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- PDB-1hpg: A glutamic acid specific serine protease utilizes a novel histidi... -

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Basic information

Entry
Database: PDB / ID: 1hpg
TitleA glutamic acid specific serine protease utilizes a novel histidine triad in substrate binding
Components
  • BOC-ALA-ALA-PRO-GLU PEPTIDE
  • Glutamic acid specific protease
KeywordsHYDROLASE/HYDROLASE INHIBITOR / SERINE PROTEASE / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Function / homology
Function and homology information


glutamyl endopeptidase II / serine-type endopeptidase activity / proteolysis / extracellular region
Similarity search - Function
Streptogrisin prodomain / Peptidase S1A, alpha-lytic prodomain / Alpha-lytic protease prodomain / Peptidase S1A, streptogrisin / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain / Trypsin ...Streptogrisin prodomain / Peptidase S1A, alpha-lytic prodomain / Alpha-lytic protease prodomain / Peptidase S1A, streptogrisin / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin family, serine active site. / 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-(tert-butoxycarbonyl)-L-alanyl-L-alanyl-L-prolyl-L-glutamic acid / Glutamyl endopeptidase 2 / Glutamic acid-specific protease
Similarity search - Component
Biological speciesStreptomyces griseus (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.5 Å
AuthorsNienaber, V.L. / Birktoft, J.J.
CitationJournal: Biochemistry / Year: 1993
Title: A glutamic acid specific serine protease utilizes a novel histidine triad in substrate binding.
Authors: Nienaber, V.L. / Breddam, K. / Birktoft, J.J.
History
DepositionApr 28, 1993Processing site: BNL
Revision 1.0Jul 10, 1995Provider: 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 1.3Dec 12, 2012Group: Other
Revision 1.4Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.5Mar 26, 2025Group: 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 / struct_conn
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 / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glutamic acid specific protease
B: BOC-ALA-ALA-PRO-GLU PEPTIDE


Theoretical massNumber of molelcules
Total (without water)18,7662
Polymers18,7662
Non-polymers00
Water2,306128
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area890 Å2
ΔGint-3 kcal/mol
Surface area7210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.260, 36.290, 51.220
Angle α, β, γ (deg.)90.00, 101.80, 90.00
Int Tables number5
Space group name H-MC121
Atom site foot note1: SER A 79 - GLY A 80 OMEGA = 320.79 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
2: CIS PROLINE - PRO A 99

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Components

#1: Protein Glutamic acid specific protease / Glutamic acid-specific protease


Mass: 18279.891 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces griseus (bacteria) / Gene: sprE
References: UniProt: Q54211, UniProt: Q07006*PLUS, glutamyl endopeptidase II
#2: Protein/peptide BOC-ALA-ALA-PRO-GLU PEPTIDE


Type: Peptide-like / Class: Inhibitor / Mass: 486.515 Da / Num. of mol.: 1 / Source method: obtained synthetically
References: N-(tert-butoxycarbonyl)-L-alanyl-L-alanyl-L-prolyl-L-glutamic acid
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsHOH 401 FITS THE CRITERIA OF A SODIUM ATOM BUT WAS REFINED AS AN ORDERED SOLVENT.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.87 Å3/Da / Density % sol: 34.3 %
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7.5 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
133 mg/mlprotein1drop
20.2 M1dropMgCl2
30.1 MHEPES1drop
450 %satsodium citrate1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.5→30 Å / Num. obs: 22913 / % possible obs: 94.4 % / Observed criterion σ(I): 2
Reflection
*PLUS
Highest resolution: 1.8 Å / Num. all: 13006 / Num. measured all: 90655 / Rmerge(I) obs: 0.083

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementRfactor Rwork: 0.181 / Rfactor obs: 0.181 / Highest resolution: 1.5 Å
Refinement stepCycle: LAST / Highest resolution: 1.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1317 0 0 128 1445
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
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_deg2.84
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
Refinement
*PLUS
Highest resolution: 2 Å / Rfactor obs: 0.17
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_deg / Dev ideal: 3.18

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