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- PDB-5fbz: Structure of subtilase SubHal from Bacillus halmapalus - complex ... -

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Basic information

Entry
Database: PDB / ID: 5fbz
TitleStructure of subtilase SubHal from Bacillus halmapalus - complex with chymotrypsin inhibitor CI2A
Components
  • Autoproteolytic fragment of enzyme subtilase SubHal
  • Enzyme subtilase SubHal from Bacillus halmapalus
  • Subtilisin-chymotrypsin inhibitor-2A
KeywordsHYDROLASE / Protease / Subtilase / Calcium binding / CI2A inhibitor
Function / homology
Function and homology information


3.4.21.14 / serine-type endopeptidase inhibitor activity / response to wounding / serine-type endopeptidase activity / proteolysis / metal ion binding
Similarity search - Function
TagA/B/C/D, peptidase domain / Jelly Rolls - #380 / : / Trypsin Inhibitor V, subunit A / Proteinase inhibitor I13, potato inhibitor I / Proteinase inhibitor I13, potato inhibitor I superfamily / Potato inhibitor I family / Potato inhibitor I family signature. / Trypsin Inhibitor V; Chain A / Peptidase, C-terminal, archaeal/bacterial ...TagA/B/C/D, peptidase domain / Jelly Rolls - #380 / : / Trypsin Inhibitor V, subunit A / Proteinase inhibitor I13, potato inhibitor I / Proteinase inhibitor I13, potato inhibitor I superfamily / Potato inhibitor I family / Potato inhibitor I family signature. / Trypsin Inhibitor V; Chain A / Peptidase, C-terminal, archaeal/bacterial / Bacterial pre-peptidase C-terminal domain / Peptidase S8/S53 domain / Peptidase S8, subtilisin, His-active site / Serine proteases, subtilase family, histidine 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 / Galactose-binding-like domain superfamily / Jelly Rolls / Sandwich / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Subtilase SubHal from Bacillus halmapalus / Subtilisin-chymotrypsin inhibitor-2A
Similarity search - Component
Biological speciesBacillus halmapalus (bacteria)
Hordeum vulgare (barley)
MethodX-RAY DIFFRACTION / MIR / Resolution: 1.9 Å
AuthorsDohnalek, J. / Brzozowski, A.M. / Svendsen, A. / Wilson, K.S.
CitationBook title: Understanding enzymes; Function, Design, Engineering and Analysis
Journal: Book / Year: 2016
Title: Stabilization of Enzymes by Metal Binding: Structures of Two Alkalophilic Bacillus Subtilases and Analysis of the Second Metal-Binding Site of the Subtilase Family
Authors: Dohnalek, J. / McAuley, K.E. / Brzozowski, A.M. / Oestergaard, P.R. / Svendsen, A. / Wilson, K.S.
History
DepositionDec 14, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 18, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 11, 2021Group: Database references / Derived calculations
Category: citation / database_2 ...citation / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _citation.journal_abbrev / _database_2.pdbx_DOI ..._citation.journal_abbrev / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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
Revision 2.0Jul 10, 2024Group: Data collection / Derived calculations ...Data collection / Derived calculations / Non-polymer description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / entity / struct_conn
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _entity.formula_weight / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Enzyme subtilase SubHal from Bacillus halmapalus
B: Subtilisin-chymotrypsin inhibitor-2A
C: Enzyme subtilase SubHal from Bacillus halmapalus
D: Subtilisin-chymotrypsin inhibitor-2A
E: Autoproteolytic fragment of enzyme subtilase SubHal
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,72711
Polymers107,4865
Non-polymers2406
Water19,7801098
1
A: Enzyme subtilase SubHal from Bacillus halmapalus
B: Subtilisin-chymotrypsin inhibitor-2A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,5855
Polymers53,4642
Non-polymers1203
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1860 Å2
ΔGint-46 kcal/mol
Surface area17700 Å2
MethodPISA
2
C: Enzyme subtilase SubHal from Bacillus halmapalus
D: Subtilisin-chymotrypsin inhibitor-2A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,5855
Polymers53,4642
Non-polymers1203
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1850 Å2
ΔGint-44 kcal/mol
Surface area17550 Å2
MethodPISA
3
E: Autoproteolytic fragment of enzyme subtilase SubHal


