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- PDB-1xbu: Streptomyces griseus aminopeptidase complexed with p-iodo-D-pheny... -

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Basic information

Entry
Database: PDB / ID: 1xbu
TitleStreptomyces griseus aminopeptidase complexed with p-iodo-D-phenylalanine
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
P-IODO-D-PHENYLALANINE / Aminopeptidase S
Similarity search - Component
Biological speciesStreptomyces griseus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Difference fourier from previously determined, related structure / Resolution: 1.2 Å
AuthorsReiland, V. / Gilboa, R. / Spungin-Bialik, A. / Schomburg, D. / Shoham, Y. / Blumberg, S. / Shoham, G.
CitationJournal: To be Published
Title: Streptomyces griseus aminopeptidase complexed with p-iodo-D-phenylalanine
Authors: Reiland, V. / Gilboa, R. / Spungin-Bialik, A. / Schomburg, D. / Shoham, Y. / Blumberg, S. / Shoham, G.
History
DepositionAug 31, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 4, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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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)30,2135
Polymers29,7511
Non-polymers4624
Water7,963442
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.970, 60.970, 144.519
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-1161-

HOH

21A-1205-

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-IOY / P-IODO-D-PHENYLALANINE / 4-IODOPHENYLALANINE


Type: D-peptide linking / Mass: 291.086 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H10INO2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 442 / 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: 2.26 Å3/Da / Density % sol: 45.13 %
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: X8C / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 22, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.2→40 Å / Num. all: 80710 / Num. obs: 80710 / % possible obs: 93.6 % / Observed criterion σ(I): 0 / Redundancy: 10 % / Rsym value: 0.081 / Net I/σ(I): 8.6
Reflection shellResolution: 1.2→1.22 Å / Redundancy: 6 % / Rsym value: 0.327 / % possible all: 63.2

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Processing

Software
NameClassification
SHELXmodel building
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
RefinementMethod to determine structure: Difference fourier from previously determined, related structure
Resolution: 1.2→40 Å / Num. parameters: 23539 / Num. restraintsaints: 29137 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.167 3982 5.3 %RANDOM
Rwork0.1269 ---
all-80710 --
obs-80710 93.6 %-
Refine analyzeNum. disordered residues: 29 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 2487.14
Refinement stepCycle: LAST / Resolution: 1.2→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2153 0 16 442 2611
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.013
X-RAY DIFFRACTIONs_angle_d0.029
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0282
X-RAY DIFFRACTIONs_zero_chiral_vol0.077
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.088
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.02
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.004
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.02
X-RAY DIFFRACTIONs_approx_iso_adps0.087

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