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- PDB-1zai: Fructose-1,6-bisphosphate Schiff base intermediate in FBP aldolas... -

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Basic information

Entry
Database: PDB / ID: 1zai
TitleFructose-1,6-bisphosphate Schiff base intermediate in FBP aldolase from rabbit muscle
ComponentsFructose-bisphosphate aldolase A
KeywordsLYASE / aldolase / substrate / schiff base intermediate
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 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_conn / 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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 600HETEROGEN 2FP ligand is covalently bound to LYS 229.

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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)158,4158
Polymers157,0554
Non-polymers1,3604
Water43,3802408
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13510 Å2
ΔGint-42 kcal/mol
Surface area51310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.996, 103.228, 84.305
Angle α, β, γ (deg.)90.00, 98.77, 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: Sugar
ChemComp-2FP / 1,6-FRUCTOSE DIPHOSPHATE (LINEAR FