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- PDB-1tf8: Streptomyces griseus aminopeptidase complexed with L-tryptophan -

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Basic information

Entry
Database: PDB / ID: 1tf8
TitleStreptomyces griseus aminopeptidase complexed with L-tryptophan
ComponentsAminopeptidase
KeywordsHYDROLASE / DOUBLE-ZINC METALLOPROTEINASE / CALCIUM ACTIVATION / PROTEIN-INHIBITOR COMPLEX
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
TRYPTOPHAN / Aminopeptidase S
Similarity search - Component
Biological speciesStreptomyces griseus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.3 Å
AuthorsReiland, V. / Gilboa, R. / Spungin-Bialik, A. / Schomburg, D. / Shoham, Y. / Blumberg, S. / Shoham, G.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2004
Title: Binding of inhibitory aromatic amino acids to Streptomyces griseus aminopeptidase.
Authors: Reiland, V. / Gilboa, R. / Spungin-Bialik, A. / Schomburg, D. / Shoham, Y. / Blumberg, S. / Shoham, G.
History
DepositionMay 27, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 31, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification / _software.name

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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)30,3306
Polymers29,7511
Non-polymers5795
Water8,071448
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.339, 61.339, 144.964
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-1163-

HOH

21A-1173-

HOH

31A-1354-

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-TRP / TRYPTOPHAN / Tryptophan


Type: L-peptide linking / Mass: 204.225 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H12N2O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 448 / Source method: isolated from a natural source / Formula: H2O

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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: 2.27 Å3/Da / Density % sol: 45.45 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: PEG 4000, sodium acetate, pH 5.5, vapor diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 1.1 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 25, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.11
21.11
ReflectionResolution: 1.3→20 Å / Num. all: 62291 / Num. obs: 62291 / % possible obs: 90.4 % / Observed criterion σ(I): 0 / Redundancy: 10 % / Rsym value: 0.091 / Net I/σ(I): 9.6
Reflection shellResolution: 1.3→1.32 Å / Redundancy: 10 % / Rsym value: 0.216 / % possible all: 60.2

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Processing

Software
NameClassification
SHELXL-97refinement
SCALEPACKdata scaling
CNSrefinement
DENZOdata reduction
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.3→20 Å / Num. parameters: 23408 / Num. restraintsaints: 29161 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.1742 3137 5.3 %RANDOM
Rwork0.1281 ---
all-62291 --
obs-62291 90.4 %-
Refine analyzeNum. disordered residues: 21 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 2494.97
Refinement stepCycle: LAST / Resolution: 1.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2024 0 33 448 2505
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.012
X-RAY DIFFRACTIONs_angle_d0.027
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0288
X-RAY DIFFRACTIONs_zero_chiral_vol0.076
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.076
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.018
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.004
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.026
X-RAY DIFFRACTIONs_approx_iso_adps0.077

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