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- PDB-5bte: Crystal structure of Ashbya gossypii Rai1 in complex with pU(S)6-Mn2+ -

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Basic information

Entry
Database: PDB / ID: 5bte
TitleCrystal structure of Ashbya gossypii Rai1 in complex with pU(S)6-Mn2+
Components
  • AFR263Cp
  • RNA (5'-R(P*UP*(U37)P*(U37)P*UP*UP*U)-3')
Keywordshydrolase/rna / Rai1 / RNA / Decapping / mRNA 5'-processing / hydrolase-rna complex
Function / homology
Function and homology information


mRNA 5'-diphosphatase activity / NAD-cap decapping / exonuclease activity / nuclear-transcribed mRNA catabolic process / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / mRNA processing / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / nucleotide binding / RNA binding / metal ion binding ...mRNA 5'-diphosphatase activity / NAD-cap decapping / exonuclease activity / nuclear-transcribed mRNA catabolic process / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / mRNA processing / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / nucleotide binding / RNA binding / metal ion binding / nucleus / cytosol
Similarity search - Function
RAI1-like / RAI1-like family / RAI1 like PD-(D/E)XK nuclease
Similarity search - Domain/homology
: / RNA / Decapping nuclease RAI1
Similarity search - Component
Biological speciesAshbya gossypii (fungus)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.4 Å
AuthorsWang, V.Y. / Tong, L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM090059 United States
CitationJournal: Nucleic Acids Res. / Year: 2015
Title: Structural and biochemical studies of the distinct activity profiles of Rai1 enzymes.
Authors: Wang, V.Y. / Jiao, X. / Kiledjian, M. / Tong, L.
History
DepositionJun 3, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 22, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 5, 2015Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Refinement description
Category: citation / pdbx_audit_support ...citation / pdbx_audit_support / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_conn_type
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_asym_id / _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.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn.ptnr2_label_seq_id / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: AFR263Cp
D: RNA (5'-R(P*UP*(U37)P*(U37)P*UP*UP*U)-3')
C: RNA (5'-R(P*UP*(U37)P*(U37)P*UP*UP*U)-3')
A: AFR263Cp
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,39412
Polymers89,8734
Non-polymers5228
Water6,431357
1
B: AFR263Cp
D: RNA (5'-R(P*UP*(U37)P*(U37)P*UP*UP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1976
Polymers44,9362
Non-polymers2614
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: RNA (5'-R(P*UP*(U37)P*(U37)P*UP*UP*U)-3')
A: AFR263Cp
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1976
Polymers44,9362
Non-polymers2614
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.655, 79.742, 160.143
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.999971, 0.00662, -0.003799), (0.006619, -0.999978, -0.000202), (-0.0038, 0.000177, -0.999993)-35.05638, 1.85463, -80.09438

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Components

#1: Protein AFR263Cp


Mass: 43112.188 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ashbya gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056) (fungus)
Strain: ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056 / Gene: AGOS_AFR263C / Production host: Escherichia coli (E. coli) / References: UniProt: Q753P9
#2: RNA chain RNA (5'-R(P*UP*(U37)P*(U37)P*UP*UP*U)-3')


Mass: 1824.169 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 357 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.47 Å3/Da / Density % sol: 50.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: AgRai1-pU(S)6-Mn2+ complex was obtained by soaking the free AgRai1 crystal with 10mM pU(s)6 and 10mM MnCl2 overnight in the presence of 20%(w/v) PEG3350 and 10%(v/v) ethylene glycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 1, 2014
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 33896 / % possible obs: 100 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.124 / Net I/σ(I): 15.3
Reflection shellResolution: 2.4→2.5 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.465 / Mean I/σ(I) obs: 3.6 / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
HKL-2000data scaling
PHASERphasing
RefinementResolution: 2.4→42.41 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.927 / SU B: 7.542 / SU ML: 0.175 / Cross valid method: THROUGHOUT / ESU R: 0.441 / ESU R Free: 0.272 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25379 1787 5 %RANDOM
Rwork0.19573 ---
obs0.19864 33896 99.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.313 Å2
Baniso -1Baniso -2Baniso -3
1--0.12 Å20 Å20 Å2
2---1.3 Å2-0 Å2
3---1.42 Å2
Refinement stepCycle: LAST / Resolution: 2.4→42.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5935 242 16 357 6550
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0196326
X-RAY DIFFRACTIONr_bond_other_d0.0010.025934
X-RAY DIFFRACTIONr_angle_refined_deg1.5831.9638562
X-RAY DIFFRACTIONr_angle_other_deg0.823313667
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7685729
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.65623.255298
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.038151098
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8521554
X-RAY DIFFRACTIONr_chiral_restr0.0840.2928
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026898
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021476
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.397→2.527 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.337 220 -
Rwork0.251 4830 -
obs--98.44 %

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