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Basic information

Entry
Database: PDB / ID: 5aqe
TitleCooperative bio-metallic selectivity in a tailored protease enables creation of a C-C cross-coupling Heckase
ComponentsSUBTILISIN SAVINASE
KeywordsHYDROLASE / PROTEASE / SUBTILISIN / CATALYSIS / PALLADIUM / METALLOENZYME / HECK REACTION / CROSS-COUPLING
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 / Peptidase S8, subtilisin-related ...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 / 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
(4-VINYLPHENYL)METHANESULFONIC ACID / Subtilisin Savinase
Similarity search - Component
Biological speciesBACILLUS LENTUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å
AuthorsSharma, M. / Diaz-Rodriguez, A. / Offen, W.A. / Palm-Espling, M.E. / Pordea, A. / Wormald, M.R. / Mcdonough, M. / Davies, G.J. / Davis, B.G.
CitationJournal: To be Published
Title: Bisubstrate Localisation by a Tailored Serine Protease Allows Creation of a Heck-Ase
Authors: Sharma, M. / Diaz-Rodriguez, A. / Offen, W.A. / Pordea, A. / Wormald, M.R. / Mcdonough, M. / Davies, G.J. / Davis, B.G.
History
DepositionSep 22, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 7, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SUBTILISIN SAVINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,2727
Polymers26,7181
Non-polymers5546
Water7,981443
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.648, 61.246, 74.615
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein SUBTILISIN SAVINASE / ALKALINE PROTEASE / SUBTILISIN


Mass: 26718.381 Da / Num. of mol.: 1 / Fragment: MATURE PEPTIDE CHAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACILLUS LENTUS (bacteria) / Production host: BACILLUS SUBTILIS (bacteria) / References: UniProt: P29600, subtilisin

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Non-polymers , 6 types, 449 molecules

#2: Chemical ChemComp-VOD / (4-VINYLPHENYL)METHANESULFONIC ACID


Mass: 198.239 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H10O3S
#3: Chemical ChemComp-SO4 / SULFATE ION


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


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


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 443 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsSEQUENCE IS SAME FOR DEPOSITED COORDINATES BUT NUMBERING IS NON- CONTIGUOUS AS IT IS BASED ON ...SEQUENCE IS SAME FOR DEPOSITED COORDINATES BUT NUMBERING IS NON- CONTIGUOUS AS IT IS BASED ON ALIGNMENT TO AN HOMOLOGOUS SECTION OF UNIPROT SEQUENCE P00782 FOR SUBTILISIN BPN' FROM BACILLUS AMYLOLIQUEFACIENS, RESIDUES 108 TO 382. THUS THERE ARE NO RESIDUES 36, 58, 158-159 OR 163-164.

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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: 2.25 Å3/Da / Density % sol: 45 % / Description: NONE
Crystal growDetails: 9% PEG 3350, 50 MM AMMONIUM SULFATE, 0.1 M BIS-TRIS PH 5.5

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763
DetectorType: ADSC CCD / Detector: CCD / Date: May 26, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.1→43.02 Å / Num. obs: 96307 / % possible obs: 98 % / Observed criterion σ(I): 2 / Redundancy: 6.3 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 33.3
Reflection shellResolution: 1.1→1.12 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.06 / Mean I/σ(I) obs: 17.9 / % possible all: 92

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Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GCI

1gci


Resolution: 1.1→47.34 Å / Cor.coef. Fo:Fc: 0.986 / Cor.coef. Fo:Fc free: 0.985 / SU B: 0.309 / SU ML: 0.007 / Cross valid method: THROUGHOUT / ESU R: 0.017 / ESU R Free: 0.017 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 4-VINYLPHENYL METHANESULFONYL IS MODELLED WITH THE C ATOMS AT AN OCCUPANCY OF 0.5 AND THE SULFONYL GROUP AT AN OCCUPANCY OF 0.75. THE SIDE ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 4-VINYLPHENYL METHANESULFONYL IS MODELLED WITH THE C ATOMS AT AN OCCUPANCY OF 0.5 AND THE SULFONYL GROUP AT AN OCCUPANCY OF 0.75. THE SIDE CHAIN OF HIS64 IS MODELLED WITH A SECOND ORIENTATION AT OCCUPANCY 0.15 BECAUSE THERE IS DIFFERENCE DENSITY IN THAT REGION IN AN FO-FC MAP IF THE SECOND CONFORMATION IS OMITTED. THERE IS UNMODELLED ELECTRON DENSITY BETWEEN THE SIDE CHAINS OF ASN155, PHE189 AND ASN218. THERE ARE 2 REGIONS OF UNMODELLED DENSITY EITHER SIDE OF THE SIDE CHAIN OF SER56, NEAR THE SIDE CHAINS OF GLU54 AND THR57. THERE IS UNMODELLED DENSITY AROUND ARG275, WHICH IS PARTIALLY OCCUPIED. THERE IS ONLY ONE CA ION, ALTHOUGH THE GENERAL ANNOTATION FOR UNIPROT ENTRY P29600 COMMENTS THAT 2 CALCIUM IONS BIND PER SUBUNIT.
RfactorNum. reflection% reflectionSelection details
Rfree0.0877 4790 5 %RANDOM
Rwork0.0764 ---
obs0.07697 91447 97.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 6.388 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20 Å20 Å2
2---0.08 Å20 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.1→47.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1880 0 31 443 2354
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0192120
X-RAY DIFFRACTIONr_bond_other_d0.0040.021966
X-RAY DIFFRACTIONr_angle_refined_deg1.7851.9472909
X-RAY DIFFRACTIONr_angle_other_deg1.08534527
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0115302
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.51824.93375
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.24415298
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.123159
X-RAY DIFFRACTIONr_chiral_restr0.1080.2338
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212566
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02487
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_it0.5740.4361172
X-RAY DIFFRACTIONr_mcbond_other0.570.4351171
X-RAY DIFFRACTIONr_mcangle_it0.7710.6651480
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.0330.57948
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_restr2.32134086
X-RAY DIFFRACTIONr_sphericity_free23.3775107
X-RAY DIFFRACTIONr_sphericity_bonded5.28354410
LS refinement shellResolution: 1.1→1.129 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.067 333 -
Rwork0.049 6233 -
obs--91.77 %

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