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- PDB-5fax: Structure of subtilase SubHal from Bacillus halmapalus -

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Basic information

Entry
Database: PDB / ID: 5fax
TitleStructure of subtilase SubHal from Bacillus halmapalus
ComponentsSubtilase SubHal from Bacillus halmapalus
KeywordsHYDROLASE / Protease / Subtilase / Calcium binding
Function / homology
Function and homology information


3.4.21.14 / serine-type endopeptidase activity / proteolysis / metal ion binding
Similarity search - Function
TagA/B/C/D, peptidase domain / Jelly Rolls - #380 / : / 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 ...TagA/B/C/D, peptidase domain / Jelly Rolls - #380 / : / 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 / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Subtilase SubHal from Bacillus halmapalus
Similarity search - Component
Biological speciesBacillus halmapalus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 12, 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 / struct_conn
Item: _citation.journal_abbrev / _database_2.pdbx_DOI ..._citation.journal_abbrev / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 1.2Jan 10, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
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: Subtilase SubHal from Bacillus halmapalus
B: Subtilase SubHal from Bacillus halmapalus
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,9548
Polymers90,7142
Non-polymers2406
Water11,926662
1
A: Subtilase SubHal from Bacillus halmapalus
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4774
Polymers45,3571
Non-polymers1203
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Subtilase SubHal from Bacillus halmapalus
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4774
Polymers45,3571
Non-polymers1203
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.224, 99.935, 96.749
Angle α, β, γ (deg.)90.00, 103.52, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Subtilase SubHal from Bacillus halmapalus


Mass: 45356.980 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: N-terminal asparagine is naturally modified to N-carboxyasparagine. There is no associated Uniprot entry, however 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: Chemical
ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 662 / 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: 2.36 Å3/Da / Density % sol: 47.8 % / Description: Elongated plates
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Protein concentration 24 mg ml-1 in 50 mM sodium cacodylate buffer, pH 6.5, 2 mM CaCl2 and 100 mM NaCl. The enzyme was crystallised by hanging drop vapour diffusion in drops containing 1 ...Details: Protein concentration 24 mg ml-1 in 50 mM sodium cacodylate buffer, pH 6.5, 2 mM CaCl2 and 100 mM NaCl. The enzyme was crystallised by hanging drop vapour diffusion in drops containing 1 microliter of protein and 1 microliter of reservoir solution over 0.5 ml of reservoir: Hampton Screen 2 no. 23 (10% dioxane, 0.1 M 2-(N-Morpholino)-ethanesulphonic acid (MES) buffer, pH 6.5, 1.6 M ammonium sulphate). Clusters of elongated plates appeared after several days.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 1, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. all: 41891 / Num. obs: 41891 / % possible obs: 74 % / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Biso Wilson estimate: 13.2 Å2 / Rmerge(I) obs: 0.101 / Net I/σ(I): 6
Reflection shellResolution: 2→2.05 Å / Rmerge(I) obs: 0.268 / Mean I/σ(I) obs: 2.4 / % possible all: 49.1

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
SCALEPACK1.97.2data scaling
MOLREPphasing
XFITmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Complex of SubHal with CI2A inhibitor, PDB ID 5FBZ

5fbz


Resolution: 2→30 Å / Cor.coef. Fo:Fc: 0.888 / SU B: 3.193 / SU ML: 0.097 / Cross valid method: FREE R-VALUE / σ(F): 0 / ESU R: 0.342 / ESU R Free: 0.287 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.303 2140 5.1 %Random selection
Rwork0.215 ---
obs0.21522 41891 74.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 14.77 Å2
Baniso -1Baniso -2Baniso -3
1--0.21 Å20 Å2-0.51 Å2
2--0.87 Å20 Å2
3----0.91 Å2
Refinement stepCycle: 1 / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6394 0 6 662 7062
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0216536
X-RAY DIFFRACTIONr_bond_other_d0.0020.025702
X-RAY DIFFRACTIONr_angle_refined_deg1.6781.9328913
X-RAY DIFFRACTIONr_angle_other_deg0.951313270
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.655864
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1010.2997
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.027572
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021290
X-RAY DIFFRACTIONr_nbd_refined0.2080.21634
X-RAY DIFFRACTIONr_nbd_other0.2430.27449
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0880.23833
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2240.2496
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1270.217
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1380.215
X-RAY DIFFRACTIONr_symmetry_vdw_other0.310.259
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2680.225
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7631.54283
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.16426849
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.04132251
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.8274.52064
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: 2→2.052 Å
RfactorNum. reflection% reflection
Rfree0.33 104 4.8 %
Rwork0.199 2155 -

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