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- PDB-2e6x: X-ray structure of TT1592 from Thermus thermophilus HB8 -

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Basic information

Entry
Database: PDB / ID: 2e6x
TitleX-ray structure of TT1592 from Thermus thermophilus HB8
ComponentsHypothetical protein TTHA1281
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / unknown function protein / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homologyProtein of unknown function DUF3248 / Protein of unknown function DUF3248 / Protein of unknown function (DUF3248) / Ubiquitin-like (UB roll) / Roll / Alpha Beta / DUF3248 domain-containing protein
Function and homology information
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsYamada, M. / Nakagawa, N. / Kanagawa, M. / Kuramitsu, S. / Kamitori, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: X-ray structure of TT1592 from Thermus thermophilus HB8
Authors: Yamada, M. / Nakagawa, N. / Kanagawa, M. / Kuramitsu, S. / Kamitori, S.
History
DepositionJan 5, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 18, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Oct 30, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hypothetical protein TTHA1281
B: Hypothetical protein TTHA1281
C: Hypothetical protein TTHA1281
D: Hypothetical protein TTHA1281


Theoretical massNumber of molelcules
Total (without water)33,1654
Polymers33,1654
Non-polymers00
Water3,153175
1
A: Hypothetical protein TTHA1281

A: Hypothetical protein TTHA1281


Theoretical massNumber of molelcules
Total (without water)16,5822
Polymers16,5822
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area2370 Å2
MethodPISA
2
B: Hypothetical protein TTHA1281
D: Hypothetical protein TTHA1281


Theoretical massNumber of molelcules
Total (without water)16,5822
Polymers16,5822
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2390 Å2
MethodPISA
3
C: Hypothetical protein TTHA1281

C: Hypothetical protein TTHA1281


Theoretical massNumber of molelcules
Total (without water)16,5822
Polymers16,5822
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area1480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.486, 56.051, 48.885
Angle α, β, γ (deg.)90.00, 93.48, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Hypothetical protein TTHA1281 / TT1592


Mass: 8291.131 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: tt1592 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5SIT3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / 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: 1.99 Å3/Da / Density % sol: 38.14 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.6M potassium thiocyanate, 0.1M sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 0.9, 0.97910, 0.97941
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Mar 11, 2004 / Details: mirrors
RadiationMonochromator: graphite / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.91
20.97911
30.979411
ReflectionResolution: 2→35.36 Å / Num. all: 17159 / Num. obs: 17159 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 11.4 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 13.7
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.192 / Mean I/σ(I) obs: 3.86 / Num. unique all: 1684 / % possible all: 96.9

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Processing

Software
NameVersionClassification
CNS1.1refinement
Rapid_auto_Sp8data collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2→35.36 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 415500.78 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.253 1703 9.9 %RANDOM
Rwork0.214 ---
all0.216 17159 --
obs0.214 17159 97.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 43.1319 Å2 / ksol: 0.342755 e/Å3
Displacement parametersBiso mean: 23.7 Å2
Baniso -1Baniso -2Baniso -3
1--3.38 Å20 Å2-0.62 Å2
2--0.96 Å20 Å2
3---2.42 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.09 Å
Refinement stepCycle: LAST / Resolution: 2→35.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2175 0 0 175 2350
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d22.8
X-RAY DIFFRACTIONc_improper_angle_d1.05
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.281 250 9.8 %
Rwork0.212 2305 -
obs-2555 87.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ion.paramion.top
X-RAY DIFFRACTION3water_rep.paramwater_rep.param
X-RAY DIFFRACTION4carbohydrate.param

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