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- PDB-1esb: DIRECT STRUCTURE OBSERVATION OF AN ACYL-ENZYME INTERMEDIATE IN TH... -

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Basic information

Entry
Database: PDB / ID: 1esb
TitleDIRECT STRUCTURE OBSERVATION OF AN ACYL-ENZYME INTERMEDIATE IN THE HYDROLYSIS OF AN ESTER SUBSTRATE BY ELASTASE
ComponentsPORCINE PANCREATIC ELASTASE
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
N-[(BENZYLOXY)CARBONYL]-L-ALANINE / Chymotrypsin-like elastase family member 1
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / Resolution: 2.3 Å
AuthorsDing, X. / Rasmussen, B. / Petsko, G.A. / Ringe, D.
Citation
Journal: Biochemistry / Year: 1994
Title: Direct structural observation of an acyl-enzyme intermediate in the hydrolysis of an ester substrate by elastase.
Authors: Ding, X. / Rasmussen, B.F. / Petsko, G.A. / Ringe, D.
#1: Journal: J.Am.Chem.Soc. / Year: 1989
Title: Crystal Structure of the Covalent Complex Formed by a Peptidyl Alpha,Alpha-Difluoro-Beta-Keto Amide with Porcine Pancreatic Elastase at 1.78 Angstroms Resolution
Authors: Takahashi, L.H. / Radhakrishnan, R. / Rosenfield Junior, R.E. / Meyer Junior, E.F. / Trainor, D.A.
#2: Journal: Acta Crystallogr.,Sect.B / Year: 1988
Title: Structure of Native Procine Pancreatic Elastase at 1.65 Angstroms Resolution
Authors: Meyer, E. / Cole, G. / Radhakrishnan, R. / Epp, O.
#3: Journal: J.Mol.Biol. / Year: 1980
Title: Structures of Product and Inhibitor Complexes of Streptomyces Griseus Protease a at 1.8 Angstroms Resolution
Authors: James, M.N.G. / Sielecki, A.R. / Brayer, G.D. / Delbaere, L.T.J.
#4: Journal: Nature / Year: 1976
Title: Formation of Stable Crystalline Enzyme-Substrate Intermediates at Sub-Zero Temperatures
Authors: Fink, A.L. / Ahmed, A.I.
#5: Journal: Nature / Year: 1976
Title: Crystal Structure of Elastase-Substrate Complex at-55 Degc
Authors: Alber, T. / Petsko, G.A. / Tsernoglou, D.
History
DepositionFeb 4, 1994Processing site: BNL
Revision 1.0Apr 30, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_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_type.id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Remark 700SHEET THE SHEETS PRESENTED AS *S1* AND *S2* ON SHEET RECORDS BELOW ARE ACTUALLY SIX-STRANDED BETA- ...SHEET THE SHEETS PRESENTED AS *S1* AND *S2* ON SHEET RECORDS BELOW ARE ACTUALLY SIX-STRANDED BETA-BARRELS. THIS IS REPRESENTED BY SEVEN-STRANDED SHEETS IN WHICH THE FIRST AND LAST STRAND OF EACH SHEET ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PORCINE PANCREATIC ELASTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2874
Polymers25,9281
Non-polymers3593
Water2,270126
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.020, 57.220, 74.660
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 PORCINE PANCREATIC ELASTASE


Mass: 25928.031 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / References: UniProt: P00772, pancreatic elastase
#2: Chemical ChemComp-BBL / N-[(BENZYLOXY)CARBONYL]-L-ALANINE / N-BENZYLOXYCARBONYL-L-SERINE-BETALACTONE


Mass: 223.225 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H13NO4
#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.: 126 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsBBL IS COVALENTLY LINKED TO SER 203. THE P-NITROPHENYL GROUP ORIGINALLY PRESENT IN BBL MOLECULE IS ...BBL IS COVALENTLY LINKED TO SER 203. THE P-NITROPHENYL GROUP ORIGINALLY PRESENT IN BBL MOLECULE IS LEAVING DURING THE REACTION.
Sequence detailsTHE RESIDUE NUMBERING SCHEME FOR THE PROTEIN IS SEQUENTIAL STARTING WITH VAL 16 AND ENDING WITH ASN ...THE RESIDUE NUMBERING SCHEME FOR THE PROTEIN IS SEQUENTIAL STARTING WITH VAL 16 AND ENDING WITH ASN 255. THE CATALYTIC TRIAD IS COMPOSED OF SER 203, HIS 60 AND ASP 108 (DENOTED BY *SITE* BELOW). SEQUENCE ADVISORY NOTICE: DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. SWISS-PROT ENTRY NAME: EL1_PIG SWISS-PROT PDB ATOM RECORDS NAME SEQ NAME CHAIN SEQ ASP 93 ASN 81 THE IDENTITY OF ASN 81 AGREES WITH THE SEQUENCE OF PDB ENTRY 3EST,

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.14 Å3/Da / Density % sol: 42.42 %
Crystal grow
*PLUS
Temperature: 2 ℃ / pH: 5 / Method: unknown / Details: Sawyer, L., (1978) J. Mol. Biol., 118, 137.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11 Msodium sulfate11
220 mg/mlprotein11
310 mMsodium acetate11

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 11 Å / Num. all: 10437 / Num. obs: 10437 / % possible obs: 97 %

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.3→10 Å / Rfactor Rwork: 0.21 / Rfactor obs: 0.21 / σ(F): 1
Refinement stepCycle: LAST / Resolution: 2.3→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1821 0 21 126 1968
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.21
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.018
X-RAY DIFFRACTIONx_angle_d3

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