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- PDB-1af0: SERRATIA PROTEASE IN COMPLEX WITH INHIBITOR -

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Basic information

Entry
Database: PDB / ID: 1af0
TitleSERRATIA PROTEASE IN COMPLEX WITH INHIBITOR
ComponentsSERRATIA PROTEASE
KeywordsHYDROLASE/HYDROLASE INHIBITOR / METALLOPROTEASE / SERRALYSIN / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


serralysin / symbiont-mediated killing of host cell / extracellular matrix / metalloendopeptidase activity / toxin activity / calcium ion binding / proteolysis / extracellular space / extracellular region / zinc ion binding
Similarity search - Function
Peptidase M10B / Serralysin-like metallopeptidase domain / Peptidase M10 serralysin, C-terminal / Peptidase M10 serralysin C terminal / Serralysin-like metalloprotease, C-terminal / 2 Solenoid / Alkaline Protease, subunit P, domain 1 / Hemolysin-type calcium-binding conserved site / Hemolysin-type calcium-binding region signature. / RTX calcium-binding nonapeptide repeat ...Peptidase M10B / Serralysin-like metallopeptidase domain / Peptidase M10 serralysin, C-terminal / Peptidase M10 serralysin C terminal / Serralysin-like metalloprotease, C-terminal / 2 Solenoid / Alkaline Protease, subunit P, domain 1 / Hemolysin-type calcium-binding conserved site / Hemolysin-type calcium-binding region signature. / RTX calcium-binding nonapeptide repeat / RTX calcium-binding nonapeptide repeat (4 copies) / Serralysin-like metalloprotease, C-terminal / Peptidase M10, metallopeptidase / Matrixin / Peptidase, metallopeptidase / Zinc-dependent metalloprotease / Collagenase (Catalytic Domain) / Collagenase (Catalytic Domain) / Metallopeptidase, catalytic domain superfamily / Neutral zinc metallopeptidases, zinc-binding region signature. / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
CBZ-LEU-ALA-NHOH / Chem-0Z9 / Serralysin
Similarity search - Component
Biological speciesSerratia marcescens (bacteria)
MethodX-RAY DIFFRACTION / DIFFERENCE FOURIER / Resolution: 1.8 Å
AuthorsBaumann, U.
Citation
Journal: To be Published
Title: Crystal Structure of the 50 kDa Metallo Protease from S. Marcescens in Complex with the Synthetic Inhibitor Cbz-Leu-Ala-Nhoh
Authors: Baumann, U.
#1: Journal: J.Mol.Biol. / Year: 1995
Title: Crystal Structure of a Complex between Serratia Marcescens Metallo-Protease and an Inhibitor from Erwinia Chrysanthemi
Authors: Baumann, U. / Bauer, M. / Letoffe, S. / Delepelaire, P. / Wandersman, C.
#2: Journal: J.Mol.Biol. / Year: 1994
Title: Crystal Structure of the 50 kDa Metallo Protease from Serratia Marcescens
Authors: Baumann, U.
#3: Journal: Embo J. / Year: 1993
Title: Three-Dimensional Structure of the Alkaline Protease of Pseudomonas Aeruginosa: A Two-Domain Protein with a Calcium Binding Parallel Beta Roll Motif
Authors: Baumann, U. / Wu, S. / Flaherty, K.M. / Mckay, D.B.
#4: Journal: Biochemistry / Year: 1997
Title: Kinetic characterization of the serralysins: a divergent catalytic mechanism pertaining to astacin-type metalloproteases.
Authors: Mock, W.L. / Yao, J.
History
DepositionMar 20, 1997Processing site: BNL
Revision 1.0Mar 25, 1998Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.3Dec 12, 2012Group: Other
Revision 1.4Aug 2, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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_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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 650 HELIX DETERMINATION METHOD: TAKEN FROM PDB ENTRY 1SAT
Remark 700 SHEET DETERMINATION METHOD: TAKEN FROM PDB ENTRY 1SAT

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SERRATIA PROTEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,11110
Polymers50,4131
Non-polymers6979
Water3,711206
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)151.000, 109.200, 42.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein SERRATIA PROTEASE


Mass: 50413.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: PURCHASED FROM SIGMA / Source: (natural) Serratia marcescens (bacteria) / Strain: NOT KNOWN, PROBABLY SM6 / References: UniProt: P23694, serralysin
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-0Z9 / N-[(benzyloxy)carbonyl]-L-leucyl-N-hydroxy-L-alaninamide


Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 351.398 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H25N3O5 / References: CBZ-LEU-ALA-NHOH
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 206 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsTHERE IS A DISORDERED N-CARBO-BENZYLOXY GROUP IN THIS STRUCTURE THAT IS ATTACHED TO LEU B 674. NO ...THERE IS A DISORDERED N-CARBO-BENZYLOXY GROUP IN THIS STRUCTURE THAT IS ATTACHED TO LEU B 674. NO COORDINATES ARE GIVEN FOR THIS GROUP.

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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: 3.53 Å3/Da / Density % sol: 62 %
Crystal growpH: 6.5 / Details: 0.2 M AMMONIUM SULFATE, 20%PEG 4K, PH 6.5

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Data collection

DiffractionMean temperature: 290 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 1, 1995 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→25 Å / Num. obs: 61944 / % possible obs: 93.7 % / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.058 / Rsym value: 0.058 / Net I/σ(I): 15.6
Reflection shellResolution: 1.8→1.85 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.251 / Mean I/σ(I) obs: 3.4 / Rsym value: 0.251 / % possible all: 81.7

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Processing

Software
NameClassification
SHELXLrefinement
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
SHELXrefinement
RefinementMethod to determine structure: DIFFERENCE FOURIER
Starting model: PDB ENTRY 1SAT

1sat


Resolution: 1.8→30 Å / Num. parameters: 15163 / Num. restraintsaints: 14700 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: ZN++ AND CA++ IONS REFINED ANISOTROPICALLY. THE N-CARBOBENZYLOXY GROUP OF THE INHIBITOR IS INVISIBLE.
RfactorNum. reflection% reflectionSelection details
all0.183 61935 --
obs0.242 -93.3 %-
Rfree-2382 4 %RANDOM
Solvent computationSolvent model: MOEWS & KRETSINGER
Refine analyzeOccupancy sum non hydrogen: 3780
Refinement stepCycle: LAST / Resolution: 1.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3551 0 23 206 3780
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.006
X-RAY DIFFRACTIONs_angle_d0.022
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes0.13
X-RAY DIFFRACTIONs_zero_chiral_vol0.072
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.112
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.007
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.038
X-RAY DIFFRACTIONs_approx_iso_adps

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