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- PDB-8fhm: RNase A-Uridine 5'-Hexaphosphate (RNaseA.p6U) -

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Basic information

Entry
Database: PDB / ID: 8fhm
TitleRNase A-Uridine 5'-Hexaphosphate (RNaseA.p6U)
ComponentsRibonuclease pancreatic
KeywordsRNA BINDING PROTEIN/INHIBITOR / RNase A / oligophosphate / inhibitor / nucleoside hexaphosphate / protein-ligan complex / RNA BINDING PROTEIN-INHIBITOR complex
Function / homology
Function and homology information


pancreatic ribonuclease / ribonuclease A activity / RNA nuclease activity / nucleic acid binding / lyase activity / defense response to Gram-positive bacterium / extracellular region
Similarity search - Function
Pancreatic ribonuclease / Ribonuclease A, active site / Ribonuclease A-domain / Ribonuclease A-like domain superfamily / Pancreatic ribonuclease / Pancreatic ribonuclease family signature. / Pancreatic ribonuclease
Similarity search - Domain/homology
Chem-U6F / Ribonuclease pancreatic
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SOLUTION SCATTERING / MOLECULAR REPLACEMENT / Resolution: 1.79 Å
AuthorsPark, G. / Cummins, C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: To Be Published
Title: Experimental and Computational Studies for the Effect of Lengthening the Phosphate Chain of Nucleotide on the RNase A inhibitors.
Authors: Park, G. / Cummins, C.
History
DepositionDec 14, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 20, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ribonuclease pancreatic
B: Ribonuclease pancreatic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5895
Polymers27,4172
Non-polymers2,1723
Water4,468248
1
A: Ribonuclease pancreatic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4322
Polymers13,7081
Non-polymers7241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ribonuclease pancreatic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,1563
Polymers13,7081
Non-polymers1,4482
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)100.069, 32.527, 72.785
Angle α, β, γ (deg.)90.000, 90.480, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11B-448-

HOH

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Components

#1: Protein Ribonuclease pancreatic / RNase 1 / RNase A


Mass: 13708.326 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: Chain C U6F U6F U6F / Source: (natural) Bos taurus (cattle) / References: UniProt: P61823, pancreatic ribonuclease
#2: Chemical ChemComp-U6F / 5'-O-[(S)-hydroxy{[(S)-hydroxy{[(R)-hydroxy{[(S)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]oxy}phosphoryl]oxy}phosphoryl]oxy}phosphoryl]uridine


Type: RNA linking / Mass: 724.081 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C9H18N2O24P6 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 248 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

Experiment
MethodNumber of used crystals
X-RAY DIFFRACTION1
SOLUTION SCATTERING

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Sample preparation

CrystalDensity Matthews: 2.16 Å3/Da / Density % sol: 43.06 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 25% PEG4000, 20 mM citrate, pH 6, crystal soaked in 50 mM ligand, 30% PEG4000, 25% glycerol, 20 mM citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR-H / Wavelength: 1.544178 Å
DetectorType: APEX II CCD / Detector: CCD / Date: Oct 23, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.544178 Å / Relative weight: 1
ReflectionResolution: 1.79→30.93 Å / Num. obs: 22299 / % possible obs: 99.29 % / Redundancy: 17.13 % / Biso Wilson estimate: 17.55 Å2 / Rsym value: 0.05 / Net I/σ(I): 3.13
Reflection shellResolution: 1.79→1.86 Å / Num. unique obs: 22299 / Rsym value: 0.05

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
SAINTdata reduction
SADABSdata scaling
PHENIX1.20.1_4487phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1AFU

1afu


Resolution: 1.79→30.93 Å / SU ML: 0.214 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.7391
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2309 1137 5.1 %
Rwork0.1782 21162 -
obs0.1808 22299 99.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.5 Å2
Refinement stepCycle: LAST / Resolution: 1.79→30.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1894 0 123 248 2265
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01192102
X-RAY DIFFRACTIONf_angle_d1.38432896
X-RAY DIFFRACTIONf_chiral_restr0.0616303
X-RAY DIFFRACTIONf_plane_restr0.0099349
X-RAY DIFFRACTIONf_dihedral_angle_d34.3247311
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.79-1.870.34491380.26052519X-RAY DIFFRACTION95.51
1.87-1.970.26341650.21612578X-RAY DIFFRACTION99.67
1.97-2.10.24661360.18232662X-RAY DIFFRACTION100
2.1-2.260.21271080.16362669X-RAY DIFFRACTION99.96
2.26-2.480.20421620.17052645X-RAY DIFFRACTION99.86
2.48-2.840.25261490.17962623X-RAY DIFFRACTION99.68
2.84-3.580.21151630.1632675X-RAY DIFFRACTION99.79
3.58-30.930.22231160.1742791X-RAY DIFFRACTION99.83
Refinement TLS params.Method: refined / Origin x: 20.8943519672 Å / Origin y: -0.591650368591 Å / Origin z: 21.2729051685 Å
111213212223313233
T0.15026433969 Å2-0.0224487975764 Å2-0.0120199533713 Å2-0.135475426637 Å20.0215280981847 Å2--0.13826372585 Å2
L1.10938423004 °20.0870057887908 °2-0.622135141397 °2-0.36698113115 °20.139291729478 °2--0.844961426518 °2
S-0.0652322815583 Å °0.217895937699 Å °0.0120610905331 Å °-0.10713212516 Å °0.0522058482457 Å °-0.0143060720638 Å °0.0338776101905 Å °-0.108668606998 Å °0.0207262444522 Å °
Refinement TLS groupSelection details: all

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