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- PDB-3myp: Crystal structure of tagatose-1,6-bisphosphate aldolase from Stap... -

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Basic information

Entry
Database: PDB / ID: 3myp
TitleCrystal structure of tagatose-1,6-bisphosphate aldolase from Staphylococcus aureus
ComponentsTagatose 1,6-diphosphate aldolase
KeywordsLYASE / beta-alpha-barrel
Function / homology
Function and homology information


tagatose-bisphosphate aldolase / tagatose-bisphosphate aldolase activity / lactose catabolic process via tagatose-6-phosphate / D-tagatose 6-phosphate catabolic process / tagatose-6-phosphate kinase activity
Similarity search - Function
Tagatose 1,6-diphosphate 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
Tagatose 1,6-diphosphate aldolase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.99 Å
AuthorsLee, S.J. / Kim, H.S. / Kim, D.J. / Yoon, H.J. / Kim, K.H. / Yoon, J.Y. / Suh, S.W.
CitationJournal: Febs Lett. / Year: 2011
Title: Crystal structures of LacD from Staphylococcus aureus and LacD.1 from Streptococcus pyogenes: Insights into substrate specificity and virulence gene regulation
Authors: Lee, S.J. / Kim, H.S. / Kim, D.J. / Yoon, H.J. / Kim, K.H. / Yoon, J.Y. / Suh, S.W.
History
DepositionMay 10, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 26, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tagatose 1,6-diphosphate aldolase
B: Tagatose 1,6-diphosphate aldolase
C: Tagatose 1,6-diphosphate aldolase
D: Tagatose 1,6-diphosphate aldolase


Theoretical massNumber of molelcules
Total (without water)151,7804
Polymers151,7804
Non-polymers00
Water1,72996
1
A: Tagatose 1,6-diphosphate aldolase
C: Tagatose 1,6-diphosphate aldolase


Theoretical massNumber of molelcules
Total (without water)75,8902
Polymers75,8902
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Tagatose 1,6-diphosphate aldolase
D: Tagatose 1,6-diphosphate aldolase


Theoretical massNumber of molelcules
Total (without water)75,8902
Polymers75,8902
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)104.899, 104.899, 115.863
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

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


Mass: 37944.980 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: COL / Gene: lacD, SACOL2183 / Plasmid: pET21a(+) / Production host: Escherichia coli (E. coli) / References: UniProt: Q5HE13, tagatose-bisphosphate aldolase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / 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: 2.42 Å3/Da / Density % sol: 49.25 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2M calcium chloride, 0.1M HEPES, 28% (v/v) PEG 400, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 287K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 6C1 / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 4, 2008
RadiationProtocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.989→20 Å / Num. obs: 28654 / Redundancy: 17.3 % / Biso Wilson estimate: 57 Å2 / Rmerge(I) obs: 0.153 / Net I/σ(I): 28.5
Reflection shellResolution: 2.989→3.05 Å / Redundancy: 15.4 % / Rmerge(I) obs: 0.589 / Mean I/σ(I) obs: 4.5 / Num. unique all: 1379

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.99→19.83 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.911 / SU B: 16.311 / SU ML: 0.306 / Cross valid method: THROUGHOUT / ESU R Free: 0.453 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24124 1444 5.1 %RANDOM
Rwork0.20279 ---
obs0.20471 27130 99.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 57.2 Å2
Baniso -1Baniso -2Baniso -3
1-4.6 Å22.3 Å20 Å2
2--4.6 Å20 Å2
3----6.9 Å2
Refinement stepCycle: LAST / Resolution: 2.99→19.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10136 0 0 96 10232
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02210388
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4831.9614044
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5151288
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.67425.591508
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.214151852
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9461544
X-RAY DIFFRACTIONr_chiral_restr0.0990.21548
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0217880
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6511.56424
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.193210304
X-RAY DIFFRACTIONr_scbond_it1.42533964
X-RAY DIFFRACTIONr_scangle_it2.4854.53740
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.989→3.065 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.338 98 -
Rwork0.252 1852 -
obs--92.99 %

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