  • defined by software
  • 558 Da, 1 polymers
Theoretical massNumber of molelcules
Total (without water)5581
Polymers5581
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.387, 151.411, 64.054
Angle α, β, γ (deg.)90.00, 117.11, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Enzyme subtilase SubHal from Bacillus halmapalus


Mass: 45356.980 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The N-terminal asparagine is carbamoylated to N-carboxyasparagine, The sequence is available in patent WO 2004083362
Source: (gene. exp.) Bacillus halmapalus (bacteria) / Production host: Bacillus subtilis (bacteria) / References: UniProt: A0A182DWC7*PLUS, 3.4.21.14
#2: Protein Subtilisin-chymotrypsin inhibitor-2A / CI-2A / Chymotrypsin inhibitor CI2A


Mass: 8107.385 Da / Num. of mol.: 2 / Fragment: UNP residues 13-84
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hordeum vulgare (barley) / Production host: Escherichia coli (E. coli) / References: UniProt: P01053
#3: Protein/peptide Autoproteolytic fragment of enzyme subtilase SubHal


Mass: 557.703 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The fragment was produced probably during crystallization. The fragment length is not known.
Source: (gene. exp.) Bacillus halmapalus (bacteria) / Production host: Bacillus subtilis (bacteria) / References: 3.4.21.14
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1098 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.38 Å3/Da / Density % sol: 48.4 % / Description: Plate-like crystal
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Plate-like crystals were grown by hanging drop vapour diffusion with the drop consisting of 2 microliters of 15-20 mg/mL concentration protein, 10 mM sodium cacodylate in HCl buffer, pH 6.5 ...Details: Plate-like crystals were grown by hanging drop vapour diffusion with the drop consisting of 2 microliters of 15-20 mg/mL concentration protein, 10 mM sodium cacodylate in HCl buffer, pH 6.5 and 1 microliter of reservoir solution: 20% w/v PEG 4000, 0.1 M HEPES buffer, pH 7.5, 10% v/v isopropanol.

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.54178 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jun 9, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. all: 59477 / Num. obs: 59477 / % possible obs: 76.6 % / Observed criterion σ(I): -3 / Redundancy: 9.2 % / Biso Wilson estimate: 25.5 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 22
Reflection shellResolution: 1.9→1.93 Å / Rmerge(I) obs: 0.128 / Mean I/σ(I) obs: 5.4 / % possible all: 14.5

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
DENZOdata reduction
SCALEPACK1.9.0data scaling
SOLVEphasing
MLPHAREphasing
MOLREPphasing
XFITmodel building
RefinementMethod to determine structure: MIR / Resolution: 1.9→19.97 Å / Cor.coef. Fo:Fc: 0.966 / SU B: 1.525 / SU ML: 0.046 / Cross valid method: FREE R-VALUE / ESU R: 0.159 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.181 3005 5.1 %Random selection
Rwork0.12881 ---
obs0.125 59448 76.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.619 Å2
Baniso -1Baniso -2Baniso -3
1-0.76 Å2-0 Å2-0.6 Å2
2---0.25 Å2-0 Å2
3----0.14 Å2
Refinement stepCycle: 1 / Resolution: 1.9→19.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7491 0 6 1098 8595
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0197736
X-RAY DIFFRACTIONr_bond_other_d0.0010.027300
X-RAY DIFFRACTIONr_angle_refined_deg1.3541.94710547
X-RAY DIFFRACTIONr_angle_other_deg0.791316766
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.21251004
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.16724.661339
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.939151194
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1281545
X-RAY DIFFRACTIONr_chiral_restr0.0820.21200
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0219046
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021777
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å
RfactorNum. reflection% reflection
Rfree0.227 60 6.4 %
Rwork0.163 940 -
obs--16.49 %

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