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- PDB-6xhd: Structure of Prolinyl-5'-O-adenosine phosphoramidate -

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Basic information

Entry
Database: PDB / ID: 6xhd
TitleStructure of Prolinyl-5'-O-adenosine phosphoramidate
ComponentsRibonuclease pancreatic
KeywordsRNA BINDING PROTEIN / RNase A complex / amino acid release / prodrug
Function / homology
Function and homology information


pancreatic ribonuclease / ribonuclease A activity / RNA nuclease activity / nucleic acid binding / defense response to Gram-positive bacterium / lyase activity / extracellular region
Similarity search - Function
Pancreatic ribonuclease / Ribonuclease A, active site / Ribonuclease A-domain / Ribonuclease A-like domain superfamily / Pancreatic ribonuclease family signature. / Pancreatic ribonuclease / Pancreatic ribonuclease
Similarity search - Domain/homology
: / Chem-V2P / Ribonuclease pancreatic
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.51 Å
AuthorsPallan, P.S. / Egli, M.
Funding support Germany, 1items
OrganizationGrant numberCountry
Volkswagen Foundationgrant Az 92 768 Germany
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2020
Title: The Enzyme-Free Release of Nucleotides from Phosphoramidates Depends Strongly on the Amino Acid.
Authors: Jovanovic, D. / Tremmel, P. / Pallan, P.S. / Egli, M. / Richert, C.
History
DepositionJun 18, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 17, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)28,0185
Polymers27,4172
Non-polymers6023
Water4,864270
1
A: Ribonuclease pancreatic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7472
Polymers13,7081
Non-polymers391
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Ribonuclease pancreatic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2713
Polymers13,7081
Non-polymers5632
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)98.532, 30.689, 68.641
Angle α, β, γ (deg.)90.000, 90.560, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-305-

HOH

21A-379-

HOH

31B-405-

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 genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Gene: RNASE1, RNS1 / Organ: PANCREAS / Production host: Bos taurus (domestic cattle) / References: UniProt: P61823, pancreatic ribonuclease
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-V2P / (2~{S})-1-[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]pyrrolidine-2-carboxylic acid


Mass: 444.336 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H21N6O8P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 270 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 1.89 Å3/Da / Density % sol: 35.01 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: PROTEIN WAS CRYSTALLIZED FROM 25% PEG 3350, 20 MM SODIUM CITRATE, PH 5.5 Prolinyl-5'-O-adenosine phosphoramidate soaking was achieved as follows. 1 uL of a stock solution of 100 mM ligand ...Details: PROTEIN WAS CRYSTALLIZED FROM 25% PEG 3350, 20 MM SODIUM CITRATE, PH 5.5 Prolinyl-5'-O-adenosine phosphoramidate soaking was achieved as follows. 1 uL of a stock solution of 100 mM ligand was added to 2uL of reservoir solution, to achieve a concentration of ~33 mM in the soaking solution. A few RNase A crystals were soaked for 45 - 90 minutes in the soaking solution

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 19, 2019 / Details: C(111)
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.51→50 Å / Num. obs: 31473 / % possible obs: 96.9 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.034 / Net I/σ(I): 25.76
Reflection shellResolution: 1.51→1.56 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.588 / Mean I/σ(I) obs: 1.38 / Num. unique obs: 2688 / Rpim(I) all: 0.372 / % possible all: 83

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AFK (using one molecule)

1afk


Resolution: 1.51→49.31 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.958 / SU B: 2.103 / SU ML: 0.073 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.085 / ESU R Free: 0.092 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2171 1576 5 %RANDOM
Rwork0.1687 ---
obs0.1711 29895 96.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 110.46 Å2 / Biso mean: 26.492 Å2 / Biso min: 14.4 Å2
Baniso -1Baniso -2Baniso -3
1--0.25 Å20 Å2-0.11 Å2
2--1.9 Å2-0 Å2
3----1.65 Å2
Refinement stepCycle: final / Resolution: 1.51→49.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1902 0 39 270 2211
Biso mean--44.78 37.61 -
Num. residues----248
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0121990
X-RAY DIFFRACTIONr_angle_refined_deg1.3481.6782698
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3685246
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.97324.08298
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.54815340
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.243158
X-RAY DIFFRACTIONr_chiral_restr0.1070.2276
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.021505
LS refinement shellResolution: 1.512→1.551 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 101 -
Rwork0.302 1721 -
all-1822 -
obs--76.78 %

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