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- PDB-1bk4: CRYSTAL STRUCTURE OF RABBIT LIVER FRUCTOSE-1,6-BISPHOSPHATASE AT ... -

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Basic information

Entry
Database: PDB / ID: 1bk4
TitleCRYSTAL STRUCTURE OF RABBIT LIVER FRUCTOSE-1,6-BISPHOSPHATASE AT 2.3 ANGSTROM RESOLUTION
ComponentsPROTEIN (FRUCTOSE-1,6-BISPHOSPHATASE)
KeywordsHYDROLASE / BISPHOSPHATASE
Function / homology
Function and homology information


cellular response to xenobiotic stimulus => GO:0071466 / fructose-bisphosphatase / fructose 1,6-bisphosphate 1-phosphatase activity / negative regulation of Ras protein signal transduction / cellular response to magnesium ion / fructose 6-phosphate metabolic process / monosaccharide binding / negative regulation of glycolytic process / regulation of gluconeogenesis / AMP binding ...cellular response to xenobiotic stimulus => GO:0071466 / fructose-bisphosphatase / fructose 1,6-bisphosphate 1-phosphatase activity / negative regulation of Ras protein signal transduction / cellular response to magnesium ion / fructose 6-phosphate metabolic process / monosaccharide binding / negative regulation of glycolytic process / regulation of gluconeogenesis / AMP binding / dephosphorylation / gluconeogenesis / negative regulation of cell growth / metal ion binding / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Fructose-1,6-bisphosphatase / Fructose-1,6-bisphosphatase, active site / Fructose-1-6-bisphosphatase class 1, C-terminal / Fructose-1-6-bisphosphatase active site. / Fructose-1,6-bisphosphatase class 1 / Fructose-1-6-bisphosphatase class I, N-terminal / Fructose-1-6-bisphosphatase, N-terminal domain / Fructose-1-6-bisphosphatase, C-terminal domain / D-Maltodextrin-Binding Protein; domain 2 - #80 / Fructose-1,6-Bisphosphatase, subunit A, domain 1 ...Fructose-1,6-bisphosphatase / Fructose-1,6-bisphosphatase, active site / Fructose-1-6-bisphosphatase class 1, C-terminal / Fructose-1-6-bisphosphatase active site. / Fructose-1,6-bisphosphatase class 1 / Fructose-1-6-bisphosphatase class I, N-terminal / Fructose-1-6-bisphosphatase, N-terminal domain / Fructose-1-6-bisphosphatase, C-terminal domain / D-Maltodextrin-Binding Protein; domain 2 - #80 / Fructose-1,6-Bisphosphatase, subunit A, domain 1 / Fructose-1,6-Bisphosphatase; Chain A, domain 1 / D-Maltodextrin-Binding Protein; domain 2 / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Fructose-1,6-bisphosphatase 1
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / MIRAS / Resolution: 2.3 Å
AuthorsGhosh, D. / Weeks, C.M. / Erman, M. / Roszak, A.W. / Kaiser, R. / Jornvall, H.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 1999
Title: Structure of rabbit liver fructose 1,6-bisphosphatase at 2.3 A resolution.
Authors: Weeks, C.M. / Roszak, A.W. / Erman, M. / Kaiser, R. / Jornvall, H. / Ghosh, D.
History
DepositionJul 14, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Jul 22, 1998Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Feb 7, 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_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_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: PROTEIN (FRUCTOSE-1,6-BISPHOSPHATASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,7074
Polymers36,4911
Non-polymers2163
Water1,54986
1
A: PROTEIN (FRUCTOSE-1,6-BISPHOSPHATASE)
hetero molecules

A: PROTEIN (FRUCTOSE-1,6-BISPHOSPHATASE)
hetero molecules

A: PROTEIN (FRUCTOSE-1,6-BISPHOSPHATASE)
hetero molecules

A: PROTEIN (FRUCTOSE-1,6-BISPHOSPHATASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,83016
Polymers145,9644
Non-polymers86612
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation7_555-x+1/2,y+1/2,-z+1/21
crystal symmetry operation8_555x+1/2,-y+1/2,-z+1/21
2
A: PROTEIN (FRUCTOSE-1,6-BISPHOSPHATASE)
hetero molecules

A: PROTEIN (FRUCTOSE-1,6-BISPHOSPHATASE)
hetero molecules

A: PROTEIN (FRUCTOSE-1,6-BISPHOSPHATASE)
hetero molecules

A: PROTEIN (FRUCTOSE-1,6-BISPHOSPHATASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,83016
Polymers145,9644
Non-polymers86612
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
Buried area16350 Å2
ΔGint-271 kcal/mol
Surface area43680 Å2
MethodPQS
Unit cell
Length a, b, c (Å)73.790, 80.050, 131.820
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein PROTEIN (FRUCTOSE-1,6-BISPHOSPHATASE) / FRUCTOSE-1 / 6-DIPHOSPHATASE


Mass: 36490.965 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Organ: LIVER / References: UniProt: P00637, fructose-bisphosphatase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 86 / 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: 2.67 Å3/Da / Density % sol: 53.86 %
Crystal growpH: 7.4
Details: 10-15% PEG 4000, 50-200 MM A.S. IN 25 MM TRIS, pH 7.4
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110-15 %PEG40001reservoir
225 mMTris-HCl1reservoirpH7.4
37-8 mg/mlprotein1drop
450-200 mMammonium sulfate1drop

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Data collection

DiffractionMean temperature: 285 K
Diffraction sourceWavelength: 1.5418
DetectorType: UCSD MARK III / Detector: AREA DETECTOR / Date: Jan 15, 1990
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→99 Å / Num. obs: 16921 / % possible obs: 93 % / Redundancy: 4 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 12.8
Reflection
*PLUS
Num. measured all: 67887

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Processing

Software
NameVersionClassification
PHASESphasing
X-PLOR3.8refinement
UCSD-systemdata reduction
UCSD-systemdata scaling
RefinementMethod to determine structure: MIRAS / Resolution: 2.3→8 Å / σ(F): 2
RfactorNum. reflection% reflection
Rwork0.177 --
obs0.177 16921 93 %
Displacement parametersBiso mean: 36.9 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: LAST / Resolution: 2.3→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2393 0 11 86 2490
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.7
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.7
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.5
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Xplor fileSerial no: 1 / Param file: PARHCSDX.PRO / Topol file: TOPHCSDX.PRO
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 8 Å / σ(F): 2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 36.9 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.7
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.7
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.5

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