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- PDB-5awe: Crystal structure of a hypothetical protein, TTHA0829 from Thermu... -

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Basic information

Entry
Database: PDB / ID: 5awe
TitleCrystal structure of a hypothetical protein, TTHA0829 from Thermus thermophilus HB8, composed of cystathionine-beta-synthase (CBS) and aspartate-kinase chorismate-mutase tyrA (ACT) domains
ComponentsPutative acetoin utilization protein, acetoin dehydrogenase
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / hypothetical protein / Thermus thermophilus HB8 / CBS domain / ACT domain / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homologyDomain in cystathionine beta-synthase and other proteins. / CBS domain / CBS domain / CBS domain profile. / Putative acetoin utilization protein, acetoin dehydrogenase
Function and homology information
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.45 Å
AuthorsNakabayashi, M. / Shibata, N. / Kanagawa, M. / Nakagawa, N. / Kuramitsu, S. / Higuchi, Y.
CitationJournal: Extremophiles / Year: 2016
Title: Crystal structure of a hypothetical protein, TTHA0829 from Thermus thermophilus HB8, composed of cystathionine-beta-synthase (CBS) and aspartate-kinase chorismate-mutase tyrA (ACT) domains.
Authors: Nakabayashi, M. / Shibata, N. / Ishido-Nakai, E. / Kanagawa, M. / Iio, Y. / Komori, H. / Ueda, Y. / Nakagawa, N. / Kuramitsu, S. / Higuchi, Y.
History
DepositionJul 3, 2015Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 18, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 28, 2016Group: Structure summary
Revision 1.2Feb 26, 2020Group: Data collection / Derived calculations / Category: diffrn_source / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative acetoin utilization protein, acetoin dehydrogenase


Theoretical massNumber of molelcules
Total (without water)23,2521
Polymers23,2521
Non-polymers00
Water95553
1
A: Putative acetoin utilization protein, acetoin dehydrogenase

A: Putative acetoin utilization protein, acetoin dehydrogenase

A: Putative acetoin utilization protein, acetoin dehydrogenase

A: Putative acetoin utilization protein, acetoin dehydrogenase


Theoretical massNumber of molelcules
Total (without water)93,0084
Polymers93,0084
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_765-x+2,-y+1,z1
crystal symmetry operation9_765-x+2,-x+y+1,-z+1/31
crystal symmetry operation12_555x,x-y,-z+1/31
Buried area13200 Å2
ΔGint-86 kcal/mol
Surface area34570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.800, 90.800, 89.750
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222

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Components

#1: Protein Putative acetoin utilization protein, acetoin dehydrogenase


Mass: 23251.953 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / Gene: TTHA0829 / Plasmid: pET11a / Production host: Escherichia coli / Strain (production host): B834 (DE3) / References: UniProt: Q5SK23
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46.44 % / Description: THE FILE CONTAINS FRIEDEL PAIRS.
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: HEPES, magnesium chloride, PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 0.97911 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Jun 25, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97911 Å / Relative weight: 1
ReflectionResolution: 2.45→40.51 Å / Num. obs: 8426 / % possible obs: 99.6 % / Redundancy: 16.4 % / Biso Wilson estimate: 29.5 Å2 / Rmerge(I) obs: 0.104 / Net I/σ(I): 31.7
Reflection shellResolution: 2.45→2.54 Å / Redundancy: 14.1 % / Rmerge(I) obs: 0.305 / Mean I/σ(I) obs: 4.6 / % possible all: 98.2

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Processing

Software
NameVersionClassification
CNS1.3refinement
HKL-2000data processing
HKL-2000data scaling
SnBphasing
RefinementMethod to determine structure: SAD / Resolution: 2.45→40.51 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 246220.86 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: THE FILE CONTAINS FRIEDEL PAIRS. BULK SOLVENT MODEL USED.
RfactorNum. reflection% reflectionSelection details
Rfree0.261 1443 9.8 %RANDOM
Rwork0.214 ---
obs0.214 8426 96.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 48.9401 Å2 / ksol: 0.38 e/Å3
Displacement parametersBiso mean: 35.8 Å2
Baniso -1Baniso -2Baniso -3
1--6.91 Å2-0 Å2-0 Å2
2---6.91 Å2-0 Å2
3---13.82 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.38 Å0.26 Å
Refinement stepCycle: 1 / Resolution: 2.45→40.51 Å /
ProteinNucleic acidLigandSolventTotal
Num. atoms0 0 0 0 0
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.017
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_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.81
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: 2.45→2.54 Å / Rfactor Rfree error: 0.043 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.447 106 8.3 %
Rwork0.286 1175 -
obs--83.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR/protein_rep.paramCNS_TOPPAR/protein.top
X-RAY DIFFRACTION2CNS_TOPPAR/dna-rna_rep.paramCNS_TOPPAR/dna-rna.top
X-RAY DIFFRACTION3CNS_TOPPAR/water_rep.paramCNS_TOPPAR/water.top
X-RAY DIFFRACTION4CNS_TOPPAR/ion.paramCNS_TOPPAR/ion.top
X-RAY DIFFRACTION5CNS_TOPPAR/carbohydrate.paramCNS_TOPPAR/carbohydrate.top

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