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- PDB-2d4r: Crystal structure of TTHA0849 from Thermus thermophilus HB8 -

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Basic information

Entry
Database: PDB / ID: 2d4r
TitleCrystal structure of TTHA0849 from Thermus thermophilus HB8
Componentshypothetical protein TTHA0849
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / START DOMAIN / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homologyCoenzyme Q-binding protein COQ10, START domain / Polyketide cyclase / dehydrase and lipid transport / START domain / Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 / START-like domain superfamily / 2-Layer Sandwich / Alpha Beta / Coenzyme Q-binding protein COQ10 START domain-containing protein
Function and homology information
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.4 Å
AuthorsNakabayashi, M. / Shibata, N. / Kuramitsu, S. / Higuchi, Y. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2005
Title: Structure of a conserved hypothetical protein, TTHA0849 from Thermus thermophilus HB8, at 2.4 A resolution: a putative member of the StAR-related lipid-transfer (START) domain superfamily.
Authors: Nakabayashi, M. / Shibata, N. / Komori, H. / Ueda, Y. / Iino, H. / Ebihara, A. / Kuramitsu, S. / Higuchi, Y.
History
DepositionOct 23, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 13, 2005Provider: 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 23, 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_site
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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: hypothetical protein TTHA0849
B: hypothetical protein TTHA0849
C: hypothetical protein TTHA0849
D: hypothetical protein TTHA0849
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,0895
Polymers68,9934
Non-polymers961
Water6,774376
1
A: hypothetical protein TTHA0849


Theoretical massNumber of molelcules
Total (without water)17,2481
Polymers17,2481
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: hypothetical protein TTHA0849


Theoretical massNumber of molelcules
Total (without water)17,2481
Polymers17,2481
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: hypothetical protein TTHA0849
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,3442
Polymers17,2481
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: hypothetical protein TTHA0849


Theoretical massNumber of molelcules
Total (without water)17,2481
Polymers17,2481
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
B: hypothetical protein TTHA0849
C: hypothetical protein TTHA0849
hetero molecules

A: hypothetical protein TTHA0849
D: hypothetical protein TTHA0849


Theoretical massNumber of molelcules
Total (without water)69,0895
Polymers68,9934
Non-polymers961
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_475x-1/2,-y+5/2,-z1
Buried area5160 Å2
ΔGint-65 kcal/mol
Surface area27260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.300, 86.490, 109.580
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
hypothetical protein TTHA0849


Mass: 17248.258 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): B834 / References: UniProt: Q5SK03
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 376 / 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: 1.93256 Å3/Da / Density % sol: 36.353859 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9.5
Details: 25% PEG4000, 0.2M ammonium sulfate, 0.1M CHES, pH 9.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 0.97911, 0.97940, 0.90000
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Oct 26, 2004
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979111
20.97941
30.91
ReflectionResolution: 2.4→46.28 Å / Num. all: 38812 / Num. obs: 38812 / % possible obs: 96.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 30.7 Å2
Reflection shellResolution: 2.4→2.49 Å / % possible all: 99

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Processing

Software
NameVersionClassification
CNS1.1refinement
d*TREKdata reduction
d*TREKdata scaling
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.4→46.29 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 250711.85 / 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
Rfree0.299 3785 9.8 %RANDOM
Rwork0.223 ---
obs0.223 38666 95.7 %-
all-38666 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 74.0206 Å2 / ksol: 0.393184 e/Å3
Displacement parametersBiso mean: 41.7 Å2
Baniso -1Baniso -2Baniso -3
1-10.94 Å20 Å20 Å2
2---5.23 Å20 Å2
3----5.71 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.43 Å0.28 Å
Refinement stepCycle: LAST / Resolution: 2.4→46.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4785 0 5 376 5166
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.71
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.4→2.49 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.338 391 9.9 %
Rwork0.249 3553 -
obs--98.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

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