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- PDB-1j2w: Tetrameric Structure of aldolase from Thermus thermophilus HB8 -

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Basic information

Entry
Database: PDB / ID: 1j2w
TitleTetrameric Structure of aldolase from Thermus thermophilus HB8
ComponentsAldolase protein
KeywordsLYASE / Schiff base / deoxyribose phospahte / carbinolamine / structural genomics / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


deoxyribose-phosphate aldolase / deoxyribose-phosphate aldolase activity / 2-deoxyribose 1-phosphate catabolic process / deoxyribonucleotide catabolic process / carbohydrate catabolic process / cytoplasm
Similarity search - Function
Deoxyribose-phosphate aldolase type I / Deoxyribose-phosphate aldolase / DeoC/LacD family aldolase / DeoC/FbaB/LacD aldolase / DeoC/LacD family aldolase / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Deoxyribose-phosphate aldolase / Deoxyribose-phosphate aldolase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.5 Å
AuthorsLokanath, N.K. / Shiromizu, I. / Miyano, M. / Yokoyama, S. / Kuramitsu, S. / Kunishima, N. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2004
Title: Structure of aldolase from Thermus thermophilus HB8 showing the contribution of oligomeric state to thermostability.
Authors: Lokanath, N.K. / Shiromizu, I. / Ohshima, N. / Nodake, Y. / Sugahara, M. / Yokoyama, S. / Kuramitsu, S. / Miyano, M. / Kunishima, N.
History
DepositionJan 14, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 8, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: 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

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Assembly

Deposited unit
A: Aldolase protein
B: Aldolase protein
C: Aldolase protein
D: Aldolase protein


Theoretical massNumber of molelcules
Total (without water)93,3434
Polymers93,3434
Non-polymers00
Water8,665481
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8290 Å2
ΔGint-50 kcal/mol
Surface area29260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.280, 97.686, 137.918
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
Aldolase protein


Mass: 23335.762 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Plasmid: pET-11a / Production host: Escherichia coli (E. coli) / References: UniProt: Q7SIC8, UniProt: Q5SJ28*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 481 / 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: 2.27 Å3/Da / Density % sol: 45.34 %
Crystal growTemperature: 295 K / Method: microbatch / pH: 7.9
Details: MPD, Tris HCl, magnesium chloride, pH 7.9, MICROBATCH, temperature 295.0K
Crystal grow
*PLUS
pH: 4.9 / Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
120 mg/mlprotein11
21 Mammonium sulfate11
31 Msodium acetate11
430 %MPD11pH4.9

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 0.8 Å
DetectorType: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Nov 25, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 1.5→30 Å / Num. all: 137192 / Num. obs: 137075 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 14.62 Å2
Reflection shellResolution: 1.5→1.55 Å / % possible all: 99.5
Reflection
*PLUS
Highest resolution: 1.5 Å / Num. obs: 137192 / % possible obs: 98.5 % / Redundancy: 4.85 % / Num. measured all: 665297 / Rmerge(I) obs: 0.067
Reflection shell
*PLUS
Highest resolution: 1.5 Å / % possible obs: 99.5 % / Rmerge(I) obs: 0.456 / Mean I/σ(I) obs: 4.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
SOLVEphasing
CNS1.1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MAD / Resolution: 1.5→30 Å / Isotropic thermal model: ANISOTROPIC / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.213 13684 -RANDOM
Rwork0.197 ---
all0.198 137192 --
obs0.198 137075 98.3 %-
Refinement stepCycle: LAST / Resolution: 1.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6338 0 0 481 6819
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_bond_d0.004
Refinement
*PLUS
Highest resolution: 1.5 Å / Rfactor Rwork: 0.196
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_angle_deg / Dev ideal: 1.29

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