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- PDB-6enp: Atomic resolution structure of human RNase 6 in the presence of p... -

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Basic information

Entry
Database: PDB / ID: 6enp
TitleAtomic resolution structure of human RNase 6 in the presence of phosphate anions in P21 space group.
ComponentsRibonuclease K6
KeywordsHYDROLASE / RNASE K6 / PANCREATIC RIBONUCLEASE
Function / homology
Function and homology information


Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / RNA catabolic process / Antimicrobial peptides / RNA nuclease activity / defense response / antimicrobial humoral immune response mediated by antimicrobial peptide / antibacterial humoral response / cytoplasmic vesicle / endonuclease activity / defense response to Gram-negative bacterium ...Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / RNA catabolic process / Antimicrobial peptides / RNA nuclease activity / defense response / antimicrobial humoral immune response mediated by antimicrobial peptide / antibacterial humoral response / cytoplasmic vesicle / endonuclease activity / defense response to Gram-negative bacterium / defense response to virus / nucleic acid binding / lysosome / defense response to Gram-positive bacterium / innate immune response / extracellular space / 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
PHOSPHATE ION / Ribonuclease K6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.042 Å
AuthorsPrats-Ejarque, G. / Moussaoui, M. / Boix, E.
Funding support Spain, 2items
OrganizationGrant numberCountry
MINECOSAF2015-66007-P Spain
Generalitat de Catalunya2014 SGR 728 Spain
Citation
Journal: Biochim Biophys Acta Gen Subj / Year: 2019
Title: Characterization of an RNase with two catalytic centers. Human RNase6 catalytic and phosphate-binding site arrangement favors the endonuclease cleavage of polymeric substrates.
Authors: Prats-Ejarque, G. / Blanco, J.A. / Salazar, V.A. / Nogues, V.M. / Moussaoui, M. / Boix, E.
#1: Journal: Biochem. J. / Year: 2016
Title: The first crystal structure of human RNase 6 reveals a novel substrate-binding and cleavage site arrangement.
Authors: Prats-Ejarque, G. / Arranz-Trullen, J. / Blanco, J.A. / Pulido, D. / Nogues, M.V. / Moussaoui, M. / Boix, E.
History
DepositionOct 5, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 24, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 11, 2019Group: Data collection / Database references / Category: citation / Item: _citation.year
Revision 1.2Jan 17, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_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_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_conn.ptnr2_symmetry
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ribonuclease K6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,2629
Polymers14,8071
Non-polymers4558
Water3,999222
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area880 Å2
ΔGint-54 kcal/mol
Surface area8230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)27.734, 38.557, 98.965
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Ribonuclease K6 / RNase K6


Mass: 14807.069 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RNASE6, RNS6 / Plasmid: PET11C / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q93091, Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters

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Non-polymers , 5 types, 230 molecules

#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 222 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 1.79 Å3/Da / Density % sol: 31.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 1 M ammonium phosphate, 100 mM sodium acetate pH 4.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9796 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 26, 2016
Details: VERTICAL FOCUSING MIRROR (VFM) AND A HORIZONTAL FOCUSING MIRROR (HFM)
RadiationMonochromator: CHANNEL-CUT DOUBLE CRYSTAL MONOCHROMATOR (CINEL), 6 MM GAP
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 1.042→35.93 Å / Num. obs: 95760 / % possible obs: 97.2 % / Redundancy: 3.5 % / Biso Wilson estimate: 12.24 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.03216 / Rpim(I) all: 0.01895 / Rrim(I) all: 0.0376 / Net I/σ(I): 17.08
Reflection shellResolution: 1.042→1.079 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.5059 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 4946 / CC1/2: 0.75 / Rpim(I) all: 0.3064 / Rrim(I) all: 0.01895 / % possible all: 97.13

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
XDS20151001data reduction
Aimless0.5.17data scaling
PHENIX1.11.1_2575phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4X09

4x09


Resolution: 1.042→35.927 Å / SU ML: 0.07 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 11.63
RfactorNum. reflection% reflection
Rfree0.1449 4800 5.01 %
Rwork0.1215 --
obs0.1227 95760 97.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 19.33 Å2
Refinement stepCycle: LAST / Resolution: 1.042→35.927 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1036 0 20 222 1278
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0131330
X-RAY DIFFRACTIONf_angle_d1.4241837
X-RAY DIFFRACTIONf_dihedral_angle_d14.911535
X-RAY DIFFRACTIONf_chiral_restr0.102186
X-RAY DIFFRACTIONf_plane_restr0.011248
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.0419-1.05370.2351770.21683045X-RAY DIFFRACTION98
1.0537-1.06610.20681830.20192943X-RAY DIFFRACTION95
1.0661-1.07910.20491410.18273077X-RAY DIFFRACTION99
1.0791-1.09280.18761900.1652998X-RAY DIFFRACTION99
1.0928-1.10720.20021660.163115X-RAY DIFFRACTION97
1.1072-1.12240.20791420.1552976X-RAY DIFFRACTION98
1.1224-1.13840.16411210.14183116X-RAY DIFFRACTION99
1.1384-1.15540.14551530.13173068X-RAY DIFFRACTION97
1.1554-1.17340.14961390.12563046X-RAY DIFFRACTION99
1.1734-1.19270.16031590.12283071X-RAY DIFFRACTION99
1.1927-1.21320.13831720.11973052X-RAY DIFFRACTION98
1.2132-1.23530.12581570.11243094X-RAY DIFFRACTION100
1.2353-1.25910.1531910.11423076X-RAY DIFFRACTION99
1.2591-1.28480.1351450.11593111X-RAY DIFFRACTION100
1.2848-1.31270.14442150.11523011X-RAY DIFFRACTION100
1.3127-1.34320.14761780.10853049X-RAY DIFFRACTION99
1.3432-1.37680.14661500.10383132X-RAY DIFFRACTION99
1.3768-1.41410.13231640.10363011X-RAY DIFFRACTION98
1.4141-1.45570.13621360.09573142X-RAY DIFFRACTION99
1.4557-1.50270.1111770.09663071X-RAY DIFFRACTION100
1.5027-1.55640.1431410.09583120X-RAY DIFFRACTION100
1.5564-1.61870.13141540.09943110X-RAY DIFFRACTION100
1.6187-1.69230.13511700.10393084X-RAY DIFFRACTION100
1.6923-1.78160.13561730.10923056X-RAY DIFFRACTION99
1.7816-1.89320.13041580.10713077X-RAY DIFFRACTION99
1.8932-2.03930.13581630.10412997X-RAY DIFFRACTION97
2.0393-2.24450.10181560.10812557X-RAY DIFFRACTION83
2.2445-2.56930.16861370.12073039X-RAY DIFFRACTION97
2.5693-3.23670.12931440.13332984X-RAY DIFFRACTION96
3.2367-35.9480.17191480.14112732X-RAY DIFFRACTION88

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