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- PDB-1cp7: AMINOPEPTIDASE FROM STREPTOMYCES GRISEUS -

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Basic information

Entry
Database: PDB / ID: 1cp7
TitleAMINOPEPTIDASE FROM STREPTOMYCES GRISEUS
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
Biological speciesStreptomyces griseus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.58 Å
AuthorsGilboa, R. / Greenblatt, H.M. / Perach, M. / Spungin-Bialik, A. / Lessel, U. / Schomburg, D. / Blumberg, S. / Shoham, G.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2000
Title: Interactions of Streptomyces griseus aminopeptidase with a methionine product analogue: a structural study at 1.53 A resolution.
Authors: Gilboa, R. / Greenblatt, H.M. / Perach, M. / Spungin-Bialik, A. / Lessel, U. / Wohlfahrt, G. / Schomburg, D. / Blumberg, S. / Shoham, G.
#1: Journal: Eur.J.Biochem. / Year: 1998
Title: Inhibition of Streptomyces Griseus Aminopeptidase and Effects of Calcium Ions on Catalysis and Binding Comparisons with the Homologous Enzyme Aeromonas Proteolytica Aminopeptidasea
Authors: Papir, G. / Spungin-Bialik, A. / Ben-Meir, D. / Fudim, E. / Gilboa, R. / Greenblatt, H.M. / Shoham, G. / Lessel, U. / Schomburg, D. / Ashkenazi, R. / Blumberg, S.
#2: Journal: J.Mol.Biol. / Year: 1997
Title: Streptomyces Griseus Aminopeptidase:X-Ray Crystallographic Structure at 1.75A Resolution
Authors: Greenblatt, H.M. / Almog, O. / Maras, B. / Spungin-Bialik, A. / Barra, D. / Blumberg, S. / Shoham, G.
#3: 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
DepositionJun 10, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0May 3, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_sheet / 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.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_sheet.number_strands / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: AMINOPEPTIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9224
Polymers29,7511
Non-polymers1713
Water4,522251
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.750, 61.750, 146.150
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein AMINOPEPTIDASE / SGAP


Mass: 29750.656 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: THE ENZYME IS ISOLATED FROM 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-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.: 251 / 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: 2.34 Å3/Da / Density % sol: 47 %
Crystal growpH: 5.5 / Details: 16% PEG 4K, 0.1 M SODIUM ACETATE PH 5.5
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion / Details: Greenblatt, H.M., (1997) J.Mol.Biol., 265, 620.
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: X26C / Wavelength: 1.083
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Oct 26, 1997 / Details: MIRROR
RadiationMonochromator: SILICON CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.083 Å / Relative weight: 1
ReflectionResolution: 1.58→32 Å / Num. obs: 37375 / % possible obs: 94 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 17 Å2 / Rmerge(I) obs: 0.045 / Rsym value: 0.045 / Net I/σ(I): 13
Reflection shellResolution: 1.58→1.61 Å / Rmerge(I) obs: 0.141 / Rsym value: 0.141 / % possible all: 63.2
Reflection
*PLUS
% possible obs: 94 %
Reflection shell
*PLUS
% possible obs: 63.2 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CCP4model building
CNSrefinement
CCP4phasing
CNSphasing
RefinementMethod to determine structure: OTHER
Starting model: PDB ENTERY 1XJO

1xjo


Resolution: 1.58→32 Å / Rfactor Rfree error: 0.003 / Data cutoff high rms absF: 1998230.6 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.171 3745 10 %RANDOM
Rwork0.144 ---
obs0.144 37354 94 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 40.22 Å2 / ksol: 0.318 e/Å3
Displacement parametersBiso mean: 19 Å2
Baniso -1Baniso -2Baniso -3
1-1.14 Å20 Å20 Å2
2--1.14 Å20 Å2
3----2.28 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.15 Å0.13 Å
Luzzati d res low-5 Å
Luzzati sigma a0.09 Å0.06 Å
Refinement stepCycle: LAST / Resolution: 1.58→32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2032 0 3 251 2286
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.019
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.9
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.27
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.371.5
X-RAY DIFFRACTIONc_mcangle_it2.122
X-RAY DIFFRACTIONc_scbond_it3.442
X-RAY DIFFRACTIONc_scangle_it4.582.5
LS refinement shellResolution: 1.58→1.68 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.202 523 9.9 %
Rwork0.171 4735 -
obs--81.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4CIS_PEPTIDE.PARAMCIS_PEPTIDE.TOP
Software
*PLUS
Name: CNS / Version: 0.3 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 19 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.9
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.27
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.202 / % reflection Rfree: 9.9 % / Rfactor Rwork: 0.171

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