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- PDB-1ft7: AAP COMPLEXED WITH L-LEUCINEPHOSPHONIC ACID -

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Basic information

Entry
Database: PDB / ID: 1ft7
TitleAAP COMPLEXED WITH L-LEUCINEPHOSPHONIC ACID
ComponentsBACTERIAL LEUCYL AMINOPEPTIDASE
KeywordsHYDROLASE / zinc / peptidase / bimetallic
Function / homology
Function and homology information


bacterial leucyl aminopeptidase / metalloexopeptidase activity / aminopeptidase activity / proteolysis / extracellular region / metal ion binding
Similarity search - Function
Peptidase M28E, aminopeptidase AP1 / Peptidase M28 family / Peptidase, C-terminal, archaeal/bacterial / Bacterial pre-peptidase C-terminal domain / Peptidase M28 / Peptidase family M28 / Zn peptidases / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / LEUCINE PHOSPHONIC ACID / Bacterial leucyl aminopeptidase
Similarity search - Component
Biological speciesVibrio proteolyticus (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsStamper, C. / Bennett, B. / Holz, R. / Petsko, G. / Ringe, D.
CitationJournal: Biochemistry / Year: 2001
Title: Inhibition of the aminopeptidase from Aeromonas proteolytica by L-leucinephosphonic acid. Spectroscopic and crystallographic characterization of the transition state of peptide hydrolysis.
Authors: Stamper, C. / Bennett, B. / Edwards, T. / Holz, R.C. / Ringe, D. / Petsko, G.
History
DepositionSep 11, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 4, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BACTERIAL LEUCYL AMINOPEPTIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7645
Polymers31,4271
Non-polymers3374
Water2,198122
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)107.000, 107.000, 102.000
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein BACTERIAL LEUCYL AMINOPEPTIDASE /


Mass: 31427.350 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vibrio proteolyticus (bacteria)
References: UniProt: Q01693, bacterial leucyl aminopeptidase
#2: Chemical ChemComp-ZN / ZINC ION


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


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-PLU / LEUCINE PHOSPHONIC ACID


Mass: 167.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H14NO3P
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 122 / 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: 2.68 Å3/Da / Density % sol: 54.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: KSCN, NaCl, Tris, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
110 mg/mlprotein1drop
210 mMTris-HCl1drop
310 mMKSCN1drop
40.4 M1dropNaCl
6100 mMTris-HCl1reservoir
7100 mMKSCN1reservoir
84.5 M1reservoirNaCl
5LPA1drop4-fold molar excess

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Data collection

DiffractionMean temperature: 4 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.1→12 Å / Num. all: 349668 / Num. obs: 349668 / % possible obs: 75 % / Observed criterion σ(F): 10 / Observed criterion σ(I): 10 / Redundancy: 6.7 % / Biso Wilson estimate: 10 Å2 / Rmerge(I) obs: 0.18 / Net I/σ(I): 6
Reflection shellResolution: 2.17→2.2 Å / Redundancy: 3 % / Rmerge(I) obs: 0.65 / % possible all: 65
Reflection
*PLUS
Num. obs: 21129 / % possible obs: 99.9 % / Num. measured all: 349668 / Rmerge(I) obs: 0.134
Reflection shell
*PLUS
% possible obs: 100 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.2→10 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.232 2000 10%
Rwork0.198 --
all0.198 349668 -
obs0.198 349668 -
Refinement stepCycle: LAST / Resolution: 2.2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2211 0 13 122 2346
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_angle_deg1.2
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.153
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.931
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.639

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