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- PDB-3mhf: Tagatose-1,6-bisphosphate aldolase from Streptococcus pyogenes -

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Basic information

Entry
Database: PDB / ID: 3mhf
TitleTagatose-1,6-bisphosphate aldolase from Streptococcus pyogenes
ComponentsTagatose 1,6-diphosphate aldolase 2
KeywordsLYASE / tagatose aldolase class I / beta barrel / streptococcus pyogenes
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 2
Similarity search - Component
Biological speciesStreptococcus pyogenes serotype M1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 Å
AuthorsLowKam, C.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Structure of a class I tagatose-1,6-bisphosphate aldolase: investigation into an apparent loss of stereospecificity.
Authors: LowKam, C. / Liotard, B. / Sygusch, J.
History
DepositionApr 7, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 28, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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 2
B: Tagatose 1,6-diphosphate aldolase 2
C: Tagatose 1,6-diphosphate aldolase 2
D: Tagatose 1,6-diphosphate aldolase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,23811
Polymers145,9574
Non-polymers2817
Water41,9932331
1
A: Tagatose 1,6-diphosphate aldolase 2
B: Tagatose 1,6-diphosphate aldolase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,1797
Polymers72,9792
Non-polymers2005
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2180 Å2
ΔGint-17 kcal/mol
Surface area27300 Å2
MethodPISA
2
C: Tagatose 1,6-diphosphate aldolase 2
D: Tagatose 1,6-diphosphate aldolase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,0594
Polymers72,9792
Non-polymers802
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2160 Å2
ΔGint-12 kcal/mol
Surface area27010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.863, 105.590, 238.160
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Tagatose 1,6-diphosphate aldolase 2 / Tagatose-bisphosphate aldolase 2 / D-tagatose-1 / 6-bisphosphate aldolase 2


Mass: 36489.262 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pyogenes serotype M1 (bacteria)
Gene: lacD.2, lacD2, M5005_Spy1635, SPy_1919 / Plasmid: pKK222 / Production host: Escherichia coli (E. coli) / References: UniProt: P63705, tagatose-bisphosphate aldolase
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2331 / 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: 2.75 Å3/Da / Density % sol: 55.29 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Tris Acetate, Calcium Acetate, PEG 4000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 4, 2008
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.87→50 Å / Num. all: 144212 / Num. obs: 131345 / % possible obs: 74.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.1 % / Rsym value: 0.092 / Net I/σ(I): 7.1
Reflection shellResolution: 1.87→1.97 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 1.4 / Num. unique all: 15756 / Rsym value: 0.513 / % possible all: 82.5

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.4_161)refinement
CNSrefinement
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.87→43.549 Å / SU ML: 0.23 / σ(F): 0.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2159 12296 10 %Random
Rwork0.1692 ---
obs0.1739 123021 91.94 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 62.478 Å2 / ksol: 0.345 e/Å3
Displacement parametersBiso mean: 32.75 Å2
Refinement stepCycle: LAST / Resolution: 1.87→43.549 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10164 0 7 2331 12502
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00510428
X-RAY DIFFRACTIONf_angle_d0.90914105
X-RAY DIFFRACTIONf_dihedral_angle_d15.23881
X-RAY DIFFRACTIONf_chiral_restr0.0631570
X-RAY DIFFRACTIONf_plane_restr0.0041834
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.87-1.89130.31062680.27462435X-RAY DIFFRACTION61
1.8913-1.91350.28433010.26132652X-RAY DIFFRACTION67
1.9135-1.93680.2932970.23833052X-RAY DIFFRACTION75
1.9368-1.96140.29123500.21993193X-RAY DIFFRACTION81
1.9614-1.98720.24463640.2183368X-RAY DIFFRACTION84
1.9872-2.01440.25414010.20873453X-RAY DIFFRACTION88
2.0144-2.04320.24714210.19443548X-RAY DIFFRACTION90
2.0432-2.07370.2294130.19553586X-RAY DIFFRACTION90
2.0737-2.10610.24973720.1953636X-RAY DIFFRACTION91
2.1061-2.14060.24964110.2023682X-RAY DIFFRACTION92
2.1406-2.17750.27394160.18623659X-RAY DIFFRACTION93
2.1775-2.21710.22874020.1883772X-RAY DIFFRACTION94
2.2171-2.25970.25844130.18013749X-RAY DIFFRACTION94
2.2597-2.30590.23884160.17673814X-RAY DIFFRACTION95
2.3059-2.3560.22774390.17163793X-RAY DIFFRACTION95
2.356-2.41080.22834210.1753818X-RAY DIFFRACTION96
2.4108-2.47110.23223960.17963903X-RAY DIFFRACTION96
2.4711-2.53790.25314370.1733817X-RAY DIFFRACTION96
2.5379-2.61260.21774740.17793825X-RAY DIFFRACTION97
2.6126-2.69690.24154040.1733973X-RAY DIFFRACTION98
2.6969-2.79320.22194630.17383905X-RAY DIFFRACTION98
2.7932-2.90510.22254210.16893952X-RAY DIFFRACTION98
2.9051-3.03720.21254460.16043952X-RAY DIFFRACTION98
3.0372-3.19730.21134620.15213952X-RAY DIFFRACTION99
3.1973-3.39760.20414370.14623967X-RAY DIFFRACTION98
3.3976-3.65980.16954680.12873925X-RAY DIFFRACTION98
3.6598-4.02780.18254230.12314036X-RAY DIFFRACTION98
4.0278-4.61010.16194670.12274025X-RAY DIFFRACTION98
4.6101-5.80610.18944710.14384065X-RAY DIFFRACTION98
5.8061-43.56110.19394220.20474218X-RAY DIFFRACTION97

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