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- PDB-3azq: Crystal structure of puromycin hydrolase S511A mutant complexed w... -

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Basic information

Entry
Database: PDB / ID: 3azq
TitleCrystal structure of puromycin hydrolase S511A mutant complexed with PGG
Components
  • Aminopeptidase
  • tripeptide PGG
KeywordsHYDROLASE / POP family
Function / homology
Function and homology information


aminopeptidase activity / serine-type peptidase activity / proteolysis
Similarity search - Function
: / Peptidase S9, prolyl oligopeptidase, catalytic domain / Prolyl oligopeptidase family / Six-bladed beta-propeller, TolB-like / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesStreptomyces morookaensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsMatoba, Y. / Sugiyama, M.
CitationJournal: Proteins / Year: 2011
Title: Structural evidence that puromycin hydrolase is a new type of aminopeptidase with a prolyl oligopeptidase family fold
Authors: Matoba, Y. / Nakayama, A. / Oda, K. / Noda, M. / Kumagai, T. / Nishimura, M. / Sugiyama, M.
History
DepositionMay 27, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 27, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 28, 2011Group: Database references
Revision 1.2Nov 1, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

Downloads & links

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Assembly

Deposited unit
A: Aminopeptidase
B: Aminopeptidase
C: tripeptide PGG
D: tripeptide PGG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,96514
Polymers143,0044
Non-polymers96110
Water9,188510
1
A: Aminopeptidase
C: tripeptide PGG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,0788
Polymers71,5022
Non-polymers5766
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Aminopeptidase
D: tripeptide PGG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,8866
Polymers71,5022
Non-polymers3844
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.430, 142.680, 156.310
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Aminopeptidase


Mass: 71272.773 Da / Num. of mol.: 2 / Mutation: S511A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces morookaensis (bacteria) / Strain: JCM4673 / Gene: pmh / Plasmid: pET-21a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q2HXD9
#2: Protein/peptide tripeptide PGG


Mass: 229.234 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: purchased
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 510 / 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: 3.29 Å3/Da / Density % sol: 62.63 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 1.7M ammonium sulfate, 0.1M Tris-HCl , pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Dec 7, 2007
RadiationMonochromator: vertically bent cylinder mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→100 Å / Num. all: 52360 / Num. obs: 52360 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Biso Wilson estimate: 50.4 Å2 / Rmerge(I) obs: 0.119 / Net I/σ(I): 10.6
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.407 / Mean I/σ(I) obs: 2.5 / Num. unique all: 5113 / % possible all: 98.6

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Processing

Software
NameVersionClassification
BSSdata collection
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
CNS1.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3AZO

3azo


Resolution: 2.7→29.8 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2399339.73 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.24 2645 5.1 %RANDOM
Rwork0.193 ---
obs0.193 52128 99.2 %-
all-52128 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 22.0099 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 24.9 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--6.87 Å20 Å2
3----6.88 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.47 Å0.38 Å
Refinement stepCycle: LAST / Resolution: 2.7→29.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10070 0 50 510 10630
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
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_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.9
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.131.5
X-RAY DIFFRACTIONc_mcangle_it1.92
X-RAY DIFFRACTIONc_scbond_it1.772
X-RAY DIFFRACTIONc_scangle_it2.72.5
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.367 421 4.9 %
Rwork0.308 8128 -
obs--99 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

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