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- PDB-1qo5: Fructose 1,6-bisphosphate Aldolase from Human Liver Tissue -

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Basic information

Entry
Database: PDB / ID: 1qo5
TitleFructose 1,6-bisphosphate Aldolase from Human Liver Tissue
ComponentsFRUCTOSE-BISPHOSPHATE ALDOLASE B
KeywordsLYASE / ALDOLASE / TIM BARREL / GLYCOLYTIC ENZYME
Function / homology
Function and homology information


Hereditary fructose intolerance / fructose-1-phosphate aldolase activity / fructose catabolic process to hydroxyacetone phosphate and glyceraldehyde-3-phosphate / fructose binding / vacuolar proton-transporting V-type ATPase complex assembly / NADH oxidation / Fructose catabolism / fructose-bisphosphate aldolase / fructose-bisphosphate aldolase activity / Gluconeogenesis ...Hereditary fructose intolerance / fructose-1-phosphate aldolase activity / fructose catabolic process to hydroxyacetone phosphate and glyceraldehyde-3-phosphate / fructose binding / vacuolar proton-transporting V-type ATPase complex assembly / NADH oxidation / Fructose catabolism / fructose-bisphosphate aldolase / fructose-bisphosphate aldolase activity / Gluconeogenesis / positive regulation of ATP-dependent activity / fructose metabolic process / fructose 1,6-bisphosphate metabolic process / negative regulation of pentose-phosphate shunt / Glycolysis / microtubule organizing center / centriolar satellite / cytoskeletal protein binding / gluconeogenesis / glycolytic process / ATPase binding / molecular adaptor activity / extracellular exosome / identical protein binding / 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
Fructose-bisphosphate aldolase B
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsDalby, A.R. / Littlechild, J.A.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2001
Title: The Structure of Human Liver Fructose-1,6-Bisphosphate Aldolase
Authors: Dalby, A.R. / Tolan, D.R. / Littlechild, J.A.
History
DepositionNov 3, 1999Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 5, 2000Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Advisory / Data collection ...Advisory / Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_data_processing_status / pdbx_database_proc / pdbx_database_status / pdbx_unobs_or_zero_occ_residues
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.4Dec 13, 2023Group: Advisory / Data collection ...Advisory / 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_unobs_or_zero_occ_residues / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: FRUCTOSE-BISPHOSPHATE ALDOLASE B
B: FRUCTOSE-BISPHOSPHATE ALDOLASE B
C: FRUCTOSE-BISPHOSPHATE ALDOLASE B
D: FRUCTOSE-BISPHOSPHATE ALDOLASE B
E: FRUCTOSE-BISPHOSPHATE ALDOLASE B
F: FRUCTOSE-BISPHOSPHATE ALDOLASE B
G: FRUCTOSE-BISPHOSPHATE ALDOLASE B
H: FRUCTOSE-BISPHOSPHATE ALDOLASE B
I: FRUCTOSE-BISPHOSPHATE ALDOLASE B
J: FRUCTOSE-BISPHOSPHATE ALDOLASE B
K: FRUCTOSE-BISPHOSPHATE ALDOLASE B
L: FRUCTOSE-BISPHOSPHATE ALDOLASE B
M: FRUCTOSE-BISPHOSPHATE ALDOLASE B
N: FRUCTOSE-BISPHOSPHATE ALDOLASE B
O: FRUCTOSE-BISPHOSPHATE ALDOLASE B
P: FRUCTOSE-BISPHOSPHATE ALDOLASE B
Q: FRUCTOSE-BISPHOSPHATE ALDOLASE B
R: FRUCTOSE-BISPHOSPHATE ALDOLASE B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)710,43933
Polymers708,99818
Non-polymers1,44115
Water21,0601169
1
A: FRUCTOSE-BISPHOSPHATE ALDOLASE B
B: FRUCTOSE-BISPHOSPHATE ALDOLASE B
C: FRUCTOSE-BISPHOSPHATE ALDOLASE B
D: FRUCTOSE-BISPHOSPHATE ALDOLASE B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,8437
Polymers157,5554
Non-polymers2883
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11480 Å2
ΔGint2.4 kcal/mol
Surface area59920 Å2
MethodPQS
2
E: FRUCTOSE-BISPHOSPHATE ALDOLASE B
F: FRUCTOSE-BISPHOSPHATE ALDOLASE B
G: FRUCTOSE-BISPHOSPHATE ALDOLASE B
H: FRUCTOSE-BISPHOSPHATE ALDOLASE B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,9398
Polymers157,5554
Non-polymers3844
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10170 Å2
ΔGint-9.6 kcal/mol
Surface area60140 Å2
MethodPQS
3
I: FRUCTOSE-BISPHOSPHATE ALDOLASE B
J: FRUCTOSE-BISPHOSPHATE ALDOLASE B
K: FRUCTOSE-BISPHOSPHATE ALDOLASE B
L: FRUCTOSE-BISPHOSPHATE ALDOLASE B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,7476
Polymers157,5554
Non-polymers1922
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9530 Å2
ΔGint-57.4 kcal/mol
Surface area59540 Å2
MethodPQS
4
M: FRUCTOSE-BISPHOSPHATE ALDOLASE B
N: FRUCTOSE-BISPHOSPHATE ALDOLASE B
O: FRUCTOSE-BISPHOSPHATE ALDOLASE B
P: FRUCTOSE-BISPHOSPHATE ALDOLASE B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,9398
Polymers157,5554
Non-polymers3844
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11990 Å2
ΔGint0.7 kcal/mol
Surface area60060 Å2
MethodPQS
5
Q: FRUCTOSE-BISPHOSPHATE ALDOLASE B
R: FRUCTOSE-BISPHOSPHATE ALDOLASE B
hetero molecules

