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- PDB-3azp: Crystal structure of puromycin hydrolase S511A mutant -

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Basic information

Entry
Database: PDB / ID: 3azp
TitleCrystal structure of puromycin hydrolase S511A mutant
ComponentsAminopeptidase
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: 2.15 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

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Assembly

Deposited unit
A: Aminopeptidase
B: Aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,0267
Polymers142,5462
Non-polymers4805
Water18,1771009
1
A: Aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,5614
Polymers71,2731
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,4653
Polymers71,2731
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)84.110, 142.620, 156.300
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: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1009 / 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: 62.59 %
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: 2.15→100 Å / Num. all: 95945 / Num. obs: 95945 / % possible obs: 93 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 20.2 Å2 / Rmerge(I) obs: 0.092 / Net I/σ(I): 12.2
Reflection shellResolution: 2.15→2.23 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.416 / Mean I/σ(I) obs: 2.1 / Num. unique all: 8464 / % possible all: 83.2

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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: 2.15→29.74 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 3224286.67 / 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
Rfree0.219 4814 5 %RANDOM
Rwork0.188 ---
obs0.188 95702 93.2 %-
all-95702 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 61.5823 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 27.7 Å2
Baniso -1Baniso -2Baniso -3
1--2.31 Å20 Å20 Å2
2--8.74 Å20 Å2
3----6.44 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.28 Å0.24 Å
Refinement stepCycle: LAST / Resolution: 2.15→29.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10054 0 25 1009 11088
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_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.83
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.151.5
X-RAY DIFFRACTIONc_mcangle_it1.772
X-RAY DIFFRACTIONc_scbond_it1.932
X-RAY DIFFRACTIONc_scangle_it2.732.5
LS refinement shellResolution: 2.15→2.28 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.27 713 4.9 %
Rwork0.252 13751 -
obs--85.7 %
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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