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- PDB-2ek8: Aminopeptidase from Aneurinibacillus sp. strain AM-1 -

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Basic information

Entry
Database: PDB / ID: 2ek8
TitleAminopeptidase from Aneurinibacillus sp. strain AM-1
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
ISOPROPYL ALCOHOL / Aminopeptidase
Similarity search - Component
Biological speciesAneurinibacillus sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 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 1.2Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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)45,7428
Polymers45,2901
Non-polymers4537
Water9,314517
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)91,48416
Polymers90,5792
Non-polymers90514
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,-y,z1
Buried area3180 Å2
ΔGint-421.8 kcal/mol
Surface area32840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.624, 68.618, 76.841
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-2464-

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-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL / Isopropyl alcohol


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 517 / 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: 4

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Sample preparation

CrystalDensity Matthews: 2.72 Å3/Da / Density % sol: 54.85 %
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

Diffraction
IDMean temperature (K)Crystal-ID
1931
21001
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
ROTATING ANODERIGAKU11.5418
SYNCHROTRONSPring-8 BL44B220.9792, 0.9788, 0.9639
Detector
TypeIDDetectorDate
RIGAKU RAXIS VII1IMAGE PLATEJul 6, 2006
ADSC QUANTUM 3152CCD
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.54181
20.97921
30.97881
40.96391
ReflectionResolution: 1.8→19.9 Å / Num. obs: 45919 / % possible obs: 98.7 % / Redundancy: 10.6 % / Biso Wilson estimate: 18.5 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 31.2
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 10.5 % / Rmerge(I) obs: 0.336 / Mean I/σ(I) obs: 6.1 / % possible all: 97.1

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Processing

Software
NameVersionClassification
CNS1.1refinement
CrystalCleardata collection
MOSFLMdata reduction
SCALAdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.8→19.85 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1875354.05 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.238 2292 5 %RANDOM
Rwork0.213 ---
obs0.213 45812 98.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 46.2604 Å2 / ksol: 0.37918 e/Å3
Displacement parametersBiso mean: 28.1 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å20 Å20 Å2
2---0.19 Å20 Å2
3---0.25 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.1 Å0.09 Å
Refinement stepCycle: LAST / Resolution: 1.8→19.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3119 0 10 517 3646
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_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.77
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.961.5
X-RAY DIFFRACTIONc_mcangle_it1.542
X-RAY DIFFRACTIONc_scbond_it2.012
X-RAY DIFFRACTIONc_scangle_it2.682.5
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.263 388 5.2 %
Rwork0.249 7026 -
obs--96.8 %
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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