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- PDB-2h1u: Porcine pancreatic elastase complexed with MetPheLeuGlu at pH 5.0 -

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Basic information

Entry
Database: PDB / ID: 2h1u
TitlePorcine pancreatic elastase complexed with MetPheLeuGlu at pH 5.0
Components
  • Elastase-1
  • MFLE
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: 1.6 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: Bioorg.Med.Chem.Lett. / Year: 2000
Title: Mass spectrometry reveals elastase inhibitors from the reactive centre loop of alpha1-antitrypsin
Authors: Wright, P.A. / Rostom, A.A. / Robinson, C.V. / Schofield, C.J.
History
DepositionMay 17, 2006Deposition 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: Version format compliance
Revision 1.3Oct 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 1.4Nov 6, 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
P: MFLE
A: Elastase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,6034
Polymers26,4672
Non-polymers1362
Water2,126118
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area690 Å2
ΔGint-28 kcal/mol
Surface area10220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.084, 57.570, 74.146
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/peptide MFLE


Mass: 538.656 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic peptide
#2: 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
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / 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: 2.02 Å3/Da / Density % sol: 39.07 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 25mm sodium sulphate, 25mm sodium acetate (ph 5.0), 25mg/ml PPE, 17.5mg/ml MFLE , 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: Oct 10, 2005 / Details: OSMIC mirrors
RadiationMonochromator: OSMIC MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.6→45.45 Å / Num. obs: 27749 / % possible obs: 96.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 16.1 Å2 / Rmerge(I) obs: 0.042 / Net I/σ(I): 21.3
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.208 / Mean I/σ(I) obs: 4.8 / Num. unique all: 3793 / % possible all: 91.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3EST

3est


Resolution: 1.6→19.54 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.945 / SU B: 1.583 / SU ML: 0.058 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.097 / ESU R Free: 0.092 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2049 1419 5.1 %RANDOM
Rwork0.18247 ---
obs0.18363 26295 95.39 %-
all-27749 --
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: 21.611 Å2
Baniso -1Baniso -2Baniso -3
1-0.86 Å20 Å20 Å2
2---0.29 Å20 Å2
3----0.57 Å2
Refinement stepCycle: LAST / Resolution: 1.6→19.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1812 0 6 118 1936
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0211858
X-RAY DIFFRACTIONr_angle_refined_deg1.4131.9182543
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0375240
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.18324.15677
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.51115266
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.269159
X-RAY DIFFRACTIONr_chiral_restr0.1010.2291
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021416
X-RAY DIFFRACTIONr_nbd_refined0.2350.2873
X-RAY DIFFRACTIONr_nbtor_refined0.310.21291
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1090.2129
X-RAY DIFFRACTIONr_metal_ion_refined0.1290.25
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.20.228
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.170.214
X-RAY DIFFRACTIONr_mcbond_it0.8891.51206
X-RAY DIFFRACTIONr_mcangle_it1.41121913
X-RAY DIFFRACTIONr_scbond_it2.1223754
X-RAY DIFFRACTIONr_scangle_it2.8764.5630
LS refinement shellResolution: 1.598→1.64 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.258 107 -
Rwork0.187 1739 -
obs--87.78 %

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