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- PDB-5hjl: Crystal structure of class I tagatose 1,6-bisphosphate aldolase L... -

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Basic information

Entry
Database: PDB / ID: 5hjl
TitleCrystal structure of class I tagatose 1,6-bisphosphate aldolase LacD from Streptococcus porcinus
ComponentsTagatose 1,6-diphosphate aldolase
KeywordsLYASE / tagatose 1 / 6-bisphosphate aldolase / LacD
Function / homologyAldolase class I / TIM Barrel / Alpha-Beta Barrel / Alpha Beta / :
Function and homology information
Biological speciesStreptococcus porcinus str. Jelinkova 176 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3 Å
AuthorsFreichels, R. / Kerff, F. / Herman, R. / Charlier, P. / Galleni, M.
Funding support Belgium, 2items
OrganizationGrant numberCountry
National Fund for Scientific Research Belgium
FRS-FNRSIISN 4.4503 Belgium
CitationJournal: To Be Published
Title: Structure and Characterization of a new class I Tagatose-1,6-bipshosphate aldolase from Streptococcus porcinus : switch in specificity directed by an Arginine
Authors: Freichels, R. / Delmarcelle, M. / Van der Heiden, E. / Herman, R. / Colarusso, A. / Wathelet, B. / Kerff, F. / Galleni, M.
History
DepositionJan 13, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 7, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tagatose 1,6-diphosphate aldolase
B: Tagatose 1,6-diphosphate aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,5028
Polymers73,9262
Non-polymers5766
Water1448
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2840 Å2
ΔGint-93 kcal/mol
Surface area26990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.660, 93.750, 88.110
Angle α, β, γ (deg.)90.000, 120.580, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: LEU / End label comp-ID: LEU / Auth seq-ID: 5 - 326 / Label seq-ID: 5 - 326

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain AAA
2chain BBB

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Components

#1: Protein Tagatose 1,6-diphosphate aldolase / D-tagatose-1 / 6-bisphosphate aldolase / Tagatose-bisphosphate aldolase


Mass: 36962.938 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus porcinus str. Jelinkova 176 (bacteria)
Gene: lacD, STRPO_0644 / Plasmid: pET28a(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: F3L835, tagatose-bisphosphate aldolase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 2.51 Å3/Da / Density % sol: 51.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Small crystals grow in 25% PEG 3350, 0.1M bistris pH 5.5, 0.2 M Ammonium Sulfate. The crystal used for data collection was obtained after micro seeding in the same condition.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 1.7101 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 21, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.7101 Å / Relative weight: 1
ReflectionResolution: 3→46.88 Å / Num. obs: 14194 / % possible obs: 99.9 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.296 / Net I/σ(I): 5.9
Reflection shellResolution: 3→3.16 Å / Redundancy: 5.6 % / Rmerge(I) obs: 1.13 / Mean I/σ(I) obs: 2.4 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
Cootmodel building
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3IV3

3iv3


Resolution: 3→46.87 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / Phase error: 25.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2292 710 5 %
Rwork0.1744 16583 -
obs-14194 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 111.76 Å2 / Biso mean: 61.6768 Å2 / Biso min: 38.61 Å2
Refinement stepCycle: final / Resolution: 3→46.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5016 0 30 8 5054
Biso mean--83.58 55.31 -
Num. residues----644
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055134
X-RAY DIFFRACTIONf_angle_d0.9146946
X-RAY DIFFRACTIONf_chiral_restr0.036776
X-RAY DIFFRACTIONf_plane_restr0.006886
X-RAY DIFFRACTIONf_dihedral_angle_d15.1951882
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2936X-RAY DIFFRACTION4.865TORSIONAL
12B2936X-RAY DIFFRACTION4.865TORSIONAL
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.23160.31771400.25672670X-RAY DIFFRACTION100
3.2316-3.55670.30111420.21642699X-RAY DIFFRACTION100
3.5567-4.07110.221420.16692688X-RAY DIFFRACTION100
4.0711-5.12810.21131410.14922689X-RAY DIFFRACTION99.9
5.1281-46.88070.18731450.15612738X-RAY DIFFRACTION99.7

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