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- PDB-6xhf: Structure of Phenylalanyl-5'-O-adenosine phosphoramidate -

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Basic information

Entry
Database: PDB / ID: 6xhf
TitleStructure of Phenylalanyl-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 / Pancreatic ribonuclease family signature. / Pancreatic ribonuclease
Similarity search - Domain/homology
Chem-V2S / Ribonuclease pancreatic
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 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)28,4766
Polymers27,4172
Non-polymers1,0604
Water3,081171
1
A: Ribonuclease pancreatic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2383
Polymers13,7081
Non-polymers5302
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Ribonuclease pancreatic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2383
Polymers13,7081
Non-polymers5302
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)100.102, 32.500, 72.945
Angle α, β, γ (deg.)90.000, 90.420, 90.000
Int Tables number5
Space group name H-MC121

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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-V2S / (2~{S})-2-[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]amino]-3-phenyl-propanoic acid


Mass: 494.395 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H23N6O8P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / 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: 2.16 Å3/Da / Density % sol: 43.16 %
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 Phenylalanyl-O5'-adenosine phosphoramidate was soaked into the crystals using a stock solution of 100 mM, to achieve ...Details: PROTEIN WAS CRYSTALLIZED FROM 25% PEG 3350, 20 MM SODIUM CITRATE, PH 5.5 Phenylalanyl-O5'-adenosine phosphoramidate was soaked into the crystals using a stock solution of 100 mM, to achieve ~35 mM 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-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jul 10, 2019 / Details: Be (Beryllium lens)
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.45→50 Å / Num. obs: 41463 / % possible obs: 98 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.031 / Rrim(I) all: 0.083 / Χ2: 1.644 / Net I/σ(I): 9.2 / Num. measured all: 271958
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.45-1.54.11.71838030.3140.8691.9370.71290.5
1.5-1.5661.37641500.5550.5941.5030.76299.1
1.56-1.636.80.95841490.750.391.0360.82498.9
1.63-1.726.80.63441180.8530.2570.6860.90898.1
1.72-1.836.80.39941020.9390.1610.4311.05197.7
1.83-1.976.80.24240970.9740.0980.2611.38997.5
1.97-2.176.80.14441830.9890.0590.1551.998.6
2.17-2.486.90.09842160.9940.040.1062.39599.9
2.48-3.127.20.06642660.9970.0270.0712.886100
3.12-507.10.04343790.9990.0170.0462.74699.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: One molecule from PDB ID 1AFK

1afk


Resolution: 1.45→30.93 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.956 / SU B: 2.005 / SU ML: 0.072 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.076 / ESU R Free: 0.08 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2311 2093 5.1 %RANDOM
Rwork0.1946 ---
obs0.1965 39307 97.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 98.14 Å2 / Biso mean: 30.032 Å2 / Biso min: 11.64 Å2
Baniso -1Baniso -2Baniso -3
1--0.84 Å2-0 Å2-0.01 Å2
2--0.53 Å2-0 Å2
3---0.31 Å2
Refinement stepCycle: final / Resolution: 1.45→30.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1902 0 70 171 2143
Biso mean--37.23 36.25 -
Num. residues----246
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0122017
X-RAY DIFFRACTIONr_angle_refined_deg1.6681.7032737
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0025246
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.12723.95896
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.17415337
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.572158
X-RAY DIFFRACTIONr_chiral_restr0.1020.2278
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.021526
LS refinement shellResolution: 1.45→1.485 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.397 130 -
Rwork0.383 2540 -
obs--85.47 %

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