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- PDB-6ald: RABBIT MUSCLE ALDOLASE A/FRUCTOSE-1,6-BISPHOSPHATE COMPLEX -

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Basic information

Entry
Database: PDB / ID: 6ald
TitleRABBIT MUSCLE ALDOLASE A/FRUCTOSE-1,6-BISPHOSPHATE COMPLEX
ComponentsFRUCTOSE-1,6-BIS(PHOSPHATE) ALDOLASE
KeywordsLYASE / ALDOLASE A / FRUCTOSE-1 / 6-BISPHOSPHATE / LINEAR HEXOSE / MICHAELIS COMPLEX
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
1,6-FRUCTOSE DIPHOSPHATE (LINEAR FORM) / Fructose-bisphosphate aldolase A
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsChoi, K.H. / Mazurkie, A.S. / Morris, A.J. / Utheza, D. / Tolan, D.R. / Allen, K.N.
CitationJournal: 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
DepositionDec 23, 1998Processing site: BNL
Revision 1.0Jan 5, 2000Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / 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 / _pdbx_database_status.process_site / _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 9, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FRUCTOSE-1,6-BIS(PHOSPHATE) ALDOLASE
B: FRUCTOSE-1,6-BIS(PHOSPHATE) ALDOLASE
C: FRUCTOSE-1,6-BIS(PHOSPHATE) ALDOLASE
D: FRUCTOSE-1,6-BIS(PHOSPHATE) ALDOLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,5036
Polymers156,8224
Non-polymers6802
Water6,936385
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10340 Å2
ΔGint-26 kcal/mol
Surface area47810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.800, 100.600, 84.500
Angle α, β, γ (deg.)90.00, 98.30, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.991391, 0.005696, 0.130811), (-0.004238, -0.999926, 0.011425), (0.130866, 0.010772, 0.991342)49.9395, 21.1793, -3.287
2given(-0.963555, -0.267435, -0.00631), (-0.267416, 0.963574, -0.003759), (0.007086, -0.001934, -0.999973)56.0683, 7.5122, 57.3238
3given(0.957877, 0.255984, -0.130166), (0.256226, -0.966498, -0.015177), (-0.12969, -0.018814, -0.991376)2.1685, 14.7508, 60.9545

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Components

#1: Protein
FRUCTOSE-1,6-BIS(PHOSPHATE) ALDOLASE / D-FRUCTOSE 1 / 6-BIS(PHOSPHATE) D-GLYCERALDEHYDE 3-PHOSPHATE LYASE


Mass: 39205.570 Da / Num. of mol.: 4 / Mutation: K146A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Tissue: MUSCLESkeletal muscle / Plasmid: PPB1 / Cellular location (production host): CYTOPLASM / Culture collection (production host): ATCC 77473 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5ALPHA / References: UniProt: P00883, fructose-bisphosphate aldolase
#2: Sugar ChemComp-2FP / 1,6-FRUCTOSE DIPHOSPHATE (LINEAR FORM)


Type: saccharideCarbohydrate / Mass: 340.116 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O12P2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 385 / 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: 2.18 Å3/Da / Density % sol: 43 %
Crystal growpH: 7.4 / Details: pH 7.4
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
17 mg/mlprotein1drop
20.2 MTris-HCl1drop
32 mMEDTA1drop
42 mMbeta-mercaptoethanol1drop
51.1 mMdithiothreitol1drop
610 %PEG60001drop
70.1 MTris-HCl1reservoir
824 %PEG60001reservoir

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Dec 1, 1997 / Details: SUPER LONG MIRRORS
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→100 Å / Num. obs: 62360 / % possible obs: 94.5 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.179 / Rsym value: 0.179 / Net I/σ(I): 7.2
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 3 % / Rmerge(I) obs: 0.459 / Mean I/σ(I) obs: 2.43 / % possible all: 74
Reflection
*PLUS
Rmerge(I) obs: 0.092
Reflection shell
*PLUS
% possible obs: 95.3 % / Rmerge(I) obs: 0.182 / Mean I/σ(I) obs: 2.4

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Processing

Software
NameVersionClassification
X-PLOR3.8model building
X-PLOR3.8refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.8phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ADO

1ado


Resolution: 2.3→100 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.274 2689 5 %RANDOM
Rwork0.228 ---
obs0.228 53783 94.5 %-
Displacement parametersBiso mean: 26.2 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.31 Å
Luzzati d res low-5 Å
Refinement stepCycle: LAST / Resolution: 2.3→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10452 0 40 385 10877
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.004
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.12
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.2
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.619
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refine LS restraints NCSNCS model details: RESTRAINTS
LS refinement shellResolution: 2.3→2.4 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.3739 282 3.72 %
Rwork0.3164 5341 -
obs--74.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPHCSDX.PRO
X-RAY DIFFRACTION2TIP3P.PARTOPH19.PEP
X-RAY DIFFRACTION3FBP.PARTIP3P.TOP
X-RAY DIFFRACTION4FBP.TOP
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.2
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.619

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