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- PDB-2p7s: Enzymatic and Structural Characterisation of Amphinase, a Novel C... -

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Basic information

Entry
Database: PDB / ID: 2p7s
TitleEnzymatic and Structural Characterisation of Amphinase, a Novel Cytotoxic Ribonuclease from Rana pipiens Oocytes
ComponentsAmphinase-2
KeywordsHYDROLASE / Amphinase / cytotoxic RNase / enzyme efficiency / substrate specificity
Function / homology
Function and homology information


Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / RNA nuclease activity / endonuclease activity / angiogenesis / defense response to Gram-negative bacterium / nucleic acid binding / defense response to Gram-positive bacterium / extracellular region
Similarity search - Function
P-30 Protein / Ribonuclease A-like domain / Pancreatic ribonuclease / Ribonuclease A, active site / Ribonuclease A-domain / Ribonuclease A-like domain superfamily / Pancreatic ribonuclease / Pancreatic ribonuclease family signature. / Pancreatic ribonuclease / Roll / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Amphinase-2
Similarity search - Component
Biological speciesRana pipiens (northern leopard frog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSingh, U.P.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Enzymatic and Structural Characterisation of Amphinase, a Novel Cytotoxic Ribonuclease from Rana pipiens Oocytes.
Authors: Singh, U.P. / Ardelt, W. / Saxena, S.K. / Holloway, D.E. / Vidunas, E. / Lee, H.S. / Saxena, A. / Shogen, K. / Acharya, K.R.
History
DepositionMar 20, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 18, 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 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 999SEQUENCE There is no UNP sequence database reference available for the protein at the time of processing.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Amphinase-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7415
Polymers13,1071
Non-polymers6354
Water1,35175
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.967, 53.967, 47.796
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein Amphinase-2


Mass: 13106.916 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Natural Glycosylated form / Source: (natural) Rana pipiens (northern leopard frog) / Cell: Oocytes
References: UniProt: P85073, Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 75 / 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: 2.65 Å3/Da / Density % sol: 53.65 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: protein 25 mg/ml, PEG 8000 30% (w/v), Na-acetate 0.2M, Na-cacodylate 0.1M, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 25, 2004 / Details: Mirrors
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 1.8→38.2 Å / Num. all: 12605 / Num. obs: 12605 / % possible obs: 98 % / Observed criterion σ(F): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.069 / Χ2: 1.065 / Net I/σ(I): 16
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.354 / Num. unique all: 1088 / Χ2: 1.052 / % possible all: 86.5

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Phasing

Phasing MRRfactor: 0.554 / Cor.coef. Fo:Fc: 0.177 / Cor.coef. Io to Ic: 0.099
Highest resolutionLowest resolution
Rotation3 Å54.233 Å
Translation3 Å54.233 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
PDB_EXTRACT2data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1ONC

1onc


Resolution: 1.8→38.2 Å / FOM work R set: 0.812 / Isotropic thermal model: Isotropic / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.241 646 5 %RANDOM
Rwork0.221 ---
all0.235 ---
obs-12588 98.1 %-
Solvent computationBsol: 57.717 Å2
Displacement parametersBiso mean: 33.165 Å2
Baniso -1Baniso -2Baniso -3
1-8.019 Å20 Å20 Å2
2--8.019 Å20 Å2
3----16.037 Å2
Refinement stepCycle: LAST / Resolution: 1.8→38.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms874 0 42 75 991
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.494
X-RAY DIFFRACTIONc_mcbond_it1.3471.5
X-RAY DIFFRACTIONc_scbond_it1.9492
X-RAY DIFFRACTIONc_mcangle_it2.0542
X-RAY DIFFRACTIONc_scangle_it2.852.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs
1.8-1.850.277460.312870916
1.85-1.910.386510.309937988
1.91-1.980.309550.2849861041
1.98-2.060.324540.28910231077
2.06-2.150.317510.2529931044
2.15-2.270.336570.26410131070
2.27-2.410.335590.25410071066
2.41-2.60.25550.22810161071
2.6-2.860.251540.22410181072
2.86-3.270.228520.21410211073
3.27-4.120.208580.20310111069
4.12-500.186540.18410471101
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4act.paramact.top
X-RAY DIFFRACTION5carbohydrate.paramcarbohydrate.top

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