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- PDB-1u4g: Elastase of Pseudomonas aeruginosa with an inhibitor -

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Basic information

Entry
Database: PDB / ID: 1u4g
TitleElastase of Pseudomonas aeruginosa with an inhibitor
ComponentsElastase
KeywordsHYDROLASE / x-ray structure / Elastase / inhibition / peptidase family M4
Function / homology
Function and homology information


pseudolysin / protein transport by the Sec complex / protein secretion by the type II secretion system / bacterial-type flagellum-dependent swarming motility / single-species biofilm formation / metalloendopeptidase activity / endopeptidase activity / proteolysis / extracellular region / metal ion binding
Similarity search - Function
Elastase; domain 1 - #10 / Elastase; domain 1 / PepSY domain / Peptidase propeptide and YPEB domain / : / Peptidase M4, C-terminal / FTP domain / Peptidase M4 domain / Peptidase M4 / Thermolysin metallopeptidase, catalytic domain ...Elastase; domain 1 - #10 / Elastase; domain 1 / PepSY domain / Peptidase propeptide and YPEB domain / : / Peptidase M4, C-terminal / FTP domain / Peptidase M4 domain / Peptidase M4 / Thermolysin metallopeptidase, catalytic domain / Thermolysin metallopeptidase, alpha-helical domain / Fungalysin/Thermolysin Propeptide Motif / Neutral Protease Domain 2 / Neutral Protease; domain 2 / Peptidase M4/M1, CTD superfamily / Neutral zinc metallopeptidases, zinc-binding region signature. / Roll / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsBitto, E. / McKay, D.B.
Citation
Journal: To be Published / Year: 2004
Title: Elastase of Pseudomonas aeruginosa with an inhibitor
Authors: Bitto, E. / McKay, D.B.
#1: Journal: J.Biol.Chem. / Year: 1991
Title: Three-dimensional structure of the elastase of Pseudomonas aeruginosa at 1.5-A resolution
Authors: Thayer, M.M. / Flaherty, K.M. / McKay, D.B.
#2: Journal: Biochemistry / Year: 1992
Title: Structural comparison suggests that thermolysin and related neutral proteases undergo hinge-bending motion during catalysis
Authors: Holland, D.R. / Tronrud, D.E. / Pley, H.W. / Flaherty, K.M. / Stark, W. / Jansonius, J.N. / McKay, D.B. / Matthews, B.W.
History
DepositionJul 25, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 24, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 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 / 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_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.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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Elastase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8195
Polymers33,1761
Non-polymers6434
Water4,089227
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)114.540, 114.540, 43.940
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Elastase / E.C.3.4.24.26 / Pseudolysin / Neutral metalloproteinase


Mass: 33175.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: protein from Nagase, Japan; isolated as extracellular protease from cultures of Pseudomonas aeruginosa
Source: (natural) Pseudomonas aeruginosa (bacteria) / Secretion: extracellular / References: UniProt: P14756, pseudolysin

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Non-polymers , 5 types, 231 molecules

#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.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-HPI / N-(1-CARBOXY-3-PHENYLPROPYL)PHENYLALANYL-ALPHA-ASPARAGINE


Mass: 441.477 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H27N3O6
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 227 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.31 Å3/Da / Density % sol: 46.4 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: ammonium sulfate 1 mM, inhibitor, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.965 Å
DetectorType: ADSC / Detector: CCD
RadiationMonochromator: ssrl bl 11-1 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.965 Å / Relative weight: 1
ReflectionResolution: 1.4→30 Å / Num. obs: 57704 / % possible obs: 89.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.07
Reflection shellResolution: 1.4→1.42 Å / Rsym value: 0.121 / % possible all: 73.7

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EZM

1ezm


Resolution: 1.4→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.1974 5828 10 %random
Rwork0.1804 ---
obs-57272 88.1 %-
Displacement parametersBiso mean: 11.82 Å2
Refine analyzeLuzzati coordinate error obs: 0.15 Å / Luzzati d res low obs: 1.4 Å / Luzzati sigma a obs: 0.16 Å
Refinement stepCycle: LAST / Resolution: 1.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2304 0 39 227 2570
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0052
X-RAY DIFFRACTIONc_angle_deg1.226

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