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- PDB-2p6z: Enzymatic and Structural Characterisation of Amphinase, a Novel C... -

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Basic information

Entry
Database: PDB / ID: 2p6z
TitleEnzymatic and Structural Characterisation of Amphinase, a Novel Cytotoxic Ribonuclease from Rana pipiens Oocytes
ComponentsRecombinant Amphinase-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 / 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
CITRIC ACID / Amphinase-2
Similarity search - Component
Biological speciesRana pipiens (northern leopard frog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 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 19, 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: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Apr 3, 2024Group: 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 / diffrn_source / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 999SEQUENCE There is no sequence reference available from UNP sequence database 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: Recombinant Amphinase-2
B: Recombinant Amphinase-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1228
Polymers26,4762
Non-polymers6456
Water5,206289
1
A: Recombinant Amphinase-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,4533
Polymers13,2381
Non-polymers2152
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Recombinant Amphinase-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,6685
Polymers13,2381
Non-polymers4304
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)29.795, 44.607, 46.054
Angle α, β, γ (deg.)116.56, 83.19, 103.68
Int Tables number1
Space group name H-MP1
DetailsBiological unit is monomer

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Components

#1: Protein Recombinant Amphinase-2


Mass: 13238.112 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rana pipiens (northern leopard frog) / Cell: Oocyte / Plasmid: pET-11d / Production host: Escherichia coli (E. coli)
References: UniProt: P85073, Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H8O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 289 / 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: 2.01 Å3/Da / Density % sol: 38.74 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5
Details: protein: 12.5 mg/ml, PEG 4000 30%, Na Citrate 0.1 M, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.807
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: May 12, 2006 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.807 Å / Relative weight: 1
ReflectionResolution: 1.91→41.2 Å / Num. all: 15432 / Num. obs: 14385 / % possible obs: 89.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 2.1 % / Biso Wilson estimate: 15 Å2 / Rmerge(I) obs: 0.037 / Net I/σ(I): 18.8
Reflection shellResolution: 1.91→2.01 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.108 / Mean I/σ(I) obs: 7.5 / Num. unique all: 1477 / % possible all: 63.5

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Phasing

Phasing MRRfactor: 0.448 / Cor.coef. Fo:Fc: 0.48
Highest resolutionLowest resolution
Rotation3 Å12.64 Å
Translation3 Å12.64 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT2data extraction
HKL-2000data collection
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Amphinase-2 (native)

Resolution: 1.93→41.2 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.939 / SU B: 3.066 / SU ML: 0.091 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.189 / ESU R Free: 0.151 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.191 727 5.1 %RANDOM
Rwork0.146 ---
all0.148 15432 --
obs0.148 14385 93.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.63 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å2-1.18 Å2-1.02 Å2
2---0.18 Å20.05 Å2
3----0.27 Å2
Refinement stepCycle: LAST / Resolution: 1.93→41.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1797 0 42 289 2128
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0221890
X-RAY DIFFRACTIONr_angle_refined_deg1.2241.9452587
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0465241
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.76224.58885
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.87915324
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3391510
X-RAY DIFFRACTIONr_chiral_restr0.0870.2289
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021446
X-RAY DIFFRACTIONr_nbd_refined0.1920.2925
X-RAY DIFFRACTIONr_nbtor_refined0.2920.21333
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1340.2248
X-RAY DIFFRACTIONr_metal_ion_refined0.1480.25
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1580.254
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1860.234
X-RAY DIFFRACTIONr_mcbond_it0.4851.51150
X-RAY DIFFRACTIONr_mcangle_it0.93221913
X-RAY DIFFRACTIONr_scbond_it1.7083756
X-RAY DIFFRACTIONr_scangle_it2.7764.5663
LS refinement shellResolution: 1.933→1.983 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.223 48 -
Rwork0.172 897 -
obs-945 80.63 %

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