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- PDB-1uo6: PORCINE PANCREATIC ELASTASE/Xe-COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1uo6
TitlePORCINE PANCREATIC ELASTASE/Xe-COMPLEX
ComponentsELASTASE 1
KeywordsHYDROLASE / CHYMOTRYPSIN-FOLD / BETA-BARREL / XENON BINDING
Function / homology
Function and homology information


pancreatic elastase / serine-type endopeptidase activity / proteolysis / extracellular space / metal ion binding
Similarity search - Function
Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases ...Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
XENON / Chymotrypsin-like elastase family member 1
Similarity search - Component
Biological speciesSUS SCROFA (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsMueller-Dieckmann, C. / Polentarutti, M. / Djinovic-Carugo, K. / Panjikar, S. / Tucker, P.A. / Weiss, M.S.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2004
Title: On the Routine Use of Soft X-Rays in Macromolecular Crystallography. Part II. Data-Collection Wavelength and Scaling Models
Authors: Mueller-Dieckmann, C. / Polentarutti, M. / Djinovic-Carugo, K. / Panjikar, S. / Tucker, P.A. / Weiss, M.S.
History
DepositionSep 16, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 14, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: 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
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.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
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ELASTASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4037
Polymers25,9291
Non-polymers4746
Water3,999222
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)50.170, 58.060, 74.340
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 ELASTASE 1 /


Mass: 25929.016 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / References: UniProt: P00772, pancreatic elastase

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Non-polymers , 6 types, 228 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-XE / XENON / Xenon


Mass: 131.293 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Xe
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 222 / 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: 2.09 Å3/Da / Density % sol: 41.09 %
Crystal growpH: 5.1 / Details: SODIUM ACETATE, SODIUM SULFATE, pH 5.10
Crystal grow
*PLUS
Temperature: 293 K / pH: 5.1 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120 mg/mlprotein1drop
2100 mMsodium acetate1reservoirpH5.1
3200 mM1reservoirNa2SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 0.8
DetectorDetector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 1.65→99 Å / Num. obs: 26987 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 14.33 % / Biso Wilson estimate: 12.5 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 46.53
Reflection shellResolution: 1.65→1.69 Å / Redundancy: 7.15 % / Rmerge(I) obs: 0.089 / Mean I/σ(I) obs: 30.25 / % possible all: 100
Reflection
*PLUS
Highest resolution: 1.65 Å / Lowest resolution: 99 Å / Num. all: 386757 / % possible obs: 99.9 % / Redundancy: 14.33 % / Num. measured all: 665506 / Rmerge(I) obs: 0.053
Reflection shell
*PLUS
Lowest resolution: 1.68 Å / % possible obs: 100 % / Rmerge(I) obs: 0.089 / Mean I/σ(I) obs: 30.25

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
TRUNCATEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1LKB

1lkb


Resolution: 1.65→40 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.208 1330 5 %RANDOM
Rwork0.174 ---
obs-27003 99 %-
Refinement stepCycle: LAST / Resolution: 1.65→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1822 0 19 222 2063
Refinement
*PLUS
Rfactor Rfree: 0.206 / Rfactor Rwork: 0.176
Solvent computation
*PLUS
Displacement parameters
*PLUS

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