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- PDB-1j4e: FRUCTOSE-1,6-BISPHOSPHATE ALDOLASE COVALENTLY BOUND TO THE SUBSTR... -

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Basic information

Entry
Database: PDB / ID: 1j4e
TitleFRUCTOSE-1,6-BISPHOSPHATE ALDOLASE COVALENTLY BOUND TO THE SUBSTRATE DIHYDROXYACETONE PHOSPHATE
ComponentsFRUCTOSE-BISPHOSPHATE ALDOLASE A
KeywordsLYASE / ALDOLASE / GLYCOLYSIS
Function / homology
Function and homology information


negative regulation of Arp2/3 complex-mediated actin nucleation / fructose-bisphosphate aldolase / fructose-bisphosphate aldolase activity / M band / I band / glycolytic process / protein homotetramerization / positive regulation of cell migration
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 / Fructose-bisphosphate aldolase A
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsChoi, K.H. / Shi, J. / Hopkins, C.E. / Tolan, D.R. / Allen, K.N.
Citation
Journal: Biochemistry / Year: 2001
Title: Snapshots of catalysis: the structure of fructose-1,6-(bis)phosphate aldolase covalently bound to the substrate dihydroxyacetone phosphate.
Authors: Choi, K.H. / Shi, J. / Hopkins, C.E. / Tolan, D.R. / Allen, K.N.
#1: Journal: Biochemistry / Year: 1999
Title: Structure of a Fructose-1,6-(Bis)Phosphate Aldolase Liganded to its Natural Substrate in a Cleavage-Defective Mutant at 2.3 A
Authors: Choi, K.H. / Mazurkie, A.S. / Morris, A.J. / Utheza, D. / Tolan, D.R. / Allen, K.N.
History
DepositionSep 19, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 13, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FRUCTOSE-BISPHOSPHATE ALDOLASE A
B: FRUCTOSE-BISPHOSPHATE ALDOLASE A
C: FRUCTOSE-BISPHOSPHATE ALDOLASE A
D: FRUCTOSE-BISPHOSPHATE ALDOLASE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,2228
Polymers156,5424
Non-polymers6804
Water2,252125
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.229, 99.388, 84.484
Angle α, β, γ (deg.)90.00, 98.29, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.9908, -0.0004, 0.1353), (0.00385, -0.99968, 0.02519), (0.13525, 0.02548, 0.99048)50.0164, 20.4706, -3.60783
2given(-0.96096, -0.27667, -0.00132), (-0.2766, 0.9608, -0.01869), (0.00644, -0.01759, -0.99982)56.13226, 8.32006, 57.68105
3given(0.95523, 0.26453, -0.13253), (0.2654, -0.96407, -0.01141), (-0.13079, -0.02427, -0.99111)2.28772, 14.37086, 61.16531

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Components

#1: Protein
FRUCTOSE-BISPHOSPHATE ALDOLASE A / MUSCLE-TYPE ALDOLASE


Mass: 39135.418 Da / Num. of mol.: 4 / Mutation: C72A, C239A, C289A, C338A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Tissue: MUSCLE / Plasmid: PPB14 / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli (E. coli) / Strain (production host): DH5ALPHA / References: UniProt: P00883, fructose-bisphosphate aldolase
#2: Chemical
ChemComp-13P / 1,3-DIHYDROXYACETONEPHOSPHATE


Mass: 170.058 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H7O6P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.18 Å3/Da / Density % sol: 43.2 %
Crystal growpH: 7.4 / Details: pH 7.4
Crystal grow
*PLUS
Temperature: 18 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
20.1 MTris-HCl1droppH7.4
30.1 mMdithiothreitol1drop
41 mMbeta-mercaptoethanol1drop
51 mMEDTA1drop
610 %PEG1drop
70.1 MTris-HCl1reservoirpH7.4
828 %PEG60001reservoir

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1
DetectorDetector: CCD / Date: Mar 1, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→100 Å / Num. obs: 35634 / % possible obs: 86 % / Redundancy: 3 % / Rsym value: 0.034 / Net I/σ(I): 20
Reflection shellResolution: 2.6→2.7 Å / Redundancy: 2 % / Mean I/σ(I) obs: 10 / Rsym value: 0.22 / % possible all: 60
Reflection
*PLUS
Lowest resolution: 9999 Å / % possible obs: 86 % / Rmerge(I) obs: 0.034
Reflection shell
*PLUS
% possible obs: 60 % / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 10

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Processing

Software
NameClassification
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 6ALD

6ald


Resolution: 2.65→100 Å / Data cutoff high rms absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: mlf
Details: WE HAVE ALTERED PROTEIN_REP.PARAM AND PROTEIN.TOP TO INCLUDE THE COVALENTLY MODIFIED LYSINE
RfactorNum. reflection% reflectionSelection details
Rfree0.249 3465 10 %RANDOM
Rwork0.213 ---
obs-34548 88 %-
Displacement parametersBiso mean: 31.9 Å2
Baniso -1Baniso -2Baniso -3
1-2.01 Å20 Å2-0.29 Å2
2---10.981 Å20 Å2
3---8.971 Å2
Refine analyzeLuzzati coordinate error obs: 0.341 Å / Luzzati d res low obs: 5 Å
Refinement stepCycle: LAST / Resolution: 2.65→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10392 0 36 125 10553
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.979
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.65→2.67 Å / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.3347 38 9.5 %
Rwork0.3068 401 -
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP_PARAMWATER.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 100 Å / σ(F): 0 / % reflection Rfree: 10 % / Rfactor obs: 0.213
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 31.9 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.303
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.463
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.979
LS refinement shell
*PLUS
% reflection Rfree: 9.5 %

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