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- PDB-2cw5: Crystal structure of a conserved hypothetical protein from Thermu... -

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Basic information

Entry
Database: PDB / ID: 2cw5
TitleCrystal structure of a conserved hypothetical protein from Thermus thermophilus HB8
ComponentsBacterial fluorinating enzyme homolog
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / alpha and beta protein (a/b) / beta barrel / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


Bacterial fluorinating enzyme like / S-adenosyl-l-methionine hydroxide adenosyltransferase, N-terminal / S-adenosyl-l-methionine hydroxide adenosyltransferase / S-adenosyl-l-methionine hydroxide adenosyltransferase, C-terminal domain superfamily / S-adenosyl-l-methionine hydroxide adenosyltransferase, N-terminal domain superfamily / SAM hydroxide adenosyltransferase N-terminal domain / Elongation Factor Tu (Ef-tu); domain 3 / Beta Barrel / Rossmann fold / 3-Layer(aba) Sandwich ...Bacterial fluorinating enzyme like / S-adenosyl-l-methionine hydroxide adenosyltransferase, N-terminal / S-adenosyl-l-methionine hydroxide adenosyltransferase / S-adenosyl-l-methionine hydroxide adenosyltransferase, C-terminal domain superfamily / S-adenosyl-l-methionine hydroxide adenosyltransferase, N-terminal domain superfamily / SAM hydroxide adenosyltransferase N-terminal domain / Elongation Factor Tu (Ef-tu); domain 3 / Beta Barrel / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Uncharacterized protein
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.94 Å
AuthorsEbihara, A. / Yokoyama, S. / Kuramitsu, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of a conserved hypothetical protein from Thermus thermophilus HB8
Authors: Ebihara, A. / Yokoyama, S. / Kuramitsu, S.
History
DepositionJun 16, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 16, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bacterial fluorinating enzyme homolog
B: Bacterial fluorinating enzyme homolog
C: Bacterial fluorinating enzyme homolog


Theoretical massNumber of molelcules
Total (without water)81,2043
Polymers81,2043
Non-polymers00
Water4,089227
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6090 Å2
ΔGint-34 kcal/mol
Surface area28460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.790, 78.120, 120.580
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 Bacterial fluorinating enzyme homolog / hypothetical protein TTHA0338


Mass: 27067.955 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q5SLF5
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 227 / 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: 2.2 Å3/Da / Density % sol: 43.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 1.4M Mg sulfate, 0.1M MES, pH 6.5, 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: 0.90000, 0.97906, 0.97941
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Oct 11, 2004
RadiationMonochromator: SI DOUBLE-CRYSTAL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.91
20.979061
30.979411
ReflectionResolution: 1.94→40 Å / Num. all: 52816 / % possible obs: 99.6 % / Redundancy: 7.12 % / Biso Wilson estimate: 25 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 14.2
Reflection shellResolution: 1.94→2.01 Å / Redundancy: 7.23 % / Rmerge(I) obs: 0.313 / Mean I/σ(I) obs: 5.4 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
CrystalCleardata reduction
CrystalCleardata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.94→37.4 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 2147718.65 / 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
Rfree0.246 5353 10.1 %RANDOM
Rwork0.212 ---
all0.215 ---
obs0.212 52815 99.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 48.2684 Å2 / ksol: 0.375871 e/Å3
Displacement parametersBiso mean: 30.1 Å2
Baniso -1Baniso -2Baniso -3
1-5.82 Å20 Å20 Å2
2---3.77 Å20 Å2
3----2.05 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.12 Å0.09 Å
Refinement stepCycle: LAST / Resolution: 1.94→37.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5233 0 0 227 5460
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
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_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.82
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.471.5
X-RAY DIFFRACTIONc_mcangle_it2.32
X-RAY DIFFRACTIONc_scbond_it2.162
X-RAY DIFFRACTIONc_scangle_it3.22.5
LS refinement shellResolution: 1.94→2.06 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.245 852 9.8 %
Rwork0.217 7860 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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