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- PDB-3bx1: Complex between the Barley alpha-Amylase/Subtilisin Inhibitor and... -

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Basic information

Entry
Database: PDB / ID: 3bx1
TitleComplex between the Barley alpha-Amylase/Subtilisin Inhibitor and the subtilisin Savinase
Components
  • Alpha-amylase/subtilisin inhibitor
  • Subtilisin Savinase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Complex (Proteinase-Inhibitor) Enzyme inhibition / Savinase / Barley alpha-Amylase/Subtilisin Inhibitor / Calcium / Hydrolase / Metal-binding / Protease / Secreted / Serine protease / Sporulation / Alpha-amylase inhibitor / Protease inhibitor / Serine protease inhibitor / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Function / homology
Function and homology information


alpha-amylase inhibitor activity / subtilisin / sporulation resulting in formation of a cellular spore / serine-type endopeptidase inhibitor activity / serine-type endopeptidase activity / proteolysis / extracellular region / metal ion binding
Similarity search - Function
Soybean trypsin inhibitor (Kunitz) protease inhibitors family signature. / Proteinase inhibitor I3, Kunitz legume / Trypsin and protease inhibitor / Soybean trypsin inhibitor (Kunitz) family of protease inhibitors / Subtilisin Carlsberg-like catalytic domain / Kunitz inhibitor STI-like 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. ...Soybean trypsin inhibitor (Kunitz) protease inhibitors family signature. / Proteinase inhibitor I3, Kunitz legume / Trypsin and protease inhibitor / Soybean trypsin inhibitor (Kunitz) family of protease inhibitors / Subtilisin Carlsberg-like catalytic domain / Kunitz inhibitor STI-like 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 / Serine proteases, subtilase domain profile. / Peptidase S8, subtilisin-related / Peptidase S8/S53 domain superfamily / Subtilase family / Peptidase S8/S53 domain / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Alpha-amylase/subtilisin inhibitor / Subtilisin Savinase
Similarity search - Component
Biological speciesBacillus lentus (bacteria)
Hordeum vulgare (barley)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsMicheelsen, P.O. / Vevodova, J. / Wilson, K. / Skjot, M.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Structural and Mutational Analyses of the Interaction between the Barley alpha-Amylase/Subtilisin Inhibitor and the Subtilisin Savinase Reveal a Novel Mode of Inhibition
Authors: Micheelsen, P.O. / Vevodova, J. / De Maria, L. / Ostergaard, P.R. / Friis, E.P. / Wilson, K. / Skjot, M.
History
DepositionJan 11, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 8, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / 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_asym_id / _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_asym_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_asym_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_asym_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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_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

Downloads & links

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Assembly

Deposited unit
A: Subtilisin Savinase
B: Subtilisin Savinase
D: Alpha-amylase/subtilisin inhibitor
C: Alpha-amylase/subtilisin inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,40338
Polymers93,2534
Non-polymers1,14934
Water10,341574
1
A: Subtilisin Savinase
C: Alpha-amylase/subtilisin inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,33123
Polymers46,6272
Non-polymers70421
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3990 Å2
ΔGint-165.4 kcal/mol
Surface area17550 Å2
MethodPISA
2
B: Subtilisin Savinase
D: Alpha-amylase/subtilisin inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,07215
Polymers46,6272
Non-polymers44513
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3170 Å2
ΔGint-120.9 kcal/mol
Surface area17260 Å2
MethodPISA
3
A: Subtilisin Savinase
B: Subtilisin Savinase
D: Alpha-amylase/subtilisin inhibitor
C: Alpha-amylase/subtilisin inhibitor
hetero molecules

A: Subtilisin Savinase
B: Subtilisin Savinase
D: Alpha-amylase/subtilisin inhibitor
C: Alpha-amylase/subtilisin inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)188,80576
Polymers186,5078
Non-polymers2,29868
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/21
Buried area27710 Å2
ΔGint-724.8 kcal/mol
Surface area56240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.637, 100.637, 216.242
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11D
21C
31D
41C
51D
61C
71D
81C
12A
22B

NCS domain segments:

Refine code: 4

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ASPASPGLYGLYDC10 - 3010 - 30
211ASPASPGLYGLYCD10 - 3010 - 30
321PHEPHEALAALADC46 - 12546 - 125
421PHEPHEALAALACD46 - 12546 - 125
531METMETGLYGLYDC142 - 152142 - 152
631METMETGLYGLYCD142 - 152142 - 152
741GLYGLYLYSLYSDC165 - 177165 - 177
841GLYGLYLYSLYSCD165 - 177165 - 177
112PROPROALAALAAA5 - 2705 - 264
212PROPROALAALABB5 - 2705 - 264

NCS ensembles :
ID
1
2

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Components

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Protein , 2 types, 4 molecules ABDC

#1: Protein Subtilisin Savinase / Alkaline protease


Mass: 26718.381 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus lentus (bacteria) / Production host: Bacillus subtilis (bacteria) / References: UniProt: P29600, subtilisin
#2: Protein Alpha-amylase/subtilisin inhibitor / BASI


Mass: 19908.314 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hordeum vulgare (barley) / Production host: Pichia pastoris (fungus) / References: UniProt: P07596

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Non-polymers , 4 types, 608 molecules

#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Chemical...
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 574 / 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: 2.94 Å3/Da / Density % sol: 58.1 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.1 M sodium acetate buffer pH 5.6 and 4 M NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 291 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.004 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 18, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.004 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. all: 95850 / Num. obs: 84089 / % possible obs: 87.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 27 Å2 / Rmerge(I) obs: 0.105 / Rsym value: 0.076 / Net I/σ(I): 16.3
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.471 / Mean I/σ(I) obs: 1.6 / Num. unique all: 3898 / Rsym value: 0.415 / % possible all: 41.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQuantumdata collection
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 1AVA and 1SVN

1ava

1svn


Resolution: 1.85→35.11 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.939 / SU B: 3.22 / SU ML: 0.096 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.15 / ESU R Free: 0.142 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23894 4208 5 %RANDOM
Rwork0.2019 ---
obs0.20379 79404 87.3 %-
all-83612 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.31 Å2
Baniso -1Baniso -2Baniso -3
1-0.81 Å20 Å20 Å2
2--0.81 Å20 Å2
3----1.61 Å2
Refinement stepCycle: LAST / Resolution: 1.85→35.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6620 0 34 574 7228
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0216791
X-RAY DIFFRACTIONr_angle_refined_deg1.9151.9379287
X-RAY DIFFRACTIONr_dihedral_angle_1_deg13.9015921
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.83223.718277
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.22215963
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.941541
X-RAY DIFFRACTIONr_chiral_restr0.1650.21029
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025315
X-RAY DIFFRACTIONr_nbd_refined0.2390.23257
X-RAY DIFFRACTIONr_nbtor_refined0.3120.24558
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1670.2453
X-RAY DIFFRACTIONr_metal_ion_refined0.1480.226
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2870.290
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3350.225
X-RAY DIFFRACTIONr_mcbond_it1.0391.54485
X-RAY DIFFRACTIONr_mcangle_it1.84727166
X-RAY DIFFRACTIONr_scbond_it2.6932368
X-RAY DIFFRACTIONr_scangle_it4.0994.52108
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1D961medium positional0.610.5
2A1829medium positional0.230.5
1D961medium thermal2.592
2A1829medium thermal3.352
LS refinement shellResolution: 1.85→1.895 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.253 120 -
Rwork0.29 2499 -
obs-2499 37.46 %

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