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- PDB-1zaj: Fructose-1,6-bisphosphate aldolase from rabbit muscle in complex ... -

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Basic information

Entry
Database: PDB / ID: 1zaj
TitleFructose-1,6-bisphosphate aldolase from rabbit muscle in complex with mannitol-1,6-bisphosphate, a competitive inhibitor
ComponentsFructose-bisphosphate aldolase A
KeywordsLYASE / aldolase / competitive inhibitor / non covalent complex / mannitol-1 / 6-bisphosphate / hexitol-1
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
D-MANNITOL-1,6-DIPHOSPHATE / Fructose-bisphosphate aldolase A
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsSt-Jean, M. / Lafrance-Vanasse, J. / Liotard, B. / Sygusch, J.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: High Resolution Reaction Intermediates of Rabbit Muscle Fructose-1,6-bisphosphate Aldolase: substrate cleavage and induced fit.
Authors: St-Jean, M. / Lafrance-Vanasse, J. / Liotard, B. / Sygusch, J.
History
DepositionApr 6, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 10, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Aug 23, 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 / 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 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)158,4238
Polymers157,0554
Non-polymers1,3694
Water47,4332633
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12840 Å2
ΔGint-33 kcal/mol
Surface area52810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.044, 103.327, 84.360
Angle α, β, γ (deg.)90.00, 98.86, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is the homotetramer found in the asymmetric unit

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Components

#1: Protein
Fructose-bisphosphate aldolase A / Muscle-type aldolase


Mass: 39263.672 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Gene: ALDOA / Plasmid: pPB14 / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21 SI (Invitrogen) / References: UniProt: P00883, fructose-bisphosphate aldolase
#2: Chemical
ChemComp-M2P / D-MANNITOL-1,6-DIPHOSPHATE / 1,6-DI-O-PHOSPHONO-D-MANNITOL


Mass: 342.132 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H16O12P2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2633 / 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: 2.28 Å3/Da / Density % sol: 46 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: sodium HEPES, PEG 4000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 10, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.75→30 Å / Num. all: 135347 / Num. obs: 118124 / % possible obs: 87.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.172 / Χ2: 2.098
Reflection shellResolution: 1.75→1.81 Å / % possible obs: 46.3 % / Num. measured obs: 6216 / Χ2: 2.187 / % possible all: 46.3

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNS1.1refinement
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ADO

1ado


Resolution: 1.89→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.204 4860 3.7 %RANDOM
Rwork0.167 ---
all-106320 --
obs-96868 86.2 %-
Solvent computationBsol: 81.193 Å2
Displacement parametersBiso mean: 24.779 Å2
Baniso -1Baniso -2Baniso -3
1--0.857 Å20 Å20.499 Å2
2---2.66 Å20 Å2
3---3.518 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.34 Å0.31 Å
Refinement stepCycle: LAST / Resolution: 1.89→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11032 0 80 2633 13745
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetWeight
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.2530
X-RAY DIFFRACTIONc_mcbond_it1.27501.5
X-RAY DIFFRACTIONc_scbond_it1.95302
X-RAY DIFFRACTIONc_mcangle_it1.94702
X-RAY DIFFRACTIONc_scangle_it2.69502.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5HBP.PARHBP.TOP

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