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- PDB-1hb0: Snapshots of serine protease catalysis: (D) acyl-enzyme intermedi... -

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Basic information

Entry
Database: PDB / ID: 1hb0
TitleSnapshots of serine protease catalysis: (D) acyl-enzyme intermediate between porcine pancreatic elastase and human beta-casomorphin-7 jumped to pH 10 for 2 minutes
ComponentsELASTASE 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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 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 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "B" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "B" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: ELASTASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1503
Polymers26,0141
Non-polymers1362
Water2,162120
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)49.630, 57.600, 73.440
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 / 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
#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.: 120 / 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: 1.78 Å3/Da / Density % sol: 30.3 %
Crystal growpH: 10
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 ℃ / pH: 5 / 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: 0.99
DetectorType: PRINCETON / Detector: CCD / Date: Jan 15, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 2.05→26.8 Å / Num. obs: 12678 / % possible obs: 93.3 % / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Biso Wilson estimate: 12.6 Å2 / Rmerge(I) obs: 0.105 / Net I/σ(I): 9.6
Reflection shellResolution: 2.05→2.1 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.254 / Mean I/σ(I) obs: 6.8 / % possible all: 85.9
Reflection
*PLUS
Num. measured all: 130629
Reflection shell
*PLUS
% possible obs: 85.9 %

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Processing

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

1qix


Resolution: 2.05→38 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: ARG B 61 AND ARG B 125, SIDE CHAIN DISORDERED
RfactorNum. reflection% reflectionSelection details
Rfree0.246 510 3.7 %RANDOM
Rwork0.199 ---
obs0.199 12678 92.3 %-
Solvent computationSolvent model: STANDARD CNS / Bsol: 50.3 Å2 / ksol: 0.42 e/Å3
Displacement parametersBiso mean: 15.6 Å2
Baniso -1Baniso -2Baniso -3
1--10.3 Å20 Å20 Å2
2--2.346 Å20 Å2
3---7.954 Å2
Refinement stepCycle: LAST / Resolution: 2.05→38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1810 0 6 120 1936
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
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_deg1.25
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_it1.2790
X-RAY DIFFRACTIONc_mcangle_it1.8510
X-RAY DIFFRACTIONc_scbond_it1.8450
X-RAY DIFFRACTIONc_scangle_it2.5640
LS refinement shellResolution: 2.05→2.12 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.28 53 4.9 %
Rwork0.216 1077 -
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
LS refinement shell
*PLUS
Rfactor Rfree: 0.28

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