Q: FRUCTOSE-BISPHOSPHATE ALDOLASE B
R: FRUCTOSE-BISPHOSPHATE ALDOLASE B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,9398
Polymers157,5554
Non-polymers3844
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area11080 Å2
ΔGint-37.6 kcal/mol
Surface area59990 Å2
MethodPQS
Unit cell
Length a, b, c (Å)291.100, 489.840, 103.360
Angle α, β, γ (deg.)90.00, 103.68, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.997097, 0.059797, -0.047146), (0.057579, 0.186908, -0.98068), (-0.049831, -0.98055, -0.189809)31.89326, 23.68275, 30.54217
2given(0.207074, 0.58658, 0.782962), (0.581788, -0.717254, 0.383487), (0.786538, 0.376107, -0.48979)-7.60802, -18.51731, 25.2832
3given(-0.216224, -0.640218, -0.737124), (-0.64009, -0.477142, 0.602172), (-0.737245, 0.602031, -0.306627)37.0628, -5.22755, 44.04025
4given(0.175317, 0.645276, 0.743549), (-0.84229, 0.489329, -0.226057), (-0.509717, -0.586651, 0.629297)33.99503, 134.25899, 31.97788
5given(-0.199484, -0.595778, -0.777971), (0.333719, 0.705164, -0.62559), (0.921325, -0.384419, 0.058153)4.14202, 148.2343, 69.562
6given(-0.852615, -0.027945, 0.521788), (0.516147, -0.20078, 0.832626), (0.081498, 0.979231, 0.185612)35.01218, 105.64614, 46.44726
7given(0.876264, -0.024725, -0.481192), (-0.020096, -0.999684, 0.014771), (-0.481412, -0.003274, -0.876483)22.53846, 129.8726, 88.42326
8given(0.137334, -0.627082, 0.766738), (-0.978069, -0.208227, 0.004884), (0.156596, -0.750595, -0.641927)154.68318, 172.33195, 100.24669
9given(-0.192802, 0.653234, -0.732185), (-0.342595, 0.654413, 0.674061), (0.919488, 0.380804, 0.097622)140.6729, 124.31854, 104.74457
10given(-0.414463, -0.84237, -0.344409), (0.84242, -0.498297, 0.205003), (-0.344312, -0.205169, 0.916156)175.63443, 161.88005, 78.30228
11given(0.48443, 0.817094, 0.312533), (0.470849, 0.057571, -0.880326), (-0.737312, 0.573612, -0.356839)171.71582, 116.91897, 100.16738
12given(-0.881863, -0.015392, 0.471249), (-0.461399, -0.177673, -0.869211), (0.097109, -0.983961, 0.149581)201.82765, 204.75586, 49.63222
13given(0.850343, 0.042395, -0.524513), (-0.230229, 0.926257, -0.298374), (0.473193, 0.374478, 0.797399)165.70456, 169.89792, 48.68849
14given(-0.376586, -0.880613, -0.287556), (-0.158175, -0.244726, 0.956594), (-0.912779, 0.405723, -0.047131)219.36765, 183.34608, 66.11924
15given(0.414615, 0.842096, 0.344896), (0.841324, -0.499163, 0.207378), (0.346798, 0.204186, -0.915439)175.575, 161.9614, 78.27222
16given(0.146885, 0.630515, 0.762135), (-0.666436, -0.506283, 0.547288), (0.730951, -0.588302, 0.345832)112.89944, 314.72992, 29.92561
17given(-0.204718, -0.626935, -0.751674), (-0.843052, 0.503132, -0.190039), (0.497348, 0.594796, -0.631539)123.99388, 304.53653, 77.53224
DetailsTHE BIOMOLECULE CONSISTS OF A HOMOTETRAMER AND 5 INDEPENDENTCOPIES ARE OBSERVED IN THE ASYMMETRIC UNIT WITH THE FIFTHTETRAMER REQUIRING CRYSTALLOGRAPHIC SYMMETRY.

