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- PDB-1ub3: Crystal Structure of Tetrameric Structure of Aldolase from thermu... -

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Basic information

Entry
Database: PDB / ID: 1ub3
TitleCrystal Structure of Tetrameric Structure of Aldolase from thermus thermophilus HB8
ComponentsAldolase protein
KeywordsLYASE / Schiff base / deoxyribose phosphate / 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 / 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
1-HYDROXY-PENTANE-3,4-DIOL-5-PHOSPHATE / Deoxyribose-phosphate aldolase / Deoxyribose-phosphate aldolase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.4 Å
AuthorsLokanath, N.K. / 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
DepositionMar 28, 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 / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: Aldolase protein
B: Aldolase protein
C: Aldolase protein
D: Aldolase protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,2088
Polymers93,3434
Non-polymers8654
Water7,963442
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10190 Å2
ΔGint-58 kcal/mol
Surface area28340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.820, 96.887, 137.925
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsMolecule is in the tetramer form. The biological assempbly is a tetramer generated from the monomer in the asymmetric unit.

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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 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3)
References: UniProt: Q7SIC8, UniProt: Q5SJ28*PLUS, deoxyribose-phosphate aldolase
#2: Chemical
ChemComp-HPD / 1-HYDROXY-PENTANE-3,4-DIOL-5-PHOSPHATE / OPEN FORM OF 2'-DEOXY-RIBOFURANOSE-5'-PHOSPHATE


Mass: 216.126 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H13O7P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 442 / 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: 2.23 Å3/Da / Density % sol: 44.52 %
Crystal growTemperature: 295 K / Method: microbatch / pH: 7.9
Details: MPD, Tris-HCl, MgCl2, Deoxyribose phosphate , pH 7.9, MICROBATCH, temperature 295.0K

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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: Dec 8, 2002 / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 1.4→30 Å / Num. all: 165080 / Num. obs: 164987 / % possible obs: 99.99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 16.6 Å2 / Rmerge(I) obs: 0.048 / Rsym value: 0.046
Reflection shellResolution: 1.4→1.49 Å / % possible all: 97.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
AMoREphasing
CNS1.1refinement
HKL-2000data reduction
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.4→29.25 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 1106896.53 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.211 16428 10 %RANDOM
Rwork0.202 ---
all0.203 165080 --
obs0.203 164987 97.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 57.9881 Å2 / ksol: 0.402301 e/Å3
Displacement parametersBiso mean: 18.2 Å2
Baniso -1Baniso -2Baniso -3
1-2.96 Å20 Å20 Å2
2--1.23 Å20 Å2
3----4.19 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.18 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.16 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 1.4→29.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6322 0 52 442 6816
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_angle_d0.004
X-RAY DIFFRACTIONc_bond_d0.017
X-RAY DIFFRACTIONc_dihedral_angle_d22.6
X-RAY DIFFRACTIONc_improper_angle_d1.27
LS refinement shellResolution: 1.4→1.49 Å / Rfactor Rfree error: 0.005 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.283 2754 10.2 %
Rwork0.269 24291 -
obs--97.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMHPD.TOP
X-RAY DIFFRACTION3HPD.PARAM

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