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- PDB-3azo: Crystal structure of puromycin hydrolase -

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Basic information

Entry
Database: PDB / ID: 3azo
TitleCrystal structure of puromycin hydrolase
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 / MAD / Resolution: 2 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 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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)143,7178
Polymers143,1402
Non-polymers5766
Water19,5641086
1
A: Aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,8584
Polymers71,5701
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,8584
Polymers71,5701
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)83.920, 142.270, 156.150
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: 71570.148 Da / Num. of mol.: 2
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): B834(DE3) / References: UniProt: Q2HXD9
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1086 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.26 Å3/Da / Density % sol: 62.22 %
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: BL41XU / Wavelength: 0.97892, 0.97912, 0.99491
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 9, 2007
RadiationMonochromator: Fixed exit double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.978921
20.979121
30.994911
ReflectionResolution: 2→100 Å / Num. all: 126640 / Num. obs: 126640 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Biso Wilson estimate: 11.7 Å2 / Rmerge(I) obs: 0.095 / Net I/σ(I): 22.5
Reflection shellResolution: 2→2.07 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.402 / Mean I/σ(I) obs: 4.2 / Num. unique all: 12493 / % possible all: 100

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Processing

Software
NameVersionClassification
BSSdata collection
SHARPphasing
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 2→29.69 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 3226881.99 / 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
Rfree0.199 6355 5 %RANDOM
Rwork0.177 ---
obs0.177 126511 99.8 %-
all-126511 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 56.6517 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 21.7 Å2
Baniso -1Baniso -2Baniso -3
1--1.1 Å20 Å20 Å2
2--4.15 Å20 Å2
3----3.05 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.15 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 2→29.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10056 0 30 1086 11172
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_d0.8
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_it1.662
X-RAY DIFFRACTIONc_scbond_it1.942
X-RAY DIFFRACTIONc_scangle_it2.752.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.007 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.222 1065 5.1 %
Rwork0.197 19750 -
obs--99.8 %
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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