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- PDB-2bd9: Porcine pancreatic elastase complexed with beta-casomorphin-7 and... -

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Basic information

Entry
Database: PDB / ID: 2bd9
TitlePorcine pancreatic elastase complexed with beta-casomorphin-7 and Arg-Phe at pH 5.0 (50 min soak) and immersed in pH 9 buffer for 28 seconds (2nd pH jump)
ComponentsElastase-1
KeywordsHYDROLASE / SERINE PROTEINASE
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
Chymotrypsin-like elastase family member 1
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsLiu, B. / Schofield, C.J. / Wilmouth, R.C.
Citation
Journal: J.Biol.Chem. / Year: 2006
Title: Structural analyses on intermediates in serine protease catalysis
Authors: Liu, B. / Schofield, C.J. / Wilmouth, R.C.
#1: Journal: Nat.Struct.Biol. / Year: 1997
Title: Structure of a specific acyl-enzyme complex formed between beta-casomorphin-7 and porcine pancreatic elastase
Authors: Wilmouth, R.C. / Clifton, I.J. / Robinson, C.V. / Roach, P.L. / Aplin, R.T. / Westwood, N.J. / Hajdu, J. / Schofield, C.J.
#2: Journal: Nat.Struct.Biol. / Year: 2001
Title: X-ray snapshots of serine protease catalysis reveal a tetrahedral intermediate
Authors: Wilmouth, R.C. / Edman, K. / Neutze, R. / Wright, P.A. / Clifton, I.J. / Schneider, T.R. / Schofield, C.J. / Hajdu, J.
History
DepositionOct 20, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 30, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Oct 25, 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 1.5Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)26,0643
Polymers25,9281
Non-polymers1362
Water2,180121
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.380, 57.590, 74.758
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 Elastase-1


Mass: 25928.031 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 121 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHIS CONFLICT IS BASED ON THE REFERENCE 3 IN SEQUENCE DATABASE, P00772 IN SWISS-PROT.

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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: 2.13 Å3/Da / Density % sol: 42.32 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 25MM SODIUM SULPHATE, 25MM SODIUM ACETATE (PH 5.0), 25 MG/ML PPE AND 17.5 MG/ML BCM7, AND THEN SOAKED WITH ARG-PHE (2 MG) IN 250MM SODIUM ACETATE (PH 5.0) (5 MICROLITRES) FOR 50 MIN , VAPOR ...Details: 25MM SODIUM SULPHATE, 25MM SODIUM ACETATE (PH 5.0), 25 MG/ML PPE AND 17.5 MG/ML BCM7, AND THEN SOAKED WITH ARG-PHE (2 MG) IN 250MM SODIUM ACETATE (PH 5.0) (5 MICROLITRES) FOR 50 MIN , VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 127 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jul 3, 2005 / Details: OSMIC mirrors
RadiationMonochromator: OSMIC MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.9→19.87 Å / Num. obs: 17944 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 23.2 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 16.1
Reflection shellResolution: 1.9→2 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.328 / Mean I/σ(I) obs: 3 / Num. unique all: 2550 / % possible all: 99

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT1.7data extraction
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3EST

3est


Resolution: 1.9→19.87 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.939 / SU B: 7.007 / SU ML: 0.103 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.152 / ESU R Free: 0.148 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: The PPE:BCM7:ARG-PHE PH 5 (50 min soak) crystal (from which PDB files 2BD7 and 2BD8 were collected) was warmed to room temperature for a second time, immersed in 250 mm ches PH 9, 25% (v/v) ...Details: The PPE:BCM7:ARG-PHE PH 5 (50 min soak) crystal (from which PDB files 2BD7 and 2BD8 were collected) was warmed to room temperature for a second time, immersed in 250 mm ches PH 9, 25% (v/v) glycerol for 28s and refrozen. Beta-casomorphin-7 and ARG-PHE were not modelled into this structure.
RfactorNum. reflection% reflectionSelection details
Rfree0.226 914 5.1 %RANDOM
Rwork0.172 ---
all0.175 17944 --
obs0.175 17910 99.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 33.436 Å2
Baniso -1Baniso -2Baniso -3
1-2.62 Å20 Å20 Å2
2---1.01 Å20 Å2
3----1.61 Å2
Refinement stepCycle: LAST / Resolution: 1.9→19.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1802 0 6 121 1929
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0211850
X-RAY DIFFRACTIONr_angle_refined_deg1.2741.9172535
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1095239
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.84324.23178
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.28215266
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.939159
X-RAY DIFFRACTIONr_chiral_restr0.0840.2289
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021416
X-RAY DIFFRACTIONr_nbd_refined0.1920.2844
X-RAY DIFFRACTIONr_nbtor_refined0.3030.21274
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1310.2147
X-RAY DIFFRACTIONr_metal_ion_refined0.1430.25
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2350.225
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2330.212
X-RAY DIFFRACTIONr_mcbond_it2.20821210
X-RAY DIFFRACTIONr_mcangle_it2.97131902
X-RAY DIFFRACTIONr_scbond_it4.484756
X-RAY DIFFRACTIONr_scangle_it5.416633
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 67 -
Rwork0.205 1215 -
all-1282 -
obs--98.69 %
Refinement TLS params.Method: refined / Origin x: -4.381 Å / Origin y: 28.074 Å / Origin z: 42.937 Å
111213212223313233
T-0.1113 Å20.0001 Å2-0.0097 Å2--0.1849 Å2-0.0065 Å2---0.0902 Å2
L1.3562 °2-0.0096 °2-0.1831 °2-1.5904 °20.0263 °2--2.4067 °2
S-0.0456 Å °-0.0095 Å °0.0508 Å °-0.0205 Å °-0.0168 Å °0.0169 Å °0.0297 Å °-0.0399 Å °0.0624 Å °
Refinement TLS groupSelection: ALL

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