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- PDB-2epg: Crystal structure of TTHA1785 -

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Basic information

Entry
Database: PDB / ID: 2epg
TitleCrystal structure of TTHA1785
ComponentsHypothetical protein TTHA1785
KeywordsLIGASE / Alpha-beta fold / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


Ligases; Forming phosphoric-ester bonds / RNA ligase (GTP) activity / RNA ligase (ATP) activity / RNA repair / RNA processing / GTP binding / metal ion binding
Similarity search - Function
tRNA-splicing ligase RtcB / tRNA-splicing ligase RtcB / Uncharacterized protein family UPF0027 signature. / RNA-splicing ligase, RtcB / tRNA-splicing ligase RtcB-like superfamily / tRNA-splicing ligase RtcB / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
tRNA-splicing ligase RtcB
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsSekine, S. / Bessho, Y. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be published
Title: Crystal structure of the RtcB-like protein from Thermus thermophilus
Authors: Sekine, S. / Bessho, Y. / Yokoyama, S.
History
DepositionMar 30, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 2, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Nov 14, 2012Group: Structure summary
Revision 1.3Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hypothetical protein TTHA1785
B: Hypothetical protein TTHA1785


Theoretical massNumber of molelcules
Total (without water)109,0032
Polymers109,0032
Non-polymers00
Water5,206289
1
A: Hypothetical protein TTHA1785


Theoretical massNumber of molelcules
Total (without water)54,5021
Polymers54,5021
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Hypothetical protein TTHA1785


Theoretical massNumber of molelcules
Total (without water)54,5021
Polymers54,5021
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.689, 66.685, 116.988
Angle α, β, γ (deg.)90.00, 101.21, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Hypothetical protein TTHA1785


Mass: 54501.742 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: TTHA1785 / Plasmid: pET-11a / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q5SHE5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 289 / Source method: isolated from a natural source / Formula: H2O
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: 2.27 Å3/Da / Density % sol: 45.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 20mM Tris (pH 8.0), 150mM NaCl, 1mM DTT, 20% PEG 3350, 0.2M MgSO4, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 0.97884, 0.97935, 0.9
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Apr 7, 2006
RadiationMonochromator: Si / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.978841
20.979351
30.91
ReflectionResolution: 2.1→50 Å / Num. obs: 56468 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 5.5 % / Biso Wilson estimate: 21.2 Å2 / Rmerge(I) obs: 0.084 / Rsym value: 0.084 / Net I/σ(I): 21.3
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.619 / Mean I/σ(I) obs: 2.32 / Num. unique all: 5640 / Rsym value: 0.619 / % possible all: 99.5

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.1→38.63 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1647752.45 / 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
Rfree0.238 2856 5.1 %RANDOM
Rwork0.199 ---
obs0.199 56372 99 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 43.4452 Å2 / ksol: 0.342049 e/Å3
Displacement parametersBiso mean: 39.5 Å2
Baniso -1Baniso -2Baniso -3
1-5.97 Å20 Å21.72 Å2
2--4 Å20 Å2
3----9.96 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.25 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 2.1→38.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6899 0 0 289 7188
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d23.6
X-RAY DIFFRACTIONc_improper_angle_d0.9
X-RAY DIFFRACTIONc_mcbond_it1.551.5
X-RAY DIFFRACTIONc_mcangle_it2.52
X-RAY DIFFRACTIONc_scbond_it2.492
X-RAY DIFFRACTIONc_scangle_it3.662.5
LS refinement shellResolution: 2.1→2.2 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.295 329 5.1 %
Rwork0.259 6151 -
obs--91.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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