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- PDB-1jcl: OBSERVATION OF COVALENT INTERMEDIATES IN AN ENZYME MECHANISM AT A... -

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Basic information

Entry
Database: PDB / ID: 1jcl
TitleOBSERVATION OF COVALENT INTERMEDIATES IN AN ENZYME MECHANISM AT ATOMIC RESOLUTION
ComponentsDEOXYRIBOSE-PHOSPHATE ALDOLASE
KeywordsLYASE / alpha-beta TIM barrel
Function / homology
Function and homology information


deoxyribose-phosphate aldolase / deoxyribose-phosphate aldolase activity / 2-deoxyribose 1-phosphate catabolic process / 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
1-HYDROXY-PENTANE-3,4-DIOL-5-PHOSPHATE / Deoxyribose-phosphate aldolase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.05 Å
AuthorsHeine, A. / DeSantis, G. / Luz, J.G. / Mitchell, M. / Wong, C.-H. / Wilson, I.A.
CitationJournal: Science / Year: 2001
Title: Observation of covalent intermediates in an enzyme mechanism at atomic resolution.
Authors: Heine, A. / DeSantis, G. / Luz, J.G. / Mitchell, M. / Wong, C.H. / Wilson, I.A.
History
DepositionJun 9, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 31, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 3, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,2464
Polymers55,8142
Non-polymers4322
Water12,755708
1
A: DEOXYRIBOSE-PHOSPHATE ALDOLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1232
Polymers27,9071
Non-polymers2161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DEOXYRIBOSE-PHOSPHATE ALDOLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1232
Polymers27,9071
Non-polymers2161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.54, 41.95, 144.98
Angle α, β, γ (deg.)90, 98.36, 90
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein DEOXYRIBOSE-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 (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P0A6L0, 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.: 2 / Source method: obtained synthetically / Formula: C5H13O7P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 708 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.62 Å3/Da / Density % sol: 52.98 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: MPEG 5000, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110-15 mg/mlenzyme11
213-18 %MPEG500012
30.1 Mcacodylate12
415-20 %glycerol12

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Data collection

DiffractionMean temperature: 97 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 5, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.05→30 Å / Num. all: 256887 / Num. obs: 256887 / % possible obs: 95.5 % / Redundancy: 2.5 % / Rsym value: 0.063 / Net I/σ(I): 14.8
Reflection shellResolution: 1.05→1.07 Å / Mean I/σ(I) obs: 1 / Rsym value: 0.667 / % possible all: 64
Reflection
*PLUS
Num. measured all: 638223 / Rmerge(I) obs: 0.063
Reflection shell
*PLUS
% possible obs: 64 % / Rmerge(I) obs: 0.667

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Processing

Software
NameClassification
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: native DERA

Resolution: 1.05→10 Å / Num. parameters: 40900 / Num. restraintsaints: 48367 / Cross valid method: R-free / σ(F): 4 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.169 12716 5 %random
obs0.143 179570 90.8 %-
all-243963 --
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201
Refine analyzeNum. disordered residues: 7
Refinement stepCycle: LAST / Resolution: 1.05→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3808 0 26 708 4542
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.014
X-RAY DIFFRACTIONs_angle_d0.029
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.03
X-RAY DIFFRACTIONs_zero_chiral_vol0.089
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.093
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.119
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.005
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.047
X-RAY DIFFRACTIONs_approx_iso_adps0.105
LS refinement shellResolution: 1.05→10 Å /
RfactorNum. reflection
Rfree0.169 12716
Rwork0.143 -
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 10 Å / % reflection Rfree: 5 % / Rfactor all: 0.143 / Rfactor Rwork: 0.143
Solvent computation
*PLUS
Displacement parameters
*PLUS

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