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- PDB-2yqy: Crystal structure of TT2238, a four-helix bundle protein -

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Basic information

Entry
Database: PDB / ID: 2yqy
TitleCrystal structure of TT2238, a four-helix bundle protein
ComponentsHypothetical protein TTHA0303
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / four-helix-bundle / NPPSFA / National Project on Protein Structural and Functional Analyses
Function / homologyDinB-like domain / DinB superfamily / dinb family like domain / DinB/YfiT-like putative metalloenzymes / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha / DinB-like domain-containing protein
Function and homology information
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsNagata, K. / Ohtsuka, J. / Iino, H. / Ebihara, A. / Yokoyama, S. / Kuramitsu, S. / Tanokura, M.
CitationJournal: Proteins / Year: 2008
Title: Crystal structure of TTHA0303 (TT2238), a four-helix bundle protein with an exposed histidine triad from Thermus thermophilus HB8 at 2.0 A
Authors: Nagata, K. / Ohtsuka, J. / Takahashi, M. / Asano, A. / Iino, H. / Ebihara, A. / Tanokura, M.
History
DepositionMar 31, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 4, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hypothetical protein TTHA0303
B: Hypothetical protein TTHA0303


Theoretical massNumber of molelcules
Total (without water)37,4792
Polymers37,4792
Non-polymers00
Water1,31573
1
A: Hypothetical protein TTHA0303


Theoretical massNumber of molelcules
Total (without water)18,7401
Polymers18,7401
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Hypothetical protein TTHA0303


Theoretical massNumber of molelcules
Total (without water)18,7401
Polymers18,7401
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Hypothetical protein TTHA0303

A: Hypothetical protein TTHA0303


Theoretical massNumber of molelcules
Total (without water)37,4792
Polymers37,4792
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area1563 Å2
ΔGint-15 kcal/mol
Surface area12359 Å2
MethodPISA
4
B: Hypothetical protein TTHA0303

B: Hypothetical protein TTHA0303


Theoretical massNumber of molelcules
Total (without water)37,4792
Polymers37,4792
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area1396 Å2
ΔGint-17 kcal/mol
Surface area12011 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.846, 104.846, 51.254
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11B-194-

HOH

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Components

#1: Protein Hypothetical protein TTHA0303 / TT2238


Mass: 18739.598 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Plasmid: pET-11a-TT2238 / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3)pLysS / References: UniProt: Q5SLJ0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / 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: 1.88 Å3/Da / Density % sol: 34.49 %
Crystal growTemperature: 291 K / Method: microbatch / pH: 7
Details: 20%(w/v) PEG 1000, 100mM Tris pH 7.0, 0.2M Zn acetate, microbatch, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 0.97914, 0.97950, 0.90000
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Apr 16, 2005
Details: A fixed exit Si double crystal monochromator followed by a two dimensional focu sing mirror which is coated in rhodium.
RadiationMonochromator: Fixed exit Si double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979141
20.97951
30.91
ReflectionResolution: 2→36 Å / Num. all: 19790 / Num. obs: 19771 / % possible obs: 99.6 % / Redundancy: 13.8 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 22.4
Reflection shellResolution: 2→2.07 Å / Redundancy: 14.2 % / Rmerge(I) obs: 0.142 / Mean I/σ(I) obs: 8.5 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
BBSdata collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2→7.98 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.91 / SU B: 7.182 / SU ML: 0.117 / Cross valid method: THROUGHOUT / ESU R: 0.178 / ESU R Free: 0.172 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25738 1002 5.1 %RANDOM
Rwork0.22032 ---
obs0.22208 18459 99.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.225 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20 Å20 Å2
2---0.04 Å20 Å2
3---0.08 Å2
Refinement stepCycle: LAST / Resolution: 2→7.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1907 0 0 73 1980
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0211946
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3751.9712644
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.4275242
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.4121.53878
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.71715292
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1491519
X-RAY DIFFRACTIONr_chiral_restr0.0820.2300
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021463
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2220.2913
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.30.21311
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1890.283
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2510.233
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1640.214
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.999→2.048 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.236 60 -
Rwork0.25 1304 -
obs--99.78 %

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