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- PDB-6dwq: Subtilisin serine protease modified with the protease inhibitor c... -

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Basic information

Entry
Database: PDB / ID: 6dwq
TitleSubtilisin serine protease modified with the protease inhibitor cyanobenzylsulfonylfluoride
ComponentsKerA
KeywordsHYDROLASE / serine protease / subtilisin
Function / homology
Function and homology information


subtilisin / serine-type endopeptidase activity / proteolysis / extracellular space / metal ion binding
Similarity search - Function
Subtilisin Carlsberg-like catalytic domain / Peptidase S8/S53 domain / Peptidase S8 propeptide/proteinase inhibitor I9 / Peptidase inhibitor I9 / Peptidase S8 propeptide/proteinase inhibitor I9 superfamily / 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. ...Subtilisin Carlsberg-like catalytic domain / Peptidase S8/S53 domain / Peptidase S8 propeptide/proteinase inhibitor I9 / Peptidase inhibitor I9 / Peptidase S8 propeptide/proteinase inhibitor I9 superfamily / 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 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NITRATE ION / Subtilisin Carlsberg / KerA
Similarity search - Component
Biological speciesBacillus licheniformis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.27 Å
AuthorsLuo, M. / Eaton, C.N. / Phillips-Piro, C.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)2R15GM093330 United States
CitationJournal: Chemistryselect / Year: 2019
Title: Paired Spectroscopic and Crystallographic Studies of Protease Active Sites
Authors: Luo, M. / Eaton, C.N. / Hess, K.R. / Phillips-Piro, C.M. / Brewer, S.H. / Fenlon, E.E.
History
DepositionJun 27, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 15, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year
Revision 1.3Oct 11, 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 / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_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_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: KerA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,50017
Polymers27,5511
Non-polymers94916
Water6,485360
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.926, 67.926, 123.481
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein KerA


Mass: 27551.430 Da / Num. of mol.: 1 / Fragment: residues 37-310 / Source method: isolated from a natural source / Source: (natural) Bacillus licheniformis (bacteria) / References: UniProt: Q9FDF2, UniProt: P00780*PLUS
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO3
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 360 / 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: 2.99 Å3/Da / Density % sol: 58.91 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 26% PEG 3350, 0.350 M NH4NO3 / PH range: 6.5 - 7.8 / Temp details: Room temperature

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 26, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.27→50 Å / Num. obs: 87671 / % possible obs: 100 % / Redundancy: 9.2 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 38.6
Reflection shellResolution: 1.27→1.29 Å / Redundancy: 6 % / Rmerge(I) obs: 0.271 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 4340 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4C3V

4c3v


Resolution: 1.27→42.589 Å / SU ML: 0.08 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 12.64
RfactorNum. reflection% reflectionSelection details
Rfree0.148 4577 5.23 %Random selection
Rwork0.122 ---
obs0.1234 87552 99.86 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.27→42.589 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1947 0 58 360 2365
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062146
X-RAY DIFFRACTIONf_angle_d1.2632925
X-RAY DIFFRACTIONf_dihedral_angle_d12.136725
X-RAY DIFFRACTIONf_chiral_restr0.085333
X-RAY DIFFRACTIONf_plane_restr0.007385
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.27-1.28410.22821270.17882723X-RAY DIFFRACTION98
1.2841-1.29920.20571580.16162701X-RAY DIFFRACTION100
1.2992-1.31510.15191470.152734X-RAY DIFFRACTION100
1.3151-1.33170.16331430.13872773X-RAY DIFFRACTION100
1.3317-1.34930.15511600.12942671X-RAY DIFFRACTION100
1.3493-1.36780.17761630.12332751X-RAY DIFFRACTION100
1.3678-1.38730.13561710.11712726X-RAY DIFFRACTION100
1.3873-1.4080.12131180.11742756X-RAY DIFFRACTION100
1.408-1.430.14851430.11262716X-RAY DIFFRACTION100
1.43-1.45350.13441550.10992762X-RAY DIFFRACTION100
1.4535-1.47850.14911680.10782734X-RAY DIFFRACTION100
1.4785-1.50540.12871440.10572766X-RAY DIFFRACTION100
1.5054-1.53440.12591600.10662706X-RAY DIFFRACTION100
1.5344-1.56570.1431250.12802X-RAY DIFFRACTION100
1.5657-1.59970.13431350.09832729X-RAY DIFFRACTION100
1.5997-1.63690.13061570.10132756X-RAY DIFFRACTION100
1.6369-1.67790.1281570.10622750X-RAY DIFFRACTION100
1.6779-1.72320.13841420.1052772X-RAY DIFFRACTION100
1.7232-1.77390.13941650.11262748X-RAY DIFFRACTION100
1.7739-1.83120.13451740.11382757X-RAY DIFFRACTION100
1.8312-1.89670.1261180.11362797X-RAY DIFFRACTION100
1.8967-1.97260.12951520.122753X-RAY DIFFRACTION100
1.9726-2.06240.1241450.11632809X-RAY DIFFRACTION100
2.0624-2.17110.1171200.11552786X-RAY DIFFRACTION100
2.1711-2.30710.14321650.11482790X-RAY DIFFRACTION100
2.3071-2.48520.14181830.11912764X-RAY DIFFRACTION100
2.4852-2.73530.14581750.1282801X-RAY DIFFRACTION100
2.7353-3.1310.15891580.12892807X-RAY DIFFRACTION100
3.131-3.94430.15971740.12112850X-RAY DIFFRACTION100
3.9443-42.5890.17541750.14492985X-RAY DIFFRACTION100

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