 39.61 %
Crystal growMethod: vapor diffusion / pH: 9
Details: CRYSTAL WERE GROWN BY VAPOR DIFFUSION OF 10 MG/ML PROTEIN IN 50 MM GLYCINE PH 9.0, 10 MM CITRATE AGAINST 10% 2-PROPANOL., vapor diffusion
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Details: Bryan, P.N., (1986) Proteins: Struct.,Funct., Genet., 1, 326.
Components of the solutions
*PLUS
Conc.: 55 % / Common name: acetone

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Data collection

DiffractionMean temperature: 290 K
Diffraction sourceSource: ROTATING ANODE / Type: ELLIOTT GX-21 / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Jul 30, 1987
RadiationMonochromator: HUBER MONOCHROMATOR / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.72→10 Å / Num. obs: 19553 / % possible obs: 84.4 % / Observed criterion σ(I): 2 / Redundancy: 3.37 % / Rsym value: 0.0496 / Net I/σ(I): 18.8
Reflection shellResolution: 1.72→1.86 Å / Mean I/σ(I) obs: 2.95 / Rsym value: 0.2531 / % possible all: 49.9

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Processing

Software
NameClassification
XENGENdata collection
XENGENdata reduction
PROLSQ/PROFFTmodel building
PROFFTrefinement
PROLSQrefinement
XENGENdata scaling
RefinementMethod to determine structure: DIFFERENCE MAP / Resolution: 1.8→10 Å / σ(F): 2 /
RfactorNum. reflection
Rwork0.151 -
all-19553
obs-17446
Refinement stepCycle: LAST / Resolution: 1.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1947 0 4 207 2158
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.020.03
X-RAY DIFFRACTIONp_angle_d0.0280.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0390.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it0.6161
X-RAY DIFFRACTIONp_mcangle_it1.0212
X-RAY DIFFRACTIONp_scbond_it1.7112
X-RAY DIFFRACTIONp_scangle_it2.5054
X-RAY DIFFRACTIONp_plane_restr0.0190.03
X-RAY DIFFRACTIONp_chiral_restr0.20.3
X-RAY DIFFRACTIONp_singtor_nbd0.1610.2
X-RAY DIFFRACTIONp_multtor_nbd0.130.2
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.130.2
X-RAY DIFFRACTIONp_planar_tor3.57.5
X-RAY DIFFRACTIONp_staggered_tor11.410
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor30.310
X-RAY DIFFRACTIONp_special_tor13.47.5
Software
*PLUS
Name: PROFFT / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.151
Solvent computation
*PLUS
Displacement parameters
*PLUS

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