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- PDB-1n7k: Unique tetrameric structure of deoxyribose phosphate aldolase fro... -

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Basic information

Entry
Database: PDB / ID: 1n7k
TitleUnique tetrameric structure of deoxyribose phosphate aldolase from Aeropyrum pernix
Componentsdeoxyribose-phosphate aldolase
KeywordsLYASE / ALDOLASE / A.pernix / TETRAMER / ALPHA-BETA TIM BARREL / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics
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 / protein tetramerization / carbohydrate metabolic 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
Similarity search - Component
Biological speciesAeropyrum pernix (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2 Å
AuthorsTsuge, H. / Sakuraba, H. / Shimoya, I. / Katunuma, N. / Ago, H. / Miyano, M. / Ohshima, T. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: J.Biol.Chem. / Year: 2003
Title: The First Crystal Structure of Archaeal Aldolase. UNIQUE TETRAMERIC STRUCTURE of 2-DEOXY-D-RIBOSE-5-PHOSPHATE ALDOLASE FROM THE HYPERTHERMOPHILIC ARCHAEA Aeropyrum pernix.
Authors: Sakuraba, H. / Tsuge, H. / Shimoya, I. / Kawakami, R. / Goda, S. / Kawarabayasi, Y. / Katunuma, N. / Ago, H. / Miyano, M. / Ohshima, T.
History
DepositionNov 15, 2002Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 25, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Dec 25, 2019Group: Data collection / Category: reflns_shell / Item: _reflns_shell.pdbx_Rsym_value
Revision 1.4Mar 13, 2024Group: 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

Downloads & links

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Assembly

Deposited unit
A: deoxyribose-phosphate aldolase
B: deoxyribose-phosphate aldolase


Theoretical massNumber of molelcules
Total (without water)48,8502
Polymers48,8502
Non-polymers00
Water3,585199
1
A: deoxyribose-phosphate aldolase
B: deoxyribose-phosphate aldolase

A: deoxyribose-phosphate aldolase
B: deoxyribose-phosphate aldolase


Theoretical massNumber of molelcules
Total (without water)97,7014
Polymers97,7014
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area9570 Å2
ΔGint-88 kcal/mol
Surface area32510 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)75.293, 84.185, 87.238
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Detailsbiological tetramer is generated by the crystallographic two fold axis

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Components

#1: Protein deoxyribose-phosphate aldolase


Mass: 24425.172 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aeropyrum pernix (archaea) / Plasmid: pET11b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q9Y948, deoxyribose-phosphate aldolase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 199 / 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: 2.83 Å3/Da / Density % sol: 56.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
120 mg/mlprotein1drop
20.7-1.2 M1reservoirNaH2PO4
3250 mM1reservoirK2HPO4
4100 mM1reservoirK2HPO4/citratepH4.2

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Data collection

DiffractionMean temperature: 283 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 28, 2002
RadiationProtocol: MIRAS / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→15 Å / Num. all: 37249 / Num. obs: 38099 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Biso Wilson estimate: 14.6 Å2 / Rsym value: 0.052 / Net I/σ(I): 9.3
Reflection shellResolution: 2→2.11 Å / Redundancy: 6.2 % / Mean I/σ(I) obs: 2 / Num. unique all: 5397 / Rsym value: 0.157 / % possible all: 98.4
Reflection
*PLUS
Highest resolution: 2 Å / Lowest resolution: 34.5 Å / Rmerge(I) obs: 0.056
Reflection shell
*PLUS
% possible obs: 98.4 % / Rmerge(I) obs: 0.157

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SOLVEphasing
RESOLVEmodel building
CNS1refinement
CCP4(SCALA)data scaling
RESOLVEphasing
RefinementMethod to determine structure: MIRAS / Resolution: 2→14.85 Å / Rfactor Rfree error: 0.004 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.263 3738 10 %RANDOM
Rwork0.224 ---
obs0.224 37249 97.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 65.4041 Å2 / ksol: 0.45023 e/Å3
Displacement parametersBiso mean: 21.1 Å2
Baniso -1Baniso -2Baniso -3
1--1.21 Å20 Å20 Å2
2--9.38 Å20 Å2
3----8.18 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.16 Å-0.02 Å
Refinement stepCycle: LAST / Resolution: 2→14.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3432 0 0 199 3631
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d21.7
X-RAY DIFFRACTIONc_improper_angle_d0.92
X-RAY DIFFRACTIONc_mcbond_it1.091.5
X-RAY DIFFRACTIONc_mcangle_it1.452
X-RAY DIFFRACTIONc_scbond_it2.332
X-RAY DIFFRACTIONc_scangle_it3.272.5
LS refinement shellResolution: 2→2.12 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.29 561 9.6 %
Rwork0.219 5259 -
obs-5259 93.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP
X-RAY DIFFRACTION3WATER_REP.PARAM
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 15 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.92

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