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- PDB-1c1m: PORCINE ELASTASE UNDER XENON PRESSURE (8 BAR) -

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Basic information

Entry
Database: PDB / ID: 1c1m
TitlePORCINE ELASTASE UNDER XENON PRESSURE (8 BAR)
ComponentsPROTEIN (PORCINE ELASTASE)
KeywordsHYDROLASE / SERINE PROTEASE / PANCREAS ELASTASE / XENON
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 / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin ...: / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / 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 / Resolution: 2.2 Å
AuthorsPrange, T. / Schiltz, M. / Pernot, L. / Colloc'h, N. / Longhi, S. / Bourguet, W. / Fourme, R.
Citation
Journal: Proteins / Year: 1998
Title: Exploring hydrophobic sites in proteins with xenon or krypton.
Authors: Prange, T. / Schiltz, M. / Pernot, L. / Colloc'h, N. / Longhi, S. / Bourguet, W. / Fourme, R.
#1: Journal: J.Synchrotron Radiat. / Year: 1997
Title: Protein Crystallography at Ultra-Short Wavelengths: Feasability Study of Anomalous-Dispersion Experiments at the Xenon K-Edge
Authors: Schiltz, M. / Kvick, A. / Svensson, O. / Shepard, W. / De La Fortelle, E. / Prange, T. / Kahn, R.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 1997
Title: High-Pressure Krypton Gas and Statistical Heavy Atom Refinement: A Successful Combination of Tools for Macromolecular Structure Determination
Authors: Schiltz, M. / Shepard, W. / Fourme, R. / Prange, T. / De La Fortelle, E. / Bricogne, G.
#3: Journal: Structure / Year: 1995
Title: The Active Site of Serine Proteinases as a Specific Binding Cavity for Xenon
Authors: Schiltz, M. / Fourme, R. / Prange, T.
#4: Journal: J.Appl.Crystallogr. / Year: 1994
Title: On the Preparation and X-Ray Data Collection of Isomorphous Xenon Derivatives
Authors: Schiltz, M. / Prange, T. / Fourme, R.
History
DepositionJul 22, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 28, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 28, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (PORCINE ELASTASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1964
Polymers25,9291
Non-polymers2673
Water2,306128
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.190, 58.220, 75.770
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 PROTEIN (PORCINE ELASTASE)


Mass: 25929.016 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: PANCREAS / References: UniProt: P00772, pancreatic elastase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-SO4 / SULFATE ION


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


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


Mass: 18.015 Da / Num. of mol.: 128 / Source method: isolated from a natural source / Formula: H2O
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: 2.22 Å3/Da / Density % sol: 44.57 %
Crystal growpH: 5.5
Details: 1.4 MG ENZYME IN 0.1 ML ACETATE BUFFER (0.05M) PLUS 0.0001 ML PRECIPITATING AGENT (SODIUM SULPHATE 1M), pH 5.50
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 5 / Method: unknown / Details: Shotton, D.M., (1968) J.Mol.Biol., 32, 155.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12 %solution of elastase11
20.01 Msodium acetate11
30.02 Msodium sulfate11

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.962
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 14, 1995
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.962 Å / Relative weight: 1
ReflectionResolution: 2.2→17.7 Å / Num. obs: 44217 / % possible obs: 93.9 % / Observed criterion σ(I): 4 / Redundancy: 4.1 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 11.4
Reflection shellResolution: 2.2→2.3 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.146 / % possible all: 64

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SHELXL-97refinement
CCP4(SCALA)data scaling
RefinementResolution: 2.2→17.7 Å / σ(F): 2 / Stereochemistry target values: ENGH & HUBER
Details: REFINED WITH A COMBINATION OF SHELXL AND WARP AUTOMATIC PROCEDURE FOR LOCALIZING AND ANALYSING THE WATER MOLECULES.
RfactorNum. reflection% reflectionSelection details
Rfree0.201 896 -RANDOM
all0.173 10937 --
obs0.162 -95 %-
Refinement stepCycle: LAST / Resolution: 2.2→17.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1822 0 7 128 1957
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.02
X-RAY DIFFRACTIONs_angle_d0.04
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes
X-RAY DIFFRACTIONs_zero_chiral_vol
X-RAY DIFFRACTIONs_non_zero_chiral_vol
X-RAY DIFFRACTIONs_anti_bump_dis_restr
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt
X-RAY DIFFRACTIONs_approx_iso_adps
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.183 / Rfactor Rwork: 0.162
Solvent computation
*PLUS
Displacement parameters
*PLUS

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