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Components

#1: Protein
FRUCTOSE-BISPHOSPHATE ALDOLASE B / LIVER-TYPE ALDOLASE


Mass: 39388.773 Da / Num. of mol.: 18
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cellular location: CYTOPLASM / Organ: LIVER / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P05062, fructose-bisphosphate aldolase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1169 / 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: 5.65 Å3/Da / Density % sol: 79 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7
Details: HANGING DROP WITH AMMONIUM SULFATE AS THE PRECIPITANT, pH 7.00

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.5 / Wavelength: 0.8
DetectorType: ADSC QUANTUM 4 CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 2.5→35 Å / Num. obs: 339612 / % possible obs: 71 % / Redundancy: 2.4 % / Biso Wilson estimate: 42.57 Å2 / Rmerge(I) obs: 0.154 / Rsym value: 0.122 / Net I/σ(I): 3.2
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.567 / Mean I/σ(I) obs: 0.4 / Rsym value: 0.438 / % possible all: 55.8

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Processing

Software
NameClassification
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2ALD

2ald


Resolution: 2.5→29 Å / SU B: 9.96 / SU ML: 0.21655 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.40088 / ESU R Free: 0.30816 / Details: NCS RESTRAINTS USED THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.276 16667 5 %RANDOM
Rwork0.224 ---
obs-316146 71 %-
Refinement stepCycle: LAST / Resolution: 2.5→29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms48034 0 75 1169 49278
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0220.01
X-RAY DIFFRACTIONp_angle_d0.0630.02
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0820.03
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it6.1474
X-RAY DIFFRACTIONp_mcangle_it7.6527
X-RAY DIFFRACTIONp_scbond_it12.2349
X-RAY DIFFRACTIONp_scangle_it13.149
X-RAY DIFFRACTIONp_plane_restr0.01880.02
X-RAY DIFFRACTIONp_chiral_restr0.2180.08
X-RAY DIFFRACTIONp_singtor_nbd0.2370.3
X-RAY DIFFRACTIONp_multtor_nbd0.3160.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.2160.3
X-RAY DIFFRACTIONp_planar_tor5.86
X-RAY DIFFRACTIONp_staggered_tor22.310
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor35.420
X-RAY DIFFRACTIONp_special_tor010

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