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- PDB-1p1x: Comparison of class I aldolase binding site architecture based on... -

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Basic information

Entry
Database: PDB / ID: 1p1x
TitleComparison of class I aldolase binding site architecture based on the crystal structure of 2-deoxyribose-5-phosphate aldolase determined at 0.99 Angstrom resolution
ComponentsDeoxyribose-phosphate aldolase
KeywordsLYASE / alpha-beta barrel / TIM barrel
Function / homology
Function and homology information


deoxyribose phosphate catabolic process / deoxyribose-phosphate aldolase / deoxyribose-phosphate aldolase activity / deoxyribonucleotide catabolic process / nucleobase-containing small molecule interconversion / carbohydrate catabolic process / lyase activity / DNA damage response / membrane / cytosol
Similarity search - Function
Deoxyribose-phosphate aldolase type II / 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 speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO / Resolution: 0.99 Å
AuthorsHeine, A. / Luz, J.G. / Wong, C.H. / Wilson, I.A.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: Analysis of the class I aldolase binding site architecture based on the crystal structure of 2-deoxyribose-5-phosphate aldolase at 0.99A resolution.
Authors: Heine, A. / Luz, J.G. / Wong, C.H. / Wilson, I.A.
History
DepositionApr 14, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 1, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 9, 2012Group: Structure summary
Revision 1.4Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.5Feb 14, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)55,8142
Polymers55,8142
Non-polymers00
Water11,602644
1
A: Deoxyribose-phosphate aldolase


Theoretical massNumber of molelcules
Total (without water)27,9071
Polymers27,9071
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Deoxyribose-phosphate aldolase


Theoretical massNumber of molelcules
Total (without water)27,9071
Polymers27,9071
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.730, 42.010, 145.410
Angle α, β, γ (deg.)90.00, 98.53, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Deoxyribose-phosphate aldolase / / DERA / 2-deoxy-D-ribose 5-phosphate aldolase / Phosphodeoxyriboaldolase / Deoxyriboaldolase


Mass: 27906.963 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12
Gene: b4381, deoC, DEOC OR DRA OR THYR OR B4381 OR C5465, dra, JW4344, thyR
Production host: Escherichia coli (E. coli) / References: UniProt: P0A6L0, deoxyribose-phosphate aldolase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 644 / 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: 2.32 Å3/Da / Density % sol: 47.45 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 13-18% MPEG 5000, 0.1M cacodylate, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 85 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.783 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.783 Å / Relative weight: 1
ReflectionResolution: 0.99→50 Å / Num. obs: 314901

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Processing

Software
NameClassification
SHELXmodel building
SHELXL-97refinement
MAR345data collection
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: AB INITIO / Resolution: 0.99→8 Å / Num. parameters: 40128 / Num. restraintsaints: 47870 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: ANISOTROPIC SCALING APPLIED BY THE METHOD OF PARKIN, MOEZZI & HOPE, J.APPL.CRYST.28(1995)53-56 ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY ?
Num. reflection% reflectionSelection details
Rfree15776 5.3 %RANDOM
all298535 --
obs-92.5 %-
Refine analyzeNum. disordered residues: 7 / Occupancy sum hydrogen: 3848 / Occupancy sum non hydrogen: 4420
Refinement stepCycle: LAST / Resolution: 0.99→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3774 0 0 644 4418
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.015
X-RAY DIFFRACTIONs_angle_d0.031
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0305
X-RAY DIFFRACTIONs_zero_chiral_vol0.093
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.101
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.129
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.006
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.046
X-RAY DIFFRACTIONs_approx_iso_adps0.105

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