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- PDB-1fdj: FRUCTOSE 1,6-BISPHOSPHATE ALDOLASE FROM RABBIT LIVER -

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Basic information

Entry
Database: PDB / ID: 1fdj
TitleFRUCTOSE 1,6-BISPHOSPHATE ALDOLASE FROM RABBIT LIVER
ComponentsFRUCTOSE 1,6-BISPHOSPHATE ALDOLASE
KeywordsLYASE / ALDOLASE / LYASE (ALDEHYDE) / SCHIFF BASE / GLYCOLYSIS
Function / homology
Function and homology information


fructose-1-phosphate aldolase activity / fructose-bisphosphate aldolase / fructose-bisphosphate aldolase activity / fructose metabolic process / glycolytic process / gluconeogenesis / centriolar satellite / cytosol
Similarity search - Function
Fructose-bisphosphate aldolase class-I active site / Fructose-bisphosphate aldolase class-I active site. / Fructose-bisphosphate aldolase, class-I / Fructose-bisphosphate aldolase class-I / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
1,3-DIHYDROXYACETONEPHOSPHATE / 1,6-FRUCTOSE DIPHOSPHATE (LINEAR FORM) / SN-GLYCEROL-3-PHOSPHATE / Fructose-bisphosphate aldolase B
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / Resolution: 2.1 Å
AuthorsBlom, N.S. / White, A. / Sygusch, J.
Citation
Journal: To be Published
Title: Reaction intermediates of Rabbit liver D-fructose 1,6-bisphosphate Aldolase
Authors: Blom, N.S. / White, A. / Sygusch, J.
#1: Journal: Nat.Struct.Biol. / Year: 1997
Title: Product binding and role of the C-terminal region in Class-I D-fructose 1,6 bisphosphate Aldolase
Authors: Blom, N.S. / Sygusch, J.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 1998
Title: Enhanced electron density envelopes by extended solvent definition
Authors: Blom, N.S. / Sygusch, J.
History
DepositionJul 20, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 25, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Dec 25, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / database_PDB_caveat / pdbx_distant_solvent_atoms / pdbx_entry_details / 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 / _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
B: FRUCTOSE 1,6-BISPHOSPHATE ALDOLASE
C: FRUCTOSE 1,6-BISPHOSPHATE ALDOLASE
D: FRUCTOSE 1,6-BISPHOSPHATE ALDOLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,95215
Polymers158,0364
Non-polymers1,91711
Water62,6383477
1
A: FRUCTOSE 1,6-BISPHOSPHATE ALDOLASE
B: FRUCTOSE 1,6-BISPHOSPHATE ALDOLASE
hetero molecules

A: FRUCTOSE 1,6-BISPHOSPHATE ALDOLASE
B: FRUCTOSE 1,6-BISPHOSPHATE ALDOLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)160,46516
Polymers158,0364
Non-polymers2,42912
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
2
C: FRUCTOSE 1,6-BISPHOSPHATE ALDOLASE
D: FRUCTOSE 1,6-BISPHOSPHATE ALDOLASE
hetero molecules

C: FRUCTOSE 1,6-BISPHOSPHATE ALDOLASE
D: FRUCTOSE 1,6-BISPHOSPHATE ALDOLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,44014
Polymers158,0364
Non-polymers1,40510
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Unit cell
Length a, b, c (Å)377.250, 130.540, 80.030
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-5149-

HOH

21A-5183-

HOH

31A-5202-

HOH

41A-5215-

HOH

51A-5238-

HOH

61A-5266-

HOH

71A-5292-

HOH

81A-5312-

HOH

91A-5763-

HOH

101B-6149-

HOH

111B-6506-

HOH

121C-7209-

HOH

131C-7228-

HOH

141C-7605-

HOH

151C-7799-

HOH

161D-8017-

HOH

171D-8083-

HOH

181D-8275-

HOH

191D-8436-

HOH

201D-8447-

HOH

211D-8469-

HOH

221D-8471-

HOH

Details2 half tetramers: one half tetramers is formed by chains A and B, the other half tetramer is formed by chains C and D

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Components

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Protein / Sugars , 2 types, 6 molecules ABCD

#1: Protein
FRUCTOSE 1,6-BISPHOSPHATE ALDOLASE


Mass: 39508.922 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Organ: LIVER / References: UniProt: P79226, fructose-bisphosphate aldolase
#3: Sugar ChemComp-2FP / 1,6-FRUCTOSE DIPHOSPHATE (LINEAR FORM)


Type: saccharide / Mass: 340.116 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O12P2

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Non-polymers , 4 types, 3486 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-13P / 1,3-DIHYDROXYACETONEPHOSPHATE


Mass: 170.058 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H7O6P
#5: Chemical ChemComp-G3P / SN-GLYCEROL-3-PHOSPHATE


Mass: 172.074 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H9O6P
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3477 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

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Sample preparation

CrystalDensity Matthews: 3.12 Å3/Da / Density % sol: 60.53 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 45% saturated ammonium sulphate solution, 100mM Tris.HCl, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418
DetectorType: XENTRONICS / Detector: AREA DETECTOR / Date: Nov 10, 1994
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.13→12 Å / Num. all: 100603 / Num. obs: 85613 / % possible obs: 85.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): -3 / Redundancy: 4.5 % / Biso Wilson estimate: 10 Å2 / Rmerge(I) obs: 0.092 / Net I/σ(I): 10.8
Reflection shellResolution: 2.13→2.25 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.18 / Num. unique all: 100603 / % possible all: 68.1

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.1refinement
X-GENdata reduction
X-GENdata scaling
X-PLORphasing
RefinementResolution: 2.1→12 Å / σ(F): 1 / σ(I): 1 / Stereochemistry target values: XPLOR parhcsdx
RfactorNum. reflection% reflection
Rfree0.214 6930 -
Rwork0.171 --
all0.193 85613 -
obs0.174 78105 8 %
Refinement stepCycle: LAST / Resolution: 2.1→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11502 0 110 3477 15089
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_angle_deg1.77
X-RAY DIFFRACTIONx_dihedral23.2

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