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- PDB-2dp9: Crystal Structure of Conserved Hypothetical Protein TTHA0113 from... -

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Basic information

Entry
Database: PDB / ID: 2dp9
TitleCrystal Structure of Conserved Hypothetical Protein TTHA0113 from Thermus thermophilus HB8
ComponentsHypothetical protein TTHA0113
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / jellyroll / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homologyHypothetical protein. / ASCH / ASCH domain / ASCH domain / Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 4 / PUA-like superfamily / Roll / Mainly Beta / ASCH domain-containing protein
Function and homology information
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsAgari, Y. / Kuramitsu, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal Structure of Conserved Hypothetical Protein TTHA0113 from Thermus thermophilus HB8
Authors: Agari, Y. / Yokoyama, S. / Kuramitsu, S.
History
DepositionMay 8, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 8, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hypothetical protein TTHA0113


Theoretical massNumber of molelcules
Total (without water)14,4611
Polymers14,4611
Non-polymers00
Water1,36976
1
A: Hypothetical protein TTHA0113

A: Hypothetical protein TTHA0113


Theoretical massNumber of molelcules
Total (without water)28,9222
Polymers28,9222
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area3100 Å2
ΔGint-33 kcal/mol
Surface area13510 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)52.369, 54.468, 42.980
Angle α, β, γ (deg.)90.00, 97.22, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Hypothetical protein TTHA0113


Mass: 14460.768 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-121
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Plasmid: pET11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q5SM30
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / 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: 2.1 Å3/Da / Density % sol: 41.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.3
Details: 0.2M Calcium Acetate, 20% w/v Polyethylene Glycol 3350 , pH 7.3, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
1,21
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Sep 28, 2004
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si Double CrystalSINGLE WAVELENGTHMx-ray1
2MADMx-ray1
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 9486 / Num. obs: 9411 / % possible obs: 99.7 % / Observed criterion σ(I): 5 / Redundancy: 5.3 % / Biso Wilson estimate: 17.9 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 32.28
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.265 / Mean I/σ(I) obs: 4.1 / % possible all: 97.8

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD
Starting model: PDB ENTRY 1WK2

1wk2


Resolution: 1.9→29.57 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 254955.91 / 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
Rfree0.25 958 10.4 %RANDOM
Rwork0.215 ---
all0.232 9184 --
obs0.215 9184 96.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 36.1682 Å2 / ksol: 0.31367 e/Å3
Displacement parametersBiso mean: 29.8 Å2
Baniso -1Baniso -2Baniso -3
1--7.31 Å20 Å2-0.5 Å2
2--5.81 Å20 Å2
3---1.51 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.24 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 1.9→29.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1021 0 0 76 1097
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d23.5
X-RAY DIFFRACTIONc_improper_angle_d0.74
X-RAY DIFFRACTIONc_mcbond_it1.551.5
X-RAY DIFFRACTIONc_mcangle_it2.472
X-RAY DIFFRACTIONc_scbond_it2.112
X-RAY DIFFRACTIONc_scangle_it3.252.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.27 146 10.8 %
Rwork0.25 1211 -
obs--86.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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