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- PDB-3mhg: Dihydroxyacetone phosphate carbanion intermediate in tagatose-1,6... -

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Basic information

Entry
Database: PDB / ID: 3mhg
TitleDihydroxyacetone phosphate carbanion intermediate in tagatose-1,6-bisphosphate aldolase from Streptococcus pyogenes
ComponentsTagatose 1,6-diphosphate aldolase 2
KeywordsLYASE / tagatose aldolase class I / beta barrel / streptococcus pyogenes / Schiff base / carbanion
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
1,3-DIHYDROXYACETONEPHOSPHATE / Tagatose 1,6-diphosphate aldolase 2
Similarity search - Component
Biological speciesStreptococcus pyogenes serotype M1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å
AuthorsLowKam, C. / Liotard, B.
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 / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.name ..._software.classification / _software.name / _software.version / _struct_conn.pdbx_leaving_atom_flag

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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)146,91815
Polymers145,9574
Non-polymers96111
Water44,2092454
1
A: Tagatose 1,6-diphosphate aldolase 2
B: Tagatose 1,6-diphosphate aldolase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,4798
Polymers72,9792
Non-polymers5006
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2810 Å2
ΔGint-13 kcal/mol
Surface area26900 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)73,4397
Polymers72,9792
Non-polymers4605
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2980 Å2
ΔGint-30 kcal/mol
Surface area26690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.092, 108.182, 238.708
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-13P / 1,3-DIHYDROXYACETONEPHOSPHATE / Dihydroxyacetone phosphate


Mass: 170.058 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H7O6P
#3: Chemical
ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 2454 / 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: 2.83 Å3/Da / Density % sol: 56.61 %
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: Nov 2, 2005
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.92→50 Å / Num. all: 142361 / Num. obs: 127313 / % possible obs: 85.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 6.1 % / Rsym value: 0.101 / Net I/σ(I): 7.8
Reflection shellResolution: 1.92→2.02 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.326 / Mean I/σ(I) obs: 2.9 / Num. unique all: 12153 / % possible all: 74.1

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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: 1.92→34.52 Å / SU ML: 0.18 / σ(F): 0.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1959 11905 9.94 %random
Rwork0.1555 ---
obs0.1596 119765 93.94 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 37.998 Å2 / ksol: 0.33 e/Å3
Displacement parametersBiso mean: 22.22 Å2
Refinement stepCycle: LAST / Resolution: 1.92→34.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10166 0 43 2454 12663
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00410467
X-RAY DIFFRACTIONf_angle_d0.86614152
X-RAY DIFFRACTIONf_dihedral_angle_d15.9253908
X-RAY DIFFRACTIONf_chiral_restr0.0611572
X-RAY DIFFRACTIONf_plane_restr0.0031834
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.92-1.94180.23932920.18782467X-RAY DIFFRACTION65
1.9418-1.96470.22842880.18352753X-RAY DIFFRACTION73
1.9647-1.98860.22233220.18412907X-RAY DIFFRACTION77
1.9886-2.01380.21753140.18063082X-RAY DIFFRACTION81
2.0138-2.04030.23553850.17793290X-RAY DIFFRACTION87
2.0403-2.06820.26113480.16623439X-RAY DIFFRACTION90
2.0682-2.09780.20233900.16843429X-RAY DIFFRACTION92
2.0978-2.12910.21363970.16773564X-RAY DIFFRACTION93
2.1291-2.16240.20363910.1653584X-RAY DIFFRACTION95
2.1624-2.19780.20664120.16313612X-RAY DIFFRACTION96
2.1978-2.23570.21524340.16313644X-RAY DIFFRACTION96
2.2357-2.27630.22394360.15533655X-RAY DIFFRACTION97
2.2763-2.32010.19873930.15283673X-RAY DIFFRACTION97
2.3201-2.36750.18223920.15253718X-RAY DIFFRACTION98
2.3675-2.41890.20684030.153688X-RAY DIFFRACTION97
2.4189-2.47520.20763890.1613756X-RAY DIFFRACTION98
2.4752-2.53710.21583890.15473731X-RAY DIFFRACTION98
2.5371-2.60560.19514260.16033719X-RAY DIFFRACTION98
2.6056-2.68230.22064280.16263773X-RAY DIFFRACTION98
2.6823-2.76880.2114330.15983699X-RAY DIFFRACTION98
2.7688-2.86770.21254420.16443767X-RAY DIFFRACTION99
2.8677-2.98250.22444170.16243813X-RAY DIFFRACTION99
2.9825-3.11820.19193980.14823799X-RAY DIFFRACTION99
3.1182-3.28240.1943930.14033875X-RAY DIFFRACTION100
3.2824-3.48790.15164040.1423855X-RAY DIFFRACTION99
3.4879-3.75690.15494520.12523824X-RAY DIFFRACTION100
3.7569-4.13440.15024240.12183840X-RAY DIFFRACTION100
4.1344-4.73140.15234330.12553898X-RAY DIFFRACTION100
4.7314-5.95610.18114320.15353946X-RAY DIFFRACTION99
5.9561-34.52510.20284480.1944060X-RAY DIFFRACTION99

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