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- PDB-1hle: CRYSTAL STRUCTURE OF CLEAVED EQUINE LEUCOCYTE ELASTASE INHIBITOR ... -

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Basic information

Entry
Database: PDB / ID: 1hle
TitleCRYSTAL STRUCTURE OF CLEAVED EQUINE LEUCOCYTE ELASTASE INHIBITOR DETERMINED AT 1.95 ANGSTROMS RESOLUTION
Components(HORSE LEUKOCYTE ELASTASE INHIBITOR) x 2
KeywordsHYDROLASE INHIBITOR(SERINE PROTEINASE)
Function / homology
Function and homology information


cytolytic granule / negative regulation of interleukin-1 beta production / serine-type endopeptidase inhibitor activity / early endosome / extracellular space
Similarity search - Function
Antithrombin; Chain I, domain 2 / Antithrombin, subunit I, domain 2 / Alpha-1-antitrypsin; domain 1 / Alpha-1-antitrypsin, domain 1 / Serpin, conserved site / Serpins signature. / Serpin superfamily, domain 2 / Serpin family / Serpin domain / Serpin superfamily ...Antithrombin; Chain I, domain 2 / Antithrombin, subunit I, domain 2 / Alpha-1-antitrypsin; domain 1 / Alpha-1-antitrypsin, domain 1 / Serpin, conserved site / Serpins signature. / Serpin superfamily, domain 2 / Serpin family / Serpin domain / Serpin superfamily / Serpin superfamily, domain 1 / Serpin (serine protease inhibitor) / SERine Proteinase INhibitors / Roll / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Leukocyte elastase inhibitor
Similarity search - Component
Biological speciesEquus caballus (horse)
MethodX-RAY DIFFRACTION / Resolution: 1.95 Å
AuthorsBaumann, U. / Bode, W. / Huber, R. / Travis, J. / Potempa, J.
CitationJournal: J.Mol.Biol. / Year: 1992
Title: Crystal structure of cleaved equine leucocyte elastase inhibitor determined at 1.95 A resolution.
Authors: Baumann, U. / Bode, W. / Huber, R. / Travis, J. / Potempa, J.
History
DepositionApr 13, 1992Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Nov 13, 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_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_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.ptnr1_symmetry / _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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_PDB_ins_code / _struct_conn.pdbx_ptnr2_PDB_ins_code / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_ins_code / _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: HORSE LEUKOCYTE ELASTASE INHIBITOR
B: HORSE LEUKOCYTE ELASTASE INHIBITOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,6373
Polymers42,5972
Non-polymers401
Water3,819212
1
A: HORSE LEUKOCYTE ELASTASE INHIBITOR
B: HORSE LEUKOCYTE ELASTASE INHIBITOR
hetero molecules

A: HORSE LEUKOCYTE ELASTASE INHIBITOR
B: HORSE LEUKOCYTE ELASTASE INHIBITOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,2736
Polymers85,1934
Non-polymers802
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Unit cell
Length a, b, c (Å)121.370, 103.570, 80.930
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein HORSE LEUKOCYTE ELASTASE INHIBITOR


Mass: 38957.539 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Equus caballus (horse) / References: UniProt: P05619
#2: Protein/peptide HORSE LEUKOCYTE ELASTASE INHIBITOR


Mass: 3639.040 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Equus caballus (horse) / References: UniProt: P05619
#3: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 212 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsA CA 2+ ION HAS BEEN IDENTIFIED (RESIDUE CA 647) WHICH MEDIATES A LATTICE CONTACT.
Sequence detailsTHE SEQUENCE USED IS THAT OF DUBIN ET AL., (J. BIOL. CHEM., 1992). BASED ON PEPTIDE SEQUENCING AND ...THE SEQUENCE USED IS THAT OF DUBIN ET AL., (J. BIOL. CHEM., 1992). BASED ON PEPTIDE SEQUENCING AND WAS NOT COMPLETELY FINISHED AT THE TIME OF DEPOSITION.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.98 Å3/Da / Density % sol: 58.78 %
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
25 mMMOPS1drop
316-18 %(w/v)PEG40001reservoir
40.18 M1reservoirCaCl2

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.95 Å / Num. obs: 38335 / % possible obs: 98.7 % / Num. measured all: 154128 / Rmerge(I) obs: 0.096
Reflection shell
*PLUS
Highest resolution: 1.95 Å / Lowest resolution: 2 Å / % possible obs: 97.1 %

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 1.95→7 Å / σ(F): 2.5 /
RfactorNum. reflection
Rwork0.176 -
obs0.176 32997
Refinement stepCycle: LAST / Resolution: 1.95→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3668 0 1 636 4305
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.015
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.57
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.95 Å / Lowest resolution: 7 Å / Num. reflection obs: 32997 / σ(F): 2.5 / Rfactor obs: 0.176
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 25.2 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_d1.57
X-RAY DIFFRACTIONx_dihedral_angle_d25.49
X-RAY DIFFRACTIONx_dihedral_angle_deg1.13
X-RAY DIFFRACTIONx_mcbond_it1.97
X-RAY DIFFRACTIONx_scbond_it3.7
X-RAY DIFFRACTIONx_mcangle_it2.92
X-RAY DIFFRACTIONx_scangle_it5.51
LS refinement shell
*PLUS
Highest resolution: 1.95 Å / Lowest resolution: 1.99 Å

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