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- PDB-1f2p: CRYSTAL STRUCTURE OF THE STREPTOMYCES GRISEUS AMINOPEPTIDASE COMP... -

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Basic information

Entry
Database: PDB / ID: 1f2p
TitleCRYSTAL STRUCTURE OF THE STREPTOMYCES GRISEUS AMINOPEPTIDASE COMPLEXED WITH L-PHENYLALANINE
ComponentsAMINOPEPTIDASE
KeywordsHYDROLASE / AMINOPEPTIDASE / DOUBLE-ZINC METALLOPROTEINASE
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
PHENYLALANINE / Aminopeptidase S
Similarity search - Component
Biological speciesStreptomyces griseus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.8 Å
AuthorsGilboa, R. / Spungin-Bialik, A. / Wohlfahrt, G. / Schomburg, D. / Blumberg, S. / Shoham, G.
Citation
Journal: Proteins / Year: 2001
Title: Interactions of Streptomyces griseus aminopeptidase with amino acid reaction products and their implications toward a catalytic mechanism.
Authors: Gilboa, R. / Spungin-Bialik, A. / Wohlfahrt, G. / Schomburg, D. / Blumberg, S. / Shoham, G.
#1: 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.
#2: 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 Aminopeptidase.
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.
#3: 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.
History
DepositionMay 28, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 22, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 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_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_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)30,0875
Polymers29,7511
Non-polymers3364
Water5,314295
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.180, 62.180, 146.980
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-690-

HOH

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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 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-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-PHE / PHENYLALANINE


Type: L-peptide linking / Mass: 165.189 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H11NO2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 295 / 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: 2.39 Å3/Da / Density % sol: 48.46 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: PEG4000, Sodium acetate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
pH: 8 / Details: used microseeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
118 mg/mlprotein1drop
210 mMTris-HCl1drop
320 mM1dropNaCl
46 mM1dropCaCl2
5100 mML-Phenylalanine1drop
618 %(w/v)PEG40001reservoir
70.1 Macetate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 1.1
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 27, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.8→48 Å / Num. all: 27246 / Num. obs: 27246 / % possible obs: 98.5 % / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Biso Wilson estimate: 8.3 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 10.6
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 4 % / Rmerge(I) obs: 0.201 / Num. unique all: 1361 / % possible all: 98.9
Reflection
*PLUS
Reflection shell
*PLUS
% possible obs: 98.9 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementResolution: 1.8→48 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 2118221.05 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.225 2715 10 %RANDOM
Rwork0.187 ---
obs0.187 27246 98.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 74.94 Å2 / ksol: 0.383 e/Å3
Displacement parametersBiso mean: 11.3 Å2
Baniso -1Baniso -2Baniso -3
1-0.85 Å20 Å20 Å2
2--0.85 Å20 Å2
3----1.7 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.16 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 1.8→48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2033 0 15 295 2343
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_deg1.7
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_d1.17
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.871.5
X-RAY DIFFRACTIONc_mcangle_it1.252
X-RAY DIFFRACTIONc_scbond_it1.32
X-RAY DIFFRACTIONc_scangle_it1.772.5
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.23 456 10.2 %
Rwork0.186 3994 -
obs--98.9 %
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.PARAM
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 48 Å / σ(F): 0 / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 11.3 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.17
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: 0.23 / % reflection Rfree: 10.2 % / Rfactor Rwork: 0.186

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