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- PDB-1ufr: Crystal Structure of TT1027 from Thermus thermophilus HB8 -

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Basic information

Entry
Database: PDB / ID: 1ufr
TitleCrystal Structure of TT1027 from Thermus thermophilus HB8
Componentspyr mRNA-binding attenuation protein
KeywordsRNA BINDING PROTEIN / pyrimidine nucleotide biosynthesis / transcriptional attenuation / RNA-binding protein / uracil phosphoribosyltransferase / STRUCTURAL GENOMICS / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


uracil phosphoribosyltransferase / uracil phosphoribosyltransferase activity / nucleoside metabolic process / DNA-templated transcription termination / regulation of DNA-templated transcription / RNA binding
Similarity search - Function
Bifunctional protein PyrR / Rossmann fold - #2020 / Phosphoribosyl transferase domain / Phosphoribosyltransferase-like / Phosphoribosyltransferase domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Bifunctional protein PyrR / Bifunctional protein PyrR
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsMatsuura, T. / Sakai, H. / Terada, T. / Shirouzu, M. / Kuramitsu, S. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal Structure of TT1027 from Thermus thermophilus HB8
Authors: Matsuura, T. / Sakai, H. / Terada, T. / Shirouzu, M. / Kuramitsu, S. / Yokoyama, S.
History
DepositionJun 8, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 8, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / 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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: pyr mRNA-binding attenuation protein
B: pyr mRNA-binding attenuation protein
C: pyr mRNA-binding attenuation protein
D: pyr mRNA-binding attenuation protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,7038
Polymers82,5614
Non-polymers1424
Water1,49583
1
A: pyr mRNA-binding attenuation protein
B: pyr mRNA-binding attenuation protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,3524
Polymers41,2812
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: pyr mRNA-binding attenuation protein
D: pyr mRNA-binding attenuation protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,3524
Polymers41,2812
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.310, 114.136, 146.190
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological unit is assumed to be a dimer: A chain and B chain, C chain and D chain, respectively.

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Components

#1: Protein
pyr mRNA-binding attenuation protein / TT1027


Mass: 20640.330 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / References: UniProt: P83822, UniProt: Q5SK65*PLUS
#2: Chemical
ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 83 / 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: 2.94 Å3/Da / Density % sol: 58.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: MPD, sodium acetate, calcium chloride, dioxane, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45PX / Wavelength: 1.02 Å
DetectorType: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Jul 1, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.02 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 30397 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 5.4 % / Biso Wilson estimate: 36.2 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 9.3
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.464 / Mean I/σ(I) obs: 2.73 / Num. unique all: 2961 / % possible all: 98.7

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1A3C

1a3c


Resolution: 2.6→45.58 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 432416.59 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.287 2928 10 %RANDOM
Rwork0.264 ---
obs0.264 29313 95.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 28.7137 Å2 / ksol: 0.308967 e/Å3
Displacement parametersBiso mean: 52.9 Å2
Baniso -1Baniso -2Baniso -3
1--4.23 Å20 Å20 Å2
2--19.93 Å20 Å2
3----15.71 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.49 Å0.42 Å
Luzzati d res low-5 Å
Luzzati sigma a0.58 Å0.5 Å
Refinement stepCycle: LAST / Resolution: 2.6→45.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5288 0 4 83 5375
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d23.8
X-RAY DIFFRACTIONc_improper_angle_d0.76
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.404 476 11.2 %
Rwork0.361 3793 -
obs--84.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4MSE.TOP

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