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- PDB-4wwv: Aminopeptidase APDkam598 from the archaeon Desulfurococcus kamcha... -

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Basic information

Entry
Database: PDB / ID: 4wwv
TitleAminopeptidase APDkam598 from the archaeon Desulfurococcus kamchatkensis
ComponentsAminopeptidase from family M42
KeywordsHYDROLASE / aminopeptidase
Function / homology
Function and homology information


aminopeptidase activity / metal ion binding
Similarity search - Function
Peptidase M42, domain 2 / Peptidase M42, domain 2 / M42 glutamyl aminopeptidase / Peptidase M42 / Zn peptidases / Elongation Factor Tu (Ef-tu); domain 3 / Aminopeptidase / Beta Barrel / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Aminopeptidase from family M42
Similarity search - Component
Biological speciesDesulfurococcus kamchatkensis (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.006 Å
AuthorsPetrova, T. / Boyko, K.M. / Rakitina, T.V. / Korzhenevskiy, D.A. / Gorbacheva, M.A. / Popov, V.O.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2015
Title: Structure of the dodecamer of the aminopeptidase APDkam598 from the archaeon Desulfurococcus kamchatkensis.
Authors: Petrova, T.E. / Slutskaya, E.S. / Boyko, K.M. / Sokolova, O.S. / Rakitina, T.V. / Korzhenevskiy, D.A. / Gorbacheva, M.A. / Bezsudnova, E.Y. / Popov, V.O.
History
DepositionNov 12, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 4, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 11, 2015Group: Database references
Revision 1.2Jul 27, 2016Group: Database references
Revision 1.3Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Aminopeptidase from family M42
B: Aminopeptidase from family M42


Theoretical massNumber of molelcules
Total (without water)86,5222
Polymers86,5222
Non-polymers00
Water46826
1
A: Aminopeptidase from family M42
x 12


Theoretical massNumber of molelcules
Total (without water)519,12912
Polymers519,12912
Non-polymers00
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_556-x,y,-z+11
crystal symmetry operation4_556x,-y,-z+11
crystal symmetry operation21_545y,z-1/2,x+1/21
crystal symmetry operation22_545-y,z-1/2,-x+1/21
crystal symmetry operation23_555y,-z+1/2,-x+1/21
crystal symmetry operation24_555-y,-z+1/2,x+1/21
crystal symmetry operation29_455z-1/2,x,y+1/21
crystal symmetry operation30_455z-1/2,-x,-y+1/21
crystal symmetry operation31_555-z+1/2,-x,y+1/21
crystal symmetry operation32_555-z+1/2,x,-y+1/21
Buried area62870 Å2
ΔGint-285 kcal/mol
Surface area130890 Å2
MethodPISA
2
B: Aminopeptidase from family M42
x 12


Theoretical massNumber of molelcules
Total (without water)519,12912
Polymers519,12912
Non-polymers00
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555-z,-x,y1
crystal symmetry operation10_555-y,z,-x1
crystal symmetry operation16_555x,-y+1/2,-z+1/21
crystal symmetry operation20_555-z,x+1/2,-y+1/21
crystal symmetry operation24_555-y,-z+1/2,x+1/21
crystal symmetry operation27_455-x-1/2,y,-z+1/21
crystal symmetry operation30_455z-1/2,-x,-y+1/21
crystal symmetry operation33_455y-1/2,z,x+1/21
crystal symmetry operation38_455-x-1/2,-y+1/2,z1
crystal symmetry operation41_455z-1/2,x+1/2,y1
crystal symmetry operation47_455y-1/2,-z+1/2,-x1
Buried area61830 Å2
ΔGint-303 kcal/mol
Surface area129130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)234.323, 234.323, 234.323
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number196
Space group name H-MF23
Components on special symmetry positions
IDModelComponents
11A-405-

HOH

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Components

#1: Protein Aminopeptidase from family M42


Mass: 43260.789 Da / Num. of mol.: 2 / Mutation: M26V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desulfurococcus kamchatkensis (archaea)
Strain: 1221n / DSM 18924 / Gene: DKAM_0589 / Plasmid: pET15b
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: B8D484
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / 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: 3.38 Å3/Da / Density % sol: 63.6 %
Crystal growTemperature: 293 K / Method: liquid diffusion / pH: 7.5
Details: The reservoir solution contained 0.1 M HEPES, pH 7.0, 0.8 M ammonium sulfate, and glycerol. The crystals were grown over a period of several months.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Sep 6, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. all: 21480 / Num. obs: 21317 / % possible obs: 99.9 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 19.4
Reflection shellResolution: 3→3.05 Å / Mean I/σ(I) obs: 2 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data reduction
PHENIXrefinement
PDB_EXTRACT3.15data extraction
HKL-2000data scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1XFO

1xfo


Resolution: 3.006→47.831 Å / FOM work R set: 0.7646 / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2634 1044 5.16 %
Rwork0.2041 19194 -
obs0.2074 20238 94.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 103.88 Å2 / Biso mean: 36.05 Å2 / Biso min: 21.82 Å2
Refinement stepCycle: final / Resolution: 3.006→47.831 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5479 0 0 26 5505
Biso mean---24.22 -
Num. residues----723
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0135579
X-RAY DIFFRACTIONf_angle_d1.467569
X-RAY DIFFRACTIONf_chiral_restr0.068883
X-RAY DIFFRACTIONf_plane_restr0.006963
X-RAY DIFFRACTIONf_dihedral_angle_d15.8322027
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.0064-3.16480.35231110.25191907201867
3.1648-3.36310.30681620.24252835299799
3.3631-3.62270.2991480.232428763024100
3.6227-3.98710.25341760.203128503026100
3.9871-4.56360.24461460.173628753021100
4.5636-5.74810.261580.19129023060100
5.7481-47.8370.231430.19872949309299

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