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- PDB-2ab4: Dissecting the Roles of a Strictly Conserved Tyrosine in Substrat... -

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Basic information

Entry
Database: PDB / ID: 2ab4
TitleDissecting the Roles of a Strictly Conserved Tyrosine in Substrate Recognition and Catalysis by Pseudouridine 55 Synthase
Components
  • 5'-R(*CP*CP*AP*CP*GP*GP*UP*(FHU)P*CP*GP*AP*AP*UP*CP*CP*GP*UP*GP*GP*C)-3'
  • tRNA pseudouridine synthase B
KeywordsIsomerase/RNA / RNA modifications / Isomerase-RNA COMPLEX
Function / homology
Function and homology information


tRNA pseudouridine55 synthase / mRNA pseudouridine synthesis / tRNA pseudouridine synthase activity / tRNA pseudouridine synthesis / pseudouridine synthase activity / tRNA modification / RNA binding
Similarity search - Function
tRNA pseudouridine synthase II, TruB / Pseudouridine synthase / Pseudouridine synthase II, N-terminal / tRNA pseudouridylate synthase B, C-terminal / TruB family pseudouridylate synthase (N terminal domain) / tRNA pseudouridylate synthase B C-terminal domain / Pseudouridine synthase / PUA domain / PUA domain / Pseudouridine synthase, catalytic domain superfamily ...tRNA pseudouridine synthase II, TruB / Pseudouridine synthase / Pseudouridine synthase II, N-terminal / tRNA pseudouridylate synthase B, C-terminal / TruB family pseudouridylate synthase (N terminal domain) / tRNA pseudouridylate synthase B C-terminal domain / Pseudouridine synthase / PUA domain / PUA domain / Pseudouridine synthase, catalytic domain superfamily / Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 4 / PUA domain / PUA domain profile. / PUA domain superfamily / PUA-like superfamily / Roll / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
RNA / RNA (> 10) / tRNA pseudouridine synthase B
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsPhannachet, K. / Elias, Y. / Huang, R.H.
CitationJournal: Biochemistry / Year: 2005
Title: Dissecting the roles of a strictly conserved tyrosine in substrate recognition and catalysis by pseudouridine 55 synthase.
Authors: Phannachet, K. / Elias, Y. / Huang, R.H.
History
DepositionJul 14, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 13, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Remark 999SEQUENCE According to the authors the conflicts at residues 296 and 307 are likely due to an error ...SEQUENCE According to the authors the conflicts at residues 296 and 307 are likely due to an error in the database sequence.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: 5'-R(*CP*CP*AP*CP*GP*GP*UP*(FHU)P*CP*GP*AP*AP*UP*CP*CP*GP*UP*GP*GP*C)-3'
A: tRNA pseudouridine synthase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0043
Polymers41,9392
Non-polymers651
Water1,47782
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)157.870, 51.870, 57.150
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: RNA chain 5'-R(*CP*CP*AP*CP*GP*GP*UP*(FHU)P*CP*GP*AP*AP*UP*CP*CP*GP*UP*GP*GP*C)-3'


Mass: 6410.837 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Protein tRNA pseudouridine synthase B / E.C.5.4.99.- / tRNA pseudouridine 55 synthase / Psi55 synthase / tRNA-uridine isomerase / tRNA pseudouridylate synthase


Mass: 35528.211 Da / Num. of mol.: 1 / Mutation: Y67F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: truB / Plasmid: PLM1-Y55S-y67F / Production host: Escherichia coli (E. coli)
References: UniProt: Q9WZW0, Isomerases; Intramolecular transferases; Transferring other groups
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 82 / Source method: isolated from a natural source / Formula: H2O

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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: 2.79 Å3/Da / Density % sol: 55.9 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG6000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 278K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG600011
2H2O11
3PEG600012
4H2O12

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 7, 2003
RadiationMonochromator: Yale Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 19086 / Num. obs: 16411 / % possible obs: 86 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.8 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 10.8

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1ZE2

1ze2


Resolution: 2.4→50 Å / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.272 1306 -random
Rwork0.222 ---
all-19086 --
obs-16411 86 %-
Refinement stepCycle: LAST / Resolution: 2.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2415 423 1 82 2921
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0062
X-RAY DIFFRACTIONc_angle_deg1.34

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