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- PDB-2cvl: Crystal structure of TTHA0137 from Thermus Thermophilus HB8 -

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Basic information

Entry
Database: PDB / ID: 2cvl
TitleCrystal structure of TTHA0137 from Thermus Thermophilus HB8
Componentsprotein translation initiation inhibitor
KeywordsStructural genomics / Unknown function / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


deaminase activity / cytosol
Similarity search - Function
RidA family / RutC-like / YjgF/YER057c/UK114 family / Endoribonuclease L-PSP / RutC-like superfamily / 60s Ribosomal Protein L30; Chain: A; / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Protein translation intiation inhibitor
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsWang, H. / Murayama, K. / Terada, T. / Shirouzu, M. / Kuramitsu, S. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of TTHA0137 from Thermus Thermophilus HB8
Authors: Wang, H. / Murayama, K. / Terada, T. / Shirouzu, M. / Kuramitsu, S. / Yokoyama, S.
History
DepositionJun 8, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 8, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 6, 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: protein translation initiation inhibitor
B: protein translation initiation inhibitor
C: protein translation initiation inhibitor
D: protein translation initiation inhibitor
E: protein translation initiation inhibitor
F: protein translation initiation inhibitor


Theoretical massNumber of molelcules
Total (without water)79,7876
Polymers79,7876
Non-polymers00
Water11,962664
1
A: protein translation initiation inhibitor
B: protein translation initiation inhibitor
C: protein translation initiation inhibitor


Theoretical massNumber of molelcules
Total (without water)39,8933
Polymers39,8933
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5570 Å2
ΔGint-51 kcal/mol
Surface area14010 Å2
MethodPISA
2
D: protein translation initiation inhibitor
E: protein translation initiation inhibitor
F: protein translation initiation inhibitor


Theoretical massNumber of molelcules
Total (without water)39,8933
Polymers39,8933
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5720 Å2
ΔGint-54 kcal/mol
Surface area13670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.055, 145.296, 50.305
Angle α, β, γ (deg.)90.00, 118.52, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
protein translation initiation inhibitor / TTHA0137


Mass: 13297.769 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / References: UniProt: Q5SM06
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 664 / 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 Å3/Da / Density % sol: 39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: PEG1500, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: May 18, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. obs: 74732 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 15.8 Å2 / Rsym value: 0.072 / Net I/σ(I): 18.2
Reflection shellResolution: 1.65→1.71 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 6.4 / Num. unique all: 7279 / Rsym value: 0.186 / % possible all: 96.1

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→37.76 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 158668.31 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.227 3772 5.1 %RANDOM
Rwork0.189 ---
obs0.189 74062 98 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 34.9382 Å2 / ksol: 0.319289 e/Å3
Displacement parametersBiso mean: 17.4 Å2
Baniso -1Baniso -2Baniso -3
1-0.34 Å20 Å2-0.13 Å2
2---0.68 Å20 Å2
3---0.34 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.14 Å0.09 Å
Refinement stepCycle: LAST / Resolution: 1.65→37.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5544 0 0 664 6208
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d24.1
X-RAY DIFFRACTIONc_improper_angle_d0.81
LS refinement shellResolution: 1.65→1.75 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.279 604 5 %
Rwork0.223 11414 -
obs--95.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3ion.param

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