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- PDB-3vg8: Crystal structure of hypothetical protein TTHB210 from Thermus th... -

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Basic information

Entry
Database: PDB / ID: 3vg8
TitleCrystal structure of hypothetical protein TTHB210 from Thermus thermophilus HB8
ComponentsHypothetical Protein TTHB210
KeywordsUNKNOWN FUNCTION / Alpha and beta proteins (a+b)
Function / homologyPhosphorylase Kinase; domain 1 - #270 / Uncharacterized protein TTHB210-like / Domain of unknown function DUF5602 / Hypothetical protein TTHB210 / Phosphorylase Kinase; domain 1 / 2-Layer Sandwich / Alpha Beta / TTHB210-like domain-containing protein
Function and homology information
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsAgari, Y. / Sakamoto, K. / Agari, K. / Kuramitsu, S. / Shinkai, A.
CitationJournal: Proteins / Year: 2012
Title: Crystal structure of hypothetical protein TTHB210, controlled by the [sigma]E/anti-[sigma]E regulatory system in Thermus thermophilus HB8, reveals a novel homodecamer
Authors: Agari, Y. / Kuramitsu, S. / Shinkai, A.
History
DepositionAug 3, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 30, 2011Provider: repository / Type: Initial release
Revision 1.1Mar 7, 2012Group: Database references
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 / 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

Downloads & links

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Assembly

Deposited unit
G: Hypothetical Protein TTHB210
H: Hypothetical Protein TTHB210
I: Hypothetical Protein TTHB210
J: Hypothetical Protein TTHB210
A: Hypothetical Protein TTHB210
B: Hypothetical Protein TTHB210
C: Hypothetical Protein TTHB210
D: Hypothetical Protein TTHB210
E: Hypothetical Protein TTHB210
F: Hypothetical Protein TTHB210


Theoretical massNumber of molelcules
Total (without water)129,14410
Polymers129,14410
Non-polymers00
Water7,638424
1
G: Hypothetical Protein TTHB210
H: Hypothetical Protein TTHB210
I: Hypothetical Protein TTHB210
J: Hypothetical Protein TTHB210
A: Hypothetical Protein TTHB210
B: Hypothetical Protein TTHB210
C: Hypothetical Protein TTHB210
D: Hypothetical Protein TTHB210
E: Hypothetical Protein TTHB210
F: Hypothetical Protein TTHB210

G: Hypothetical Protein TTHB210
H: Hypothetical Protein TTHB210
I: Hypothetical Protein TTHB210
J: Hypothetical Protein TTHB210
A: Hypothetical Protein TTHB210
B: Hypothetical Protein TTHB210
C: Hypothetical Protein TTHB210
D: Hypothetical Protein TTHB210
E: Hypothetical Protein TTHB210
F: Hypothetical Protein TTHB210


Theoretical massNumber of molelcules
Total (without water)258,28920
Polymers258,28920
Non-polymers00
Water36020
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area59740 Å2
ΔGint-471 kcal/mol
Surface area86000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)154.977, 100.160, 106.366
Angle α, β, γ (deg.)90.00, 131.19, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Hypothetical Protein TTHB210


Mass: 12914.449 Da / Num. of mol.: 10 / Mutation: L81M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: TTHB210 / Plasmid: pET-11a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 834(DE3)pLysS / References: UniProt: Q53VW9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 424 / 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: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.4148.86
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2931vapor diffusion, hanging drop8.80.9M K/Na tartrate, 0.1M Tris-HCl, 40mM magnesium chloride, pH 8.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K
2932vapor diffusion, hanging drop8.80.95M K/Na tartrate, 0.1M Tris-HCl, 45mM magnesium chloride, pH 8.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21002
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSPring-8 BL26B210.9789, 0.9, 0.9795
SYNCHROTRONSPring-8 BL26B220.9789, 0.9, 0.9795
Detector
TypeIDDetectorDateDetails
RAYONIX MX-2251CCDSep 29, 2007vertically bent two dimensional focusing mirror coated in Rhodium
RAYONIX MX-2252CCDOct 6, 2007vertically bent two dimensional focusing mirror coated in Rhodium
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si (111)MADMx-ray1
2Si (111)MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.97891
20.91
30.97951
ReflectionResolution: 2.2→50 Å / Num. obs: 61889 / % possible obs: 99.4 % / Redundancy: 5.2 % / Biso Wilson estimate: 22.1 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 40.2
Reflection shellRedundancy: 4.8 % / Rmerge(I) obs: 0.272 / Mean I/σ(I) obs: 5.35 / Num. unique all: 5576 / % possible all: 97

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Processing

Software
NameVersionClassification
BSSdata collection
SOLVEphasing
CNS1.3refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.2→46.11 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 3795966.05 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.252 6258 10.1 %RANDOM
Rwork0.201 ---
all0.207 ---
obs0.201 61889 99.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 69.2475 Å2 / ksol: 0.38 e/Å3
Displacement parametersBiso mean: 40.2 Å2
Baniso -1Baniso -2Baniso -3
1-4.25 Å20 Å25.96 Å2
2---4.27 Å20 Å2
3---0.01 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.28 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 2.2→46.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8469 0 0 424 8893
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
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_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.01
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it3.51.5
X-RAY DIFFRACTIONc_mcangle_it4.662
X-RAY DIFFRACTIONc_scbond_it5.672
X-RAY DIFFRACTIONc_scangle_it6.792.5
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.299 1029 10.1 %
Rwork0.224 9200 -
obs-10229 99.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5carbohydrate.paramcarbohydrate.top

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