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- PDB-1xjo: STRUCTURE OF AMINOPEPTIDASE -

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Basic information

Entry
Database: PDB / ID: 1xjo
TitleSTRUCTURE OF AMINOPEPTIDASE
ComponentsAMINOPEPTIDASE
KeywordsHYDROLASE / AMINOPEPTIDASE / ZYMOGEN / ZINC
Function / homology
Function and homology information


aminopeptidase S / metalloexopeptidase activity / aminopeptidase activity / serine-type endopeptidase activity / proteolysis / extracellular region / metal ion binding
Similarity search - Function
Peptidase M28, SGAP-like / Peptidase M28 family / P domain / Proprotein convertase P-domain / P/Homo B domain profile. / Peptidase M28 / Peptidase family M28 / Zn peptidases / Aminopeptidase / Galactose-binding-like domain superfamily ...Peptidase M28, SGAP-like / Peptidase M28 family / P domain / Proprotein convertase P-domain / P/Homo B domain profile. / Peptidase M28 / Peptidase family M28 / Zn peptidases / Aminopeptidase / Galactose-binding-like domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Aminopeptidase S
Similarity search - Component
Biological speciesStreptomyces griseus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.75 Å
AuthorsGreenblatt, H.M. / Barra, D. / Blumberg, S. / Shoham, G.
Citation
Journal: J.Mol.Biol. / Year: 1997
Title: Streptomyces griseus aminopeptidase: X-ray crystallographic structure at 1.75 A resolution.
Authors: Greenblatt, H.M. / Almog, O. / Maras, B. / Spungin-Bialik, A. / Barra, D. / Blumberg, S. / Shoham, G.
#1: Journal: Eur.J.Biochem. / Year: 1996
Title: Aminopeptidase from S. Griseus: Primary Structure and Comparison with Other Zinc-Containing Aminopeptidases
Authors: Maras, B. / Greenblatt, H.M. / Shoham, G. / Spungin-Bialik, A. / Blumberg, S. / Barra, D.
History
DepositionOct 9, 1996Processing site: BNL
Revision 1.0Apr 1, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 30, 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_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.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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.pdbx_leaving_atom_flag / _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_ref_seq_dif.details / _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: AMINOPEPTIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0335
Polymers29,7671
Non-polymers2664
Water4,486249
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.810, 61.810, 146.300
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-520-

HOH

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Components

#1: Protein AMINOPEPTIDASE / SGAP


Mass: 29766.656 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: THE ENZYME IS ISOLATED FROM THE COMMERCIALLY AVAILABLE ENZYME MIXTURE "PRONASE E"
Source: (natural) Streptomyces griseus (bacteria)
References: UniProt: P80561, Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 249 / 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: 2.35 Å3/Da / Density % sol: 47.57 %
Crystal growpH: 5.5 / Details: 16% PEG 4K, 0.1 M SODIUM ACETATE, pH 5.5
Crystal grow
*PLUS
Method: vapor diffusion / pH: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mg/mlprotein1drop
20.1 Msodium acetate1reservoir
316 %(w/v)PEG40001reservoir
410 mMTris1drop
520 mM1dropNaCl
61 mM1dropCaCl2

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 0.949
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Mar 25, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.949 Å / Relative weight: 1
ReflectionNum. obs: 28606 / % possible obs: 97 % / Observed criterion σ(I): 0 / Redundancy: 7 % / Biso Wilson estimate: 15.2 Å2 / Rmerge(I) obs: 0.054
Reflection
*PLUS
Highest resolution: 1.75 Å / Lowest resolution: 20 Å / Num. measured all: 244396

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
TNT5Erefinement
RefinementResolution: 1.75→20 Å / σ(F): 0 / Stereochemistry target values: DEFAULT TNT
RfactorNum. reflection% reflection
Rwork0.141 --
obs-28587 97 %
Solvent computationSolvent model: DEFAULT TNT / Bsol: 295.5 Å2 / ksol: 0.765 e/Å3
Refinement stepCycle: LAST / Resolution: 1.75→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2001 0 8 249 2258
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.0220540.8
X-RAY DIFFRACTIONt_angle_deg2.8227841.3
X-RAY DIFFRACTIONt_dihedral_angle_d15.711920
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.015492
X-RAY DIFFRACTIONt_gen_planes0.0183095
X-RAY DIFFRACTIONt_it5.620500
X-RAY DIFFRACTIONt_nbd0.0261610
Software
*PLUS
Name: TNT / Version: 5E / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.141
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg15.70
X-RAY DIFFRACTIONt_plane_restr0.018

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