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- PDB-1mcv: Crystal Structure Analysis of a Hybrid Squash Inhibitor in Comple... -

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Basic information

Entry
Database: PDB / ID: 1mcv
TitleCrystal Structure Analysis of a Hybrid Squash Inhibitor in Complex with Porcine Pancreatic Elastase
Components
  • Elastase 1
  • HEI-TOE I
KeywordsHYDROLASE / elastase-inhibitor complex / hybrid squash inhibitor
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsAy, J. / Hilpert, K. / Krauss, N. / Schneider-Mergener, J. / Hoehne, W.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2003
Title: Structure of a hybrid squash inhibitor in complex with porcine pancreatic elastase at 1.8 A resolution.
Authors: Ay, J. / Hilpert, K. / Krauss, N. / Schneider-Mergener, J. / Hohne, W.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2000
Title: Atomic Resolution Structure of native porcine pancreatic elastase at 1.1 A
Authors: Wurtele, M. / Hahn, M. / Hilpert, K. / Hohne, W.
#2: Journal: Embo J. / Year: 1986
Title: X-ray crystal structure of the complex of human leukocyte elastase (PMN elastase) and the third DOMAIN OF the turkey ovomucoid inhibitor
Authors: Bode, W. / Wei, A.Z. / Huber, R. / Meyer, E. / Travis, J. / Neumann, S.
#3: Journal: FEBS Lett. / Year: 1989
Title: THE REFINED 2.0 ANGSTROMS X-RAY CRYSTAL STRUCTURE OF THE COMPLEX FORMED BETWEEN BOVINE BETA-TRYPSIN AND CMTI-I, A TRYPSIN INHIBITOR FROM SQUASH SEEDS (CUCURBITA MAXIMA). TOPOLOGICAL SIMILARITY ...Title: THE REFINED 2.0 ANGSTROMS X-RAY CRYSTAL STRUCTURE OF THE COMPLEX FORMED BETWEEN BOVINE BETA-TRYPSIN AND CMTI-I, A TRYPSIN INHIBITOR FROM SQUASH SEEDS (CUCURBITA MAXIMA). TOPOLOGICAL SIMILARITY OF THE SQUASH SEED INHIBITORS WITH THE CARBOXYPEPTIDASE A INHIBITOR FROM POTATOES
Authors: Bode, W. / Greyling, H.J. / Huber, R. / Otlewski, J. / Wilusz, T.
History
DepositionAug 6, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 4, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_sheet / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _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.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_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 400COMPOUND RESIDUE NUMBERING FOR ELASTASE FOLLOWS THE NUMBERING OF BOVINE CHYMOTRYPSINOGEN A.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Elastase 1
I: HEI-TOE I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0394
Polymers28,9022
Non-polymers1362
Water6,359353
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1940 Å2
ΔGint-36 kcal/mol
Surface area11230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.330, 56.440, 72.760
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: 25929.016 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: P00772, pancreatic elastase
#2: Protein/peptide HEI-TOE I / Hybrid squash inhibitor HEI-TOE 1


Mass: 2973.452 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: The peptide was chemically synthesized using solid phase peptide synthesis. It was constructed using the trypsin binding loop of squash inhibitor EETI II, substituted by the sequence of a ...Details: The peptide was chemically synthesized using solid phase peptide synthesis. It was constructed using the trypsin binding loop of squash inhibitor EETI II, substituted by the sequence of a peptide that was derived from the third domain of the turkey ovomucoid inhibitor.
Keywords: trypsin binding loop of squash inhibitor EETI II, substituted by the sequence of a peptide that was derived from the third domain of the turkey ovomucoid inhibitor
#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.: 353 / 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 Å3/Da / Density % sol: 38.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: sodium citrate, ammonium acetate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Crystal grow
*PLUS
Temperature: 293 K
Components of the solutions
*PLUS
Conc.: 0.02 M / Common name: citrate / Details: pH6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.9073 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 4, 2002
RadiationMonochromator: triangular monochromator, bent mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9073 Å / Relative weight: 1
ReflectionResolution: 1.8→14 Å / Num. all: 22112 / Num. obs: 21938 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 13.5 Å2 / Rsym value: 0.037 / Net I/σ(I): 21
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 4.5 / Num. unique all: 1941 / Rsym value: 0.116 / % possible all: 87.8
Reflection
*PLUS
Num. obs: 22112 / Num. measured all: 79096 / Rmerge(I) obs: 0.037
Reflection shell
*PLUS
% possible obs: 87.8 % / Num. unique obs: 1941 / Rmerge(I) obs: 0.116

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS0.9refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QNJ

1qnj


Resolution: 1.8→14 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.221 1103 RANDOM
Rwork0.182 --
all0.184 21938 -
obs0.184 21938 -
Solvent computationSolvent model: bulk solvent / Bsol: 40.2 Å2 / ksol: 0.32 e/Å3
Displacement parametersBiso mean: 15.3 Å2
Baniso -1Baniso -2Baniso -3
1-3.6 Å20 Å20 Å2
2---3.1 Å20 Å2
3----0.5 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.11 Å0.11 Å
Refinement stepCycle: LAST / Resolution: 1.8→14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2098 0 6 353 2457
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0046
X-RAY DIFFRACTIONc_angle_deg1.26
X-RAY DIFFRACTIONc_dihedral_angle_d25.56
X-RAY DIFFRACTIONc_improper_angle_d0.676
X-RAY DIFFRACTIONc_mcbond_it0.584
X-RAY DIFFRACTIONc_mcangle_it0.979
X-RAY DIFFRACTIONc_scbond_it0.867
X-RAY DIFFRACTIONc_scangle_it1.322
LS refinement shellResolution: 1.8→1.86 Å
RfactorNum. reflection% reflection
Rfree0.247 100 -
Rwork0.21 --
obs-2138 99 %
Refinement
*PLUS
Lowest resolution: 14 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.56
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.676

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