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- PDB-1hax: Snapshots of serine protease catalysis: (A) acyl-enzyme intermedi... -

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Basic information

Entry
Database: PDB / ID: 1hax
TitleSnapshots of serine protease catalysis: (A) acyl-enzyme intermediate between porcine pancreatic elastase and human beta-casomorphin-7 at pH 5
Components
  • BETA-CASOMORPHIN-7
  • ELASTASE 1
KeywordsHYDROLASE / SERINE 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 / 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)
HOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsWilmouth, R.C. / Edman, K. / Neutze, R. / Wright, P.A. / Clifton, I.J. / Schneider, T.R. / Schofield, C.J. / Hajdu, J.
Citation
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.
#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: 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.
History
DepositionApr 10, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 2, 2001Provider: repository / Type: Initial release
Revision 1.1May 7, 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 / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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
Revision 1.4Nov 20, 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: BETA-CASOMORPHIN-7
B: ELASTASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,6074
Polymers26,4712
Non-polymers1362
Water3,351186
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)50.320, 58.220, 74.410
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsCOMPLEX OF ELASTASE 1 AND BETA-CASOMORPHIN- 7

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Components

#1: Protein/peptide BETA-CASOMORPHIN-7 / BCM7


Mass: 456.532 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human)
#2: Protein ELASTASE 1 / PPE


Mass: 26014.148 Da / Num. of mol.: 1 / Source method: isolated from a natural source / 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


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.: 186 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE CARBOXYL TERMINUS OF THE BETA-CASOMORPHIN-7 PEPTIDE AND THE HYDROXYL SIDE CHAIN OF SER-195 ARE ...THE CARBOXYL TERMINUS OF THE BETA-CASOMORPHIN-7 PEPTIDE AND THE HYDROXYL SIDE CHAIN OF SER-195 ARE COVALENTLY LINKED VIA THE CARBONYL CARBON OF ILE A7 AND THE OG OF SER B195
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: 1.85 Å3/Da / Density % sol: 32.9 %
Crystal growpH: 5
Details: 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: Wilmouth, R.C., (1997) Nat.Struct.Biol., 4, 456.
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: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.933
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 15, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.6→33.9 Å / Num. obs: 29359 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 12.7 Å2 / Rmerge(I) obs: 0.034 / Net I/σ(I): 33.4
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.09 / Mean I/σ(I) obs: 15.2 / % possible all: 98.7
Reflection
*PLUS
Num. measured all: 211556
Reflection shell
*PLUS
Highest resolution: 1.6 Å / % possible obs: 98.7 % / Rmerge(I) obs: 0.09

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Processing

Software
NameVersionClassification
CNS1refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QIX

1qix


Resolution: 1.6→38.1 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.201 1206 4.1 %RANDOM
Rwork0.186 ---
obs0.186 29519 99.8 %-
Solvent computationSolvent model: STANDARD CNS / Bsol: 39.5 Å2 / ksol: 0.38 e/Å3
Displacement parametersBiso mean: 13.2 Å2
Baniso -1Baniso -2Baniso -3
1--0.756 Å20 Å20 Å2
2--0.064 Å20 Å2
3---0.692 Å2
Refinement stepCycle: LAST / Resolution: 1.6→38.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1841 0 6 186 2033
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.041
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.26
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.0070
X-RAY DIFFRACTIONc_mcangle_it1.5520
X-RAY DIFFRACTIONc_scbond_it1.7120
X-RAY DIFFRACTIONc_scangle_it2.4660
LS refinement shellResolution: 1.6→1.62 Å / Total num. of bins used: 24
RfactorNum. reflection% reflection
Rfree0.2 40 3.8 %
Rwork0.222 1052 -
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4EST_GERG.PAREST_GERG.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
LS refinement shell
*PLUS
Rfactor Rfree: 0.2

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