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- PDB-5gk7: Structure of E.Coli fructose 1,6-bisphosphate aldolase bound to Tris -

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Basic information

Entry
Database: PDB / ID: 5gk7
TitleStructure of E.Coli fructose 1,6-bisphosphate aldolase bound to Tris
ComponentsFructose-bisphosphate aldolase class 2
KeywordsLYASE / FBA Tris bound / LYASE Aldolase EC 4.1.2.13 Fructose 1 / 6-bisphosphate Glycolysis Anabolic pathways Catabolic pathways
Function / homology
Function and homology information


fructose-bisphosphate aldolase / fructose-bisphosphate aldolase activity / gluconeogenesis / glycolytic process / protein homodimerization activity / zinc ion binding / identical protein binding / cytosol
Similarity search - Function
Fructose-bisphosphate aldolase, class II, yeast/E. coli subtype / Fructose-bisphosphate aldolase class-II signature 1. / Fructose-bisphosphate aldolase class-II signature 2. / Fructose-bisphosphate aldolase, class-II / Fructose-bisphosphate aldolase class-II / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Fructose-bisphosphate aldolase class 2
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsTran, T.H. / Huynh, K.H. / Ho, T.H. / Kang, L.W.
CitationJournal: To Be Published
Title: Structure of E.Coli fructose 1,6-bisphosphate aldolase, Tris bound form
Authors: Tran, T.H. / Huynh, K.H. / Ho, T.H. / Kang, L.W.
History
DepositionJul 3, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 5, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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 / refine_hist / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_low / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fructose-bisphosphate aldolase class 2
B: Fructose-bisphosphate aldolase class 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,9568
Polymers78,3822
Non-polymers5736
Water5,278293
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5990 Å2
ΔGint-95 kcal/mol
Surface area24800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.422, 72.671, 73.052
Angle α, β, γ (deg.)90.00, 103.16, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Fructose-bisphosphate aldolase class 2 / FBPA / Fructose-1 / 6-bisphosphate aldolase / Fructose-bisphosphate aldolase class II


Mass: 39191.152 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: fbaA, fba, fda, b2925, JW2892 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0AB71, fructose-bisphosphate aldolase

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Non-polymers , 5 types, 299 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 293 / 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: 2.32 Å3/Da / Density % sol: 46.96 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.2 M ammonium acetate, 5mM fructose 1,6-bisphosphatase, 0.1 M Tris/HCl pH 7.0, and 15% PEG 4000
PH range: 5.6-7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 28, 2015
RadiationMonochromator: DCM Si (111) Crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.79→50 Å / Num. obs: 67264 / % possible obs: 97.7 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 38.6
Reflection shellResolution: 1.8→1.85 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.488 / Mean I/σ(I) obs: 5 / % possible all: 96.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DOS

1dos


Resolution: 1.8→50 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.948 / SU B: 2.114 / SU ML: 0.067 / Cross valid method: THROUGHOUT / ESU R: 0.108 / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19701 3408 5.1 %RANDOM
Rwork0.16254 ---
obs0.16435 63833 97.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.087 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2---0 Å2-0 Å2
3----0 Å2
Refinement stepCycle: LAST / Resolution: 1.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5124 0 31 293 5448
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0195272
X-RAY DIFFRACTIONr_bond_other_d0.0040.024996
X-RAY DIFFRACTIONr_angle_refined_deg2.031.9557129
X-RAY DIFFRACTIONr_angle_other_deg1.169311517
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1025658
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.81625.478230
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.08415881
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.631512
X-RAY DIFFRACTIONr_chiral_restr0.1490.2794
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0215964
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021160
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_it2.4941.9572652
X-RAY DIFFRACTIONr_mcbond_other2.4871.9562650
X-RAY DIFFRACTIONr_mcangle_it3.5712.9123302
X-RAY DIFFRACTIONr_mcangle_other3.5722.9123303
X-RAY DIFFRACTIONr_scbond_it3.5512.342620
X-RAY DIFFRACTIONr_scbond_other3.5512.342621
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.2653.3353828
X-RAY DIFFRACTIONr_long_range_B_refined7.2716.476190
X-RAY DIFFRACTIONr_long_range_B_other7.26716.4316153
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.795→1.842 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.262 247 -
Rwork0.227 4501 -
obs--92.54 %

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