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- PDB-5dbt: Crystal structure of C-terminal truncated 2-deoxyribose-5-phospha... -

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Basic information

Entry
Database: PDB / ID: 5dbt
TitleCrystal structure of C-terminal truncated 2-deoxyribose-5-phosphate aldolase (1-201) from Streptococcus suis
ComponentsDeoxyribose-phosphate aldolase
KeywordsLYASE / 2-deoxyribose-5-phosphate aldolase / Streptococcus
Function / homology
Function and homology information


deoxyribose phosphate catabolic process / deoxyribose-phosphate aldolase / deoxyribose-phosphate aldolase activity / 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
Similarity search - Component
Biological speciesStreptococcus suis GZ1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.811 Å
AuthorsCao, T.-P. / Choi, J.M. / Lee, S.H.
Funding support Korea, Republic Of, 2items
OrganizationGrant numberCountry
National Research Fund (NRF)2010-0005114 Korea, Republic Of
National Research Fund (NRF)2013R1A1A2057465 Korea, Republic Of
CitationJournal: J. Microbiol. / Year: 2016
Title: Structural insight for substrate tolerance to 2-deoxyribose-5-phosphate aldolase from the pathogen Streptococcus suis
Authors: Cao, T.-P. / Kim, J.-S. / Woo, M.-H. / Choi, J.M. / Jun, Y. / Lee, K.H. / Lee, S.H.
History
DepositionAug 22, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 13, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: 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 / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.country / _database_2.pdbx_DOI ..._citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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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
C: Deoxyribose-phosphate aldolase
D: Deoxyribose-phosphate aldolase
E: Deoxyribose-phosphate aldolase
F: Deoxyribose-phosphate aldolase
G: Deoxyribose-phosphate aldolase
H: Deoxyribose-phosphate aldolase
I: Deoxyribose-phosphate aldolase
J: Deoxyribose-phosphate aldolase
K: Deoxyribose-phosphate aldolase
L: Deoxyribose-phosphate aldolase


Theoretical massNumber of molelcules
Total (without water)257,99312
Polymers257,99312
Non-polymers00
Water543
1
A: Deoxyribose-phosphate aldolase
B: Deoxyribose-phosphate aldolase


Theoretical massNumber of molelcules
Total (without water)42,9992
Polymers42,9992
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2570 Å2
ΔGint-23 kcal/mol
Surface area16510 Å2
MethodPISA
2
C: Deoxyribose-phosphate aldolase
D: Deoxyribose-phosphate aldolase


Theoretical massNumber of molelcules
Total (without water)42,9992
Polymers42,9992
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2620 Å2
ΔGint-23 kcal/mol
Surface area16360 Å2
MethodPISA
3
E: Deoxyribose-phosphate aldolase
F: Deoxyribose-phosphate aldolase


Theoretical massNumber of molelcules
Total (without water)42,9992
Polymers42,9992
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2620 Å2
ΔGint-23 kcal/mol
Surface area16410 Å2
MethodPISA
4
G: Deoxyribose-phosphate aldolase
H: Deoxyribose-phosphate aldolase


Theoretical massNumber of molelcules
Total (without water)42,9992
Polymers42,9992
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2570 Å2
ΔGint-23 kcal/mol
Surface area16510 Å2
MethodPISA
5
I: Deoxyribose-phosphate aldolase
J: Deoxyribose-phosphate aldolase


Theoretical massNumber of molelcules
Total (without water)42,9992
Polymers42,9992
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2570 Å2
ΔGint-23 kcal/mol
Surface area16600 Å2
MethodPISA
6
K: Deoxyribose-phosphate aldolase
L: Deoxyribose-phosphate aldolase


Theoretical massNumber of molelcules
Total (without water)42,9992
Polymers42,9992
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2590 Å2
ΔGint-23 kcal/mol
Surface area16520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.993, 163.662, 169.448
Angle α, β, γ (deg.)90.00, 91.05, 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


Mass: 21499.428 Da / Num. of mol.: 12 / Fragment: UNP residues 1-201
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus suis GZ1 (bacteria) / Strain: GZ1 / Gene: deoC / Plasmid: pET28a(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: D5AHU8, deoxyribose-phosphate aldolase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 2.31 Å3/Da / Density % sol: 46.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.2 M sodium formate, 20%(w/v) PEG 3350, 40% pentaerythritol ethoxylate (3/4 EO/OH)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 1.0015 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 16, 2013
RadiationMonochromator: DCM Si (111) Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0015 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 69858 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.4 % / Rmerge(I) obs: 0.118 / Net I/σ(I): 15.067
Reflection shellResolution: 2.8→2.85 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.448 / Mean I/σ(I) obs: 3.706 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
Coot0.7model building
HKL-2000data processing
MOLREP11phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NG3

3ng3


Resolution: 2.811→45.294 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2425 3414 4.95 %Random
Rwork0.2032 ---
obs0.2051 68949 98.27 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.811→45.294 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17796 0 0 3 17799
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00418000
X-RAY DIFFRACTIONf_angle_d0.92124372
X-RAY DIFFRACTIONf_dihedral_angle_d12.4826528
X-RAY DIFFRACTIONf_chiral_restr0.0352964
X-RAY DIFFRACTIONf_plane_restr0.0043120
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8107-2.85080.33341420.29352157X-RAY DIFFRACTION80
2.8508-2.89340.341500.28742489X-RAY DIFFRACTION91
2.8934-2.93860.31991290.28582684X-RAY DIFFRACTION94
2.9386-2.98670.32241430.26612640X-RAY DIFFRACTION97
2.9867-3.03820.34111450.26252714X-RAY DIFFRACTION99
3.0382-3.09350.30551400.26922807X-RAY DIFFRACTION99
3.0935-3.15290.31241620.26812710X-RAY DIFFRACTION99
3.1529-3.21730.26171450.25472744X-RAY DIFFRACTION100
3.2173-3.28720.33271070.25672829X-RAY DIFFRACTION100
3.2872-3.36370.26921260.24652787X-RAY DIFFRACTION100
3.3637-3.44770.27751610.2342728X-RAY DIFFRACTION100
3.4477-3.54090.26691870.23272793X-RAY DIFFRACTION100
3.5409-3.64510.25991630.21432678X-RAY DIFFRACTION100
3.6451-3.76270.25381480.19932824X-RAY DIFFRACTION100
3.7627-3.89710.23311530.19962738X-RAY DIFFRACTION100
3.8971-4.0530.21851360.19432820X-RAY DIFFRACTION100
4.053-4.23740.19481090.17612777X-RAY DIFFRACTION100
4.2374-4.46060.20841220.15912832X-RAY DIFFRACTION100
4.4606-4.73980.17641240.15472772X-RAY DIFFRACTION100
4.7398-5.10530.20211550.15652783X-RAY DIFFRACTION100
5.1053-5.61820.20091210.16562805X-RAY DIFFRACTION100
5.6182-6.42920.20481500.17152793X-RAY DIFFRACTION100
6.4292-8.09260.16761510.15242809X-RAY DIFFRACTION100
8.0926-45.29980.17411450.14892822X-RAY DIFFRACTION99

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