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- PDB-2ek9: Aminopeptidase from Aneurinibacillus sp. strain AM-1 with Bestatin -

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Basic information

Entry
Database: PDB / ID: 2ek9
TitleAminopeptidase from Aneurinibacillus sp. strain AM-1 with Bestatin
ComponentsAminopeptidase
KeywordsHYDROLASE / METALLOPROTEINASE
Function / homology
Function and homology information


metalloexopeptidase activity / aminopeptidase activity / proteolysis / metal ion binding
Similarity search - Function
Peptidase M28 family / Glucose Oxidase; domain 1 - #30 / PA domain superfamily / PA domain / PA domain / Glucose Oxidase; domain 1 / Peptidase M28 / Peptidase family M28 / Zn peptidases / Aminopeptidase ...Peptidase M28 family / Glucose Oxidase; domain 1 - #30 / PA domain superfamily / PA domain / PA domain / Glucose Oxidase; domain 1 / Peptidase M28 / Peptidase family M28 / Zn peptidases / Aminopeptidase / 3-Layer(bba) Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-BES / ISOPROPYL ALCOHOL / Aminopeptidase
Similarity search - Component
Biological speciesAneurinibacillus sp. (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsAkioka, M. / Nakano, H. / Watanabe, K.
Citation
Journal: To be published
Title: Structural characterization of a novel bacterial aminopeptidase with an apical domain from aneurinibacillus sp. strain AM-1
Authors: Akioka, M. / Nakano, H. / Tsujimoto, Y. / Matsui, H. / Nakatsu, T. / Kato, H. / Watanabe, K.
#1: Journal: ACTA CRYSTALLOGR.,SECT.F / Year: 2006
Title: Overexpression, purification, crystallization and preliminary X-ray crystallographic studies of a proline-specific aminopeptidase from Aneurinibacillus sp. strain AM-1
Authors: Akioka, M. / Nakano, H. / Horikiri, A. / Tsujimoto, Y. / Matsui, H. / Shimizu, T. / Nakatsu, T. / Kato, H. / Watanabe, K.
History
DepositionMar 22, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 25, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Oct 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0519
Polymers45,2901
Non-polymers7618
Water9,080504
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Aminopeptidase
hetero molecules

A: Aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,10118
Polymers90,5792
Non-polymers1,52216
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area4590 Å2
ΔGint-416.8 kcal/mol
Surface area32620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.813, 68.678, 77.044
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-3273-

HOH

21A-3300-

HOH

31A-3495-

HOH

41A-3502-

HOH

51A-3503-

HOH

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Components

#1: Protein Aminopeptidase


Mass: 45289.699 Da / Num. of mol.: 1 / Fragment: Residues 1-421
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aneurinibacillus sp. (bacteria) / Strain: AM-1 / Plasmid: PET-11A / Production host: Escherichia coli (E. coli) / References: UniProt: A2V759
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / 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
#4: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 504 / 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: 2.74 Å3/Da / Density % sol: 55.09 %
Crystal growTemperature: 299 K / Method: vapor diffusion / pH: 5.8
Details: 13% PEG 8000, 0.1M MES-NaOH, 0.2M Zinc acetate, pH 5.8, VAPOR DIFFUSION, temperature 299K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Aug 29, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.97→15 Å / Num. obs: 35820 / % possible obs: 99.8 % / Redundancy: 4.75 % / Biso Wilson estimate: 17.3 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 18.9
Reflection shellResolution: 1.97→2.08 Å / Rmerge(I) obs: 0.292 / Mean I/σ(I) obs: 4.9 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
CrystalCleardata collection
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2EK8

2ek8


Resolution: 1.97→15 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2014166.97 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.219 1777 5 %RANDOM
Rwork0.199 ---
obs0.199 35768 99.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 59.7327 Å2 / ksol: 0.393232 e/Å3
Displacement parametersBiso mean: 28.5 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å20 Å20 Å2
2---0.09 Å20 Å2
3---0.15 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.13 Å0.1 Å
Refinement stepCycle: LAST / Resolution: 1.97→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3119 0 32 504 3655
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
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_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d2.08
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.031.5
X-RAY DIFFRACTIONc_mcangle_it1.652
X-RAY DIFFRACTIONc_scbond_it2.132
X-RAY DIFFRACTIONc_scangle_it2.812.5
LS refinement shellResolution: 1.97→2.09 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.236 272 4.6 %
Rwork0.219 5605 -
obs--99.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2zn.paramzn.top
X-RAY DIFFRACTION3hoh.paramhoh.top
X-RAY DIFFRACTION4ipa.paramipa.top
X-RAY DIFFRACTION5cis_peptide.param

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