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- PDB-1xry: Crystal structure of Aeromonas proteolytica aminopeptidase in com... -

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Basic information

Entry
Database: PDB / ID: 1xry
TitleCrystal structure of Aeromonas proteolytica aminopeptidase in complex with bestatin
ComponentsBacterial leucyl aminopeptidase
KeywordsHYDROLASE / Aeromonas proteolytica aminopeptidase / di-zinc metalloproteinases / bestatin
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
Chem-BES / Bacterial leucyl aminopeptidase
Similarity search - Component
Biological speciesVibrio proteolyticus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsGilboa, R. / Rondeau, J.-M. / Blumberg, S. / Tarnus, C. / Shoham, G.
CitationJournal: To be Published
Title: Interactions of Streptomyces griseus Aminopeptidase and Aeromonas proteolytica Aminopeptidase with Bestatin. Structural analysis of homologous enzymes with different binding modes.
Authors: Gilboa, R. / Rondeau, J.-M. / Blumberg, S. / Tarnus, C. / Shoham, G.
History
DepositionOct 17, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 27, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Oct 25, 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_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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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

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Assembly

Deposited unit
A: Bacterial leucyl aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6774
Polymers32,2381
Non-polymers4393
Water3,099172
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)107.390, 107.390, 103.060
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Detailsthe biological assembly is a monomer

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Components

#1: Protein Bacterial leucyl aminopeptidase


Mass: 32238.150 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-BES / 2-(3-AMINO-2-HYDROXY-4-PHENYL-BUTYRYLAMINO)-4-METHYL-PENTANOIC ACID / BESTATIN


Mass: 308.373 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H24N2O4 / Comment: protease inhibitor*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 172 / 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: 2.66 Å3/Da / Density % sol: 53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: NaCl, KSCN, HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418 Å
DetectorType: XENTRONICS / Detector: AREA DETECTOR / Date: Dec 14, 1992
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→29.7 Å / Num. all: 20836 / Num. obs: 20836 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 15.6 % / Biso Wilson estimate: 19.2 Å2 / Rsym value: 0.064 / Net I/σ(I): 31.1
Reflection shellResolution: 2.1→2.2 Å / Num. unique all: 2519 / Rsym value: 0.339 / % possible all: 94.7

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Processing

Software
NameVersionClassification
CNX2002refinement
X-GENdata reduction
XDSdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AMP

1amp


Resolution: 2.1→29.69 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 43544184.54 / 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
Rfree0.197 2041 9.9 %RANDOM
Rwork0.164 ---
all0.168 20680 --
obs0.168 20680 98.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 74.6938 Å2 / ksol: 0.431785 e/Å3
Displacement parametersBiso mean: 23.9 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å22.86 Å20 Å2
2---0.02 Å20 Å2
3---0.04 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 2.1→29.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2210 0 24 172 2406
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d22.9
X-RAY DIFFRACTIONc_improper_angle_d0.8
X-RAY DIFFRACTIONc_mcbond_it1.641.5
X-RAY DIFFRACTIONc_mcangle_it2.452
X-RAY DIFFRACTIONc_scbond_it2.632
X-RAY DIFFRACTIONc_scangle_it3.72.5
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.229 345 10.9 %
Rwork0.188 2817 -
obs-3162 92.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3BESTATIN.PARAMION.TOP
X-RAY DIFFRACTION4CIS_PEPTIDE.PARAM
X-RAY DIFFRACTION5ION.PARAM

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