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- PDB-2cwj: crystal structure of APE1501, a putative endonuclease from Aeropy... -

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Basic information

Entry
Database: PDB / ID: 2cwj
Titlecrystal structure of APE1501, a putative endonuclease from Aeropyrum pernix
Componentsputative endonuclease
KeywordsHYDROLASE / endoribonucrease / Aeropyrum pernix / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


Hydrolases; Acting on ester bonds / hydrolase activity
Similarity search - Function
RidA family / YjgF/YER057c/UK114 family / Endoribonuclease L-PSP / RutC-like / RutC-like superfamily / 60s Ribosomal Protein L30; Chain: A; / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Ribonuclease UK114
Similarity search - Component
Biological speciesAeropyrum pernix (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.6 Å
AuthorsTakemoto-hori, C. / Suetsugu-hanawa, K. / Murayama, K. / Shirouzu, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: crystal structure of APE1501, a putative endonuclease from Aeropyrum pernix
Authors: Takemoto-hori, C. / Suetsugu-hanawa, K. / Murayama, K. / Shirouzu, M. / Yokoyama, S.
History
DepositionJun 21, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 21, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: putative endonuclease


Theoretical massNumber of molelcules
Total (without water)13,4841
Polymers13,4841
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: putative endonuclease

A: putative endonuclease

A: putative endonuclease


Theoretical massNumber of molelcules
Total (without water)40,4533
Polymers40,4533
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_564z,x+1,y-11
crystal symmetry operation9_465y-1,z+1,x1
Buried area4970 Å2
ΔGint-40 kcal/mol
Surface area14200 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)109.026, 109.026, 109.026
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number199
Space group name H-MI213

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Components

#1: Protein putative endonuclease


Mass: 13484.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aeropyrum pernix (archaea) / Strain: K1 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE2)pRARE
References: GenBank: 5105186, UniProt: Q9YBU8*PLUS, Hydrolases; Acting on ester bonds

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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: 4 Å3/Da / Density % sol: 69.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 2.5M Ammonium sulphate, 0.2M Sodium malonate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 25, 2005
RadiationMonochromator: conforcal mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.6→50 Å / Num. obs: 2592 / % possible obs: 99.3 % / Observed criterion σ(I): -3
Reflection shellResolution: 3.6→3.83 Å / % possible all: 100

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT1.601data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.6→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.337 242 9.3 %RANDOM
Rwork0.326 ---
obs-2574 98.5 %-
Solvent computationBsol: 69.055 Å2
Displacement parametersBiso mean: 121.628 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.82 Å0.69 Å
Luzzati d res low-5 Å
Luzzati sigma a0.83 Å0.74 Å
Refinement stepCycle: LAST / Resolution: 3.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms886 0 0 0 886
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.7
Xplor fileSerial no: 1 / Param file: protein_rep.param

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