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- PDB-1elt: STRUCTURE OF NATIVE PANCREATIC ELASTASE FROM NORTH ATLANTIC SALMO... -

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Basic information

Entry
Database: PDB / ID: 1elt
TitleSTRUCTURE OF NATIVE PANCREATIC ELASTASE FROM NORTH ATLANTIC SALMON AT 1.61 ANGSTROMS RESOLUTION
ComponentsELASTASE
KeywordsSERINE 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
Biological speciesSalmo salar (Atlantic salmon)
MethodX-RAY DIFFRACTION / Resolution: 1.61 Å
AuthorsBerglund, G.I. / Smalaas, A.O.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 1995
Title: Structure of native pancreatic elastase from North Atlantic salmon at 1.61 A resolution.
Authors: Berglund, G.I. / Willassen, N.P. / Hordvik, A. / Smalas, A.O.
#1: Journal: To be Published
Title: Crystallization and Preliminary X-Ray Crystallographic Studies of Native Elastase from North Atlantic Salmon (Salmo Salar)
Authors: Berglund, G.I. / Smalaas, A.O. / Hansen, L.Kr. / Willassen, N.P.
#2: Journal: Biochemistry / Year: 1989
Title: Human Leukocyte and Porcine Pancreatic Elastase: X-Ray Crystal Structures, Mechanism, Substrate Specificity, and Mechanism-Based Inhibitors
Authors: Bode, W. / Meyer, E. / Powers, J.C.
#3: Journal: Acta Crystallogr.,Sect.B / Year: 1988
Title: Structure of Native Porcine Pancreatic Elastase at 1.65 Angstroms Resolution
Authors: Meyer, E. / Cole, G. / Radhakrishnan, R.
History
DepositionJan 2, 1995Processing site: BNL
Revision 1.0Jan 1, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 18, 2018Group: Data collection / Other / Category: diffrn_detector / pdbx_database_status
Item: _diffrn_detector.detector / _pdbx_database_status.process_site
Revision 1.4Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _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_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: ELASTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0742
Polymers25,0341
Non-polymers401
Water2,810156
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.000, 68.000, 83.980
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-410-

HOH

21A-452-

HOH

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Components

#1: Protein ELASTASE


Mass: 25033.883 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Salmo salar (Atlantic salmon) / Organ: PANCREAS / Tissue: PANCREAS / References: UniProt: Q7SIG3, pancreatic elastase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 156 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsCALCIUM IS STRUCTURALLY BOUND IN THE SAME SEQUENTIAL POSITION AS FOR PORCINE ELASTASE (SEE REF 3).
Sequence detailsTHE AMINO ACID NUMBERING SYSTEM IS THE ONE ADOPTED FROM CHYMOTRYPSINOGEN A.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.94 Å3/Da / Density % sol: 36.54 %
Crystal grow
*PLUS
pH: 7.3 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
19.5 mg/mlelastase1drop
220 %(v/v)MPD1drop
30.1 Msodium citrate1drop
450 mMHEPES1drop
510 %(w/v)PEG40001reservoir
65 %(v/v)2-propanol1reservoir
750 mMHEPES1reservoir

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER / Date: Jul 8, 1993
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 21574 / % possible obs: 83.6 % / Redundancy: 1.7 % / Rmerge(I) obs: 0.024
Reflection
*PLUS
Highest resolution: 1.61 Å / Lowest resolution: 4.82 Å / Num. measured all: 36833 / Rmerge(I) obs: 0.024
Reflection shell
*PLUS
Highest resolution: 1.61 Å / Lowest resolution: 1.71 Å / % possible obs: 46.1 % / Redundancy: 1.2 % / Num. unique obs: 1660 / Num. measured obs: 2002 / Rmerge(I) obs: 0.174 / Mean I/σ(I) obs: 60.8

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Processing

Software
NameVersionClassification
PROCOR(KABSCH)data collection
X-PLORmodel building
PROLSQrefinement
X-PLORrefinement
PROCOR(KABSCH)data reduction
X-PLORphasing
RefinementResolution: 1.61→8 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.239 --
obs0.172 21389 82.6 %
Displacement parametersBiso mean: 14.6 Å2
Refine analyzeLuzzati coordinate error obs: 0.15 Å
Refinement stepCycle: LAST / Resolution: 1.61→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1763 0 1 156 1920
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.008
X-RAY DIFFRACTIONp_angle_d1.5
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_dihedral_angle_d
X-RAY DIFFRACTIONp_dihedral_angle_deg26.3
X-RAY DIFFRACTIONp_improper_angle_d
X-RAY DIFFRACTIONp_improper_angle_deg1.2

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