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- PDB-3r1m: Structure of bifunctional fructose 1,6-bisphosphate aldolase/phos... -

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Basic information

Entry
Database: PDB / ID: 3r1m
TitleStructure of bifunctional fructose 1,6-bisphosphate aldolase/phosphatase (aldolase form)
ComponentsPutative uncharacterized protein ST0318
KeywordsMETAL BINDING PROTEIN / Sulfolobus fructose-1 / 6-bisphosphatase-like fold / Hydrolase/aldolase / Mg binding
Function / homology
Function and homology information


NADPH regeneration / fructose-bisphosphate aldolase / fructose-bisphosphate aldolase activity / fructose-bisphosphatase / fructose 1,6-bisphosphate 1-phosphatase activity / dephosphorylation / gluconeogenesis / magnesium ion binding
Similarity search - Function
Fructose-1,6-bisphosphatase, class V / Fructose-1,6-bisphosphatase, class V superfamily / Fructose-1,6-bisphosphatase
Similarity search - Domain/homology
1,3-DIHYDROXYACETONEPHOSPHATE / Fructose-1,6-bisphosphate aldolase/phosphatase / :
Similarity search - Component
Biological speciesSulfolobus tokodaii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.5 Å
AuthorsFushinobu, S. / Nishimasu, H. / Hattori, D. / Song, H.-J. / Wakagi, T.
CitationJournal: Nature / Year: 2011
Title: Structural basis for the bifunctionality of fructose-1,6-bisphosphate aldolase/phosphatase.
Authors: Fushinobu, S. / Nishimasu, H. / Hattori, D. / Song, H.-J. / Wakagi, T.
History
DepositionMar 10, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 12, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2011Group: Structure summary
Revision 1.2Nov 9, 2011Group: Database references
Revision 1.3Feb 8, 2017Group: Structure summary
Revision 1.4Nov 1, 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_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.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.pdbx_leaving_atom_flag / _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_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: Putative uncharacterized protein ST0318
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,1216
Polymers42,7601
Non-polymers3615
Water4,756264
1
A: Putative uncharacterized protein ST0318
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)344,96948
Polymers342,0808
Non-polymers2,88940
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation4_565y,-x+1,z1
crystal symmetry operation5_655-x+1,y,-z1
crystal symmetry operation6_565x,-y+1,-z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation8_665-y+1,-x+1,-z1
Buried area55340 Å2
ΔGint-612 kcal/mol
Surface area74490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.543, 112.543, 153.608
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-630-

HOH

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Components

#1: Protein Putative uncharacterized protein ST0318


Mass: 42759.969 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus tokodaii (archaea) / Strain: 7 / Gene: ST0318 / Plasmid: pET17b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q975V5, UniProt: F9VMT6*PLUS
#2: Chemical ChemComp-13P / 1,3-DIHYDROXYACETONEPHOSPHATE / Dihydroxyacetone phosphate


Mass: 170.058 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7O6P
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 264 / 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: 2.84 Å3/Da / Density % sol: 56.75 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 10% PEG 20000, 0.1M bicine pH 9.0, 2% dioxane, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 7, 2010
RadiationMonochromator: Numerical link type Si(111) double crystal monochromator, liquid nitrogen cooling
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. all: 78670 / Num. obs: 78613 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.6 % / Biso Wilson estimate: 16 Å2 / Rsym value: 0.064 / Net I/σ(I): 51.5
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 14.6 % / Mean I/σ(I) obs: 5.1 / Num. unique all: 7768 / Rsym value: 0.531 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
REFMAC5.5.0066refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 1UMG
Resolution: 1.5→26.22 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.953 / SU B: 1.116 / SU ML: 0.042 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.067 / ESU R Free: 0.067 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21461 3922 5 %RANDOM
Rwork0.19614 ---
obs0.19708 74120 99.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 19.345 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.065 Å0.062 Å
Refinement stepCycle: LAST / Resolution: 1.5→26.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2770 0 20 264 3054
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222876
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4311.9813907
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2145362
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.04523.543127
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.15315476
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.41520
X-RAY DIFFRACTIONr_chiral_restr0.0910.2430
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212193
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_it0.7861.51787
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.36722878
X-RAY DIFFRACTIONr_scbond_it2.18531089
X-RAY DIFFRACTIONr_scangle_it3.4544.51026
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 294 -
Rwork0.247 5434 -
obs--99.77 %

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