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- PDB-5gk5: Apo structure of fructose 1,6-bisphosphate aldolase from Escheric... -

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Basic information

Entry
Database: PDB / ID: 5gk5
TitleApo structure of fructose 1,6-bisphosphate aldolase from Escherichia coli at 1.9 angstrom resolution
ComponentsFructose-bisphosphate aldolase class 2
KeywordsLYASE / FBA apo3
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: 1.9 Å
AuthorsTran, T.H. / Huynh, K.H. / Ho, T.H. / Kang, L.W.
CitationJournal: To Be Published
Title: Apo structure of fructose 1,6-bisphosphate aldolase from Escherichia coli at 1.9 angstrom resolution
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 / pdbx_struct_conn_angle / struct_conn
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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

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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
C: Fructose-bisphosphate aldolase class 2
D: Fructose-bisphosphate aldolase class 2
E: Fructose-bisphosphate aldolase class 2
F: Fructose-bisphosphate aldolase class 2
G: Fructose-bisphosphate aldolase class 2
H: Fructose-bisphosphate aldolase class 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)315,72635
Polymers313,5298
Non-polymers2,19727
Water20,5191139
1
A: Fructose-bisphosphate aldolase class 2
B: Fructose-bisphosphate aldolase class 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,8698
Polymers78,3822
Non-polymers4876
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5930 Å2
ΔGint-144 kcal/mol
Surface area24910 Å2
MethodPISA
2
C: Fructose-bisphosphate aldolase class 2
D: Fructose-bisphosphate aldolase class 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,04010
Polymers78,3822
Non-polymers6588
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6400 Å2
ΔGint-179 kcal/mol
Surface area24860 Å2
MethodPISA
3
E: Fructose-bisphosphate aldolase class 2
F: Fructose-bisphosphate aldolase class 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,7777
Polymers78,3822
Non-polymers3945
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5690 Å2
ΔGint-143 kcal/mol
Surface area24930 Å2
MethodPISA
4
G: Fructose-bisphosphate aldolase class 2
H: Fructose-bisphosphate aldolase class 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,04010
Polymers78,3822
Non-polymers6588
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6390 Å2
ΔGint-176 kcal/mol
Surface area24820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.834, 90.535, 113.733
Angle α, β, γ (deg.)90.07, 90.01, 90.21
Int Tables number1
Space group name H-MP1

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Components

#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.: 8
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
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1139 / 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: 47.04 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.2M ammonium acetate, 1mM Docosahexaenoic acid , 0.1M Tris 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: Dec 13, 2014
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: 1.9→50 Å / Num. obs: 220041 / % possible obs: 95.9 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.096 / Net I/σ(I): 22.6
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.492 / Mean I/σ(I) obs: 3.3 / % possible all: 94.3

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DOS

1dos


Resolution: 1.9→22.055 Å / SU ML: 0.19 / Cross valid method: NONE / σ(F): 1.97 / Phase error: 21.15
RfactorNum. reflection% reflection
Rfree0.2068 10965 4.98 %
Rwork0.1723 --
obs0.174 220023 95.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.9→22.055 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20552 0 98 1139 21789
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00721071
X-RAY DIFFRACTIONf_angle_d0.87728527
X-RAY DIFFRACTIONf_dihedral_angle_d13.81112508
X-RAY DIFFRACTIONf_chiral_restr0.0543169
X-RAY DIFFRACTIONf_plane_restr0.0053685
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8965-1.91810.2782950.22786134X-RAY DIFFRACTION84
1.9181-1.94060.26483530.21516857X-RAY DIFFRACTION94
1.9406-1.96430.2663570.20826988X-RAY DIFFRACTION94
1.9643-1.98910.26133450.20796799X-RAY DIFFRACTION94
1.9891-2.01530.26013670.19016907X-RAY DIFFRACTION94
2.0153-2.04280.24133910.19626811X-RAY DIFFRACTION94
2.0428-2.0720.2323580.19016945X-RAY DIFFRACTION95
2.072-2.10290.24643460.18886906X-RAY DIFFRACTION95
2.1029-2.13580.24373590.18696931X-RAY DIFFRACTION95
2.1358-2.17070.21843380.17916949X-RAY DIFFRACTION95
2.1707-2.20810.23063420.17636934X-RAY DIFFRACTION95
2.2081-2.24820.23233790.17636866X-RAY DIFFRACTION95
2.2482-2.29140.21853830.17386859X-RAY DIFFRACTION95
2.2914-2.33820.22853970.17286897X-RAY DIFFRACTION95
2.3382-2.3890.2273960.18076871X-RAY DIFFRACTION95
2.389-2.44450.21683580.18436905X-RAY DIFFRACTION95
2.4445-2.50550.24613810.18476999X-RAY DIFFRACTION95
2.5055-2.57310.21693590.17886879X-RAY DIFFRACTION95
2.5731-2.64870.22173730.18177001X-RAY DIFFRACTION96
2.6487-2.73410.2493600.18426924X-RAY DIFFRACTION96
2.7341-2.83160.21123380.18977088X-RAY DIFFRACTION96
2.8316-2.94470.22953690.18447092X-RAY DIFFRACTION97
2.9447-3.07840.21013630.18197120X-RAY DIFFRACTION97
3.0784-3.24020.19263650.17787198X-RAY DIFFRACTION98
3.2402-3.44260.20243850.17527127X-RAY DIFFRACTION98
3.4426-3.70720.21253840.17267200X-RAY DIFFRACTION99
3.7072-4.07820.17483790.15137212X-RAY DIFFRACTION99
4.0782-4.66340.15813990.13827229X-RAY DIFFRACTION99
4.6634-5.85710.16753960.14997210X-RAY DIFFRACTION99
5.8571-22.05610.16123500.15177220X-RAY DIFFRACTION99

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