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- PDB-1qix: Porcine pancreatic elastase complexed with human beta-casomorphin-7 -

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Basic information

Entry
Database: PDB / ID: 1qix
TitlePorcine pancreatic elastase complexed with human beta-casomorphin-7
Components
  • BETA-CASOMORPHIN-7Casomorphin
  • ELASTASE
KeywordsSERINE PROTEINASE / HYDROLASE (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 / 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
Chymotrypsin-like elastase family member 1
Similarity search - Component
Biological speciesSUS SCROFA (pig)
HOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsWilmouth, R.C. / Clifton, I.J. / Hajdu, J. / Schofield, C.J.
Citation
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.
#1: Journal: Acta Crystallogr.,Sect.B / Year: 1988
Title: Structure of Native Porcine Pancreatic Elastase at 1.65A Resolution
Authors: Meyer, E. / Cole, G. / Radhakrishnan, R. / Epp, O.
#2: Journal: J.Biol.Chem. / Year: 1984
Title: Human Beta-Casein
Authors: Greenberg, R. / Groves, M.L. / Dower, H.J.
History
DepositionJun 18, 1999Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 14, 1999Provider: 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 / 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_ref_seq / 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_ref_seq.db_align_beg / _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

Downloads & links

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Assembly

Deposited unit
A: BETA-CASOMORPHIN-7
B: ELASTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,9284
Polymers26,7922
Non-polymers1362
Water2,090116
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area780 Å2
ΔGint-8.1 kcal/mol
Surface area12370 Å2
MethodPQS
Unit cell
Length a, b, c (Å)51.282, 58.240, 75.437
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 BETA-CASOMORPHIN-7 / Casomorphin


Mass: 863.995 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human)
#2: Protein ELASTASE / / PPE


Mass: 25928.031 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: PORCINE PANCREATIC ELASTASE / Source: (natural) SUS SCROFA (pig) / Organ: PANCREAS / References: UniProt: P00772, EC: 3.4.21.11
#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 / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 116 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHERE IS AN ESTER BOND BETWEEN THE CARBOXYL TERMINUS OF THE BETA-CASOMORPHIN-7 PEPTIDE AND THE ...THERE IS AN ESTER BOND BETWEEN THE CARBOXYL TERMINUS OF THE BETA-CASOMORPHIN-7 PEPTIDE AND THE HYDROXYL SIDE CHAIN OF SER-195 THE RESIDUE NUMBERING SCHEME USED FOR ELASTASE WAS CHOSEN TO MAXIMISE HOMOLOGY WITH THE NUMBERING FOR CHYMOTRYPSINOGEN A.

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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: 2.15 Å3/Da / Density % sol: 33 %
Crystal growpH: 5
Details: CRYSTALLISED FROM 25MM SODIUM SULPHATE, 25MM SODIUM ACETATE (PH 5.0), 25 MG/ML PPE AND 25 MG/ML BCM7.
Crystal grow
*PLUS
Temperature: 17 ℃ / Method: vapor diffusion, hanging drop
Details: drop solution was mixed with an equal volume of reservoir solution
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.04 mMsodium acetate1drop
250 mg/mlPPE1drop
350 mg/mlBCM71drop
450 mMammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 290 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 15, 1995
RadiationMonochromator: GRAPHITE(002) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→38.5 Å / Num. obs: 18368 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 15.29 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 19.48
Reflection shellResolution: 1.9→2 Å / Redundancy: 4 % / Rmerge(I) obs: 0.285 / Mean I/σ(I) obs: 4.56 / % possible all: 99.1
Reflection shell
*PLUS
% possible obs: 99.1 %

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Processing

Software
NameVersionClassification
REFMACrefinement
MOSFLMV. 6.0data reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3EST

3est


Resolution: 1.9→38.5 Å / SU B: 2.88082 / SU ML: 0.08656 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.14853 / ESU R Free: 0.14056
Details: CNS ALSO USED. THIS STRUCTURE HAS BEEN RE-PROCESSED SINCE THE ORIGINAL PAPER WAS PUBLISHED AND THEREFORE SOME OF THE DISTANCES AND ANGLES BETWEEN THE ATOMS IN THIS PDB ENTRY MAY NOT EXACTLY ...Details: CNS ALSO USED. THIS STRUCTURE HAS BEEN RE-PROCESSED SINCE THE ORIGINAL PAPER WAS PUBLISHED AND THEREFORE SOME OF THE DISTANCES AND ANGLES BETWEEN THE ATOMS IN THIS PDB ENTRY MAY NOT EXACTLY AGREE WITH THOSE QUOTED
RfactorNum. reflection% reflectionSelection details
Rfree0.219 772 4 %RANDOM
Rwork0.172 ---
obs-18368 99.9 %-
Displacement parametersBiso mean: 17.52 Å2
Refinement stepCycle: LAST / Resolution: 1.9→38.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1833 0 6 116 1955
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0140.02
X-RAY DIFFRACTIONp_angle_d0.0310.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0320.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.822
X-RAY DIFFRACTIONp_mcangle_it2.4973
X-RAY DIFFRACTIONp_scbond_it2.342
X-RAY DIFFRACTIONp_scangle_it3.6433
X-RAY DIFFRACTIONp_plane_restr0.02290.03
X-RAY DIFFRACTIONp_chiral_restr0.150.15
X-RAY DIFFRACTIONp_singtor_nbd0.1730.3
X-RAY DIFFRACTIONp_multtor_nbd0.2570.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1360.3
X-RAY DIFFRACTIONp_planar_tor3.77
X-RAY DIFFRACTIONp_staggered_tor13.315
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor18.820
X-RAY DIFFRACTIONp_special_tor15

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