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- PDB-3t2g: Fructose-1,6-bisphosphate aldolase/phosphatase from Thermoproteus... -

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Basic information

Entry
Database: PDB / ID: 3t2g
TitleFructose-1,6-bisphosphate aldolase/phosphatase from Thermoproteus neutrophilus, Y229F variant with DHAP
ComponentsFructose-1,6-bisphosphate aldolase/phosphatase
KeywordsLYASE / HYDROLASE / (beta/alpha)8 TIM barrel / FBP / F6P / DHAP / GAP / phosphorylation
Function / homology
Function and homology information


fructose-bisphosphate aldolase / fructose-bisphosphate aldolase activity / fructose-bisphosphatase / fructose 1,6-bisphosphate 1-phosphatase activity / gluconeogenesis / magnesium ion binding
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1180 / Fructose-1,6-bisphosphatase, class V / Fructose-1,6-bisphosphatase, class V superfamily / Fructose-1,6-bisphosphatase / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special
Similarity search - Domain/homology
1,3-DIHYDROXYACETONEPHOSPHATE / Fructose-1,6-bisphosphate aldolase/phosphatase
Similarity search - Component
Biological speciesThermoproteus neutrophilus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsDu, J. / Say, R. / Lue, W. / Fuchs, G. / Einsle, O.
CitationJournal: Nature / Year: 2011
Title: Active-site remodelling in the bifunctional fructose-1,6-bisphosphate aldolase/phosphatase.
Authors: Du, J. / Say, R.F. / Lu, W. / Fuchs, G. / Einsle, O.
History
DepositionJul 22, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 26, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 9, 2011Group: Database references
Revision 1.2Sep 13, 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 / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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_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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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_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_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_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: Fructose-1,6-bisphosphate aldolase/phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,8345
Polymers45,4451
Non-polymers3894
Water905
1
A: Fructose-1,6-bisphosphate aldolase/phosphatase
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)366,67040
Polymers363,5608
Non-polymers3,11032
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_465-x-1,-y+1,z1
crystal symmetry operation3_565-y,x+1,z1
crystal symmetry operation4_455y-1,-x,z1
crystal symmetry operation5_455-x-1,y,-z1
crystal symmetry operation6_565x,-y+1,-z1
crystal symmetry operation7_465y-1,x+1,-z1
crystal symmetry operation8_555-y,-x,-z1
Buried area65850 Å2
ΔGint-575 kcal/mol
Surface area81260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.430, 112.430, 151.520
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422

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Components

#1: Protein Fructose-1,6-bisphosphate aldolase/phosphatase


Mass: 45445.031 Da / Num. of mol.: 1 / Mutation: Y229F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoproteus neutrophilus (archaea) / Strain: DSM 2338 / JCM 9278 / V24Sta / Gene: Tneu_0133 / Plasmid: pET23b / Production host: Escherichia coli (E. coli)
References: UniProt: B1YAL1, fructose-bisphosphate aldolase, fructose-bisphosphatase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-13P / 1,3-DIHYDROXYACETONEPHOSPHATE


Mass: 170.058 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H7O6P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / 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: 2.63 Å3/Da / Density % sol: 53.3 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 8% PEG3350, 0.1 M HEPES/NaOH, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Aug 1, 2010
RadiationMonochromator: Fixed-exit LN2 cooled Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.998→47.721 Å / Num. all: 10089 / Num. obs: 10089 / % possible obs: 99.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.4 % / Rmerge(I) obs: 0.18 / Rsym value: 0.18 / Net I/σ(I): 10.7
Reflection shellResolution: 3→3.16 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.599 / Mean I/σ(I) obs: 3 / Rsym value: 0.599 / % possible all: 99.6

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
MOLREPphasing
REFMAC5.5.0110refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3T2B

3t2b


Resolution: 3→47.72 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.897 / SU B: 15.728 / SU ML: 0.295 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R Free: 0.401 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.23403 505 5 %RANDOM
Rwork0.17487 ---
obs0.1779 9573 100 %-
all-9583 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.404 Å2
Baniso -1Baniso -2Baniso -3
1-1.45 Å2-0 Å2-0 Å2
2--1.45 Å20 Å2
3----2.89 Å2
Refinement stepCycle: LAST / Resolution: 3→47.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3005 0 22 5 3032
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0223093
X-RAY DIFFRACTIONr_angle_refined_deg1.61.9784189
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3785381
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.05123.333138
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.00515508
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.131521
X-RAY DIFFRACTIONr_chiral_restr0.0980.2446
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212375
X-RAY DIFFRACTIONr_mcbond_it0.6421.51908
X-RAY DIFFRACTIONr_mcangle_it1.2423067
X-RAY DIFFRACTIONr_scbond_it1.7331185
X-RAY DIFFRACTIONr_scangle_it3.064.51122
LS refinement shellResolution: 2.998→3.076 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 36 -
Rwork0.198 680 -
obs--100 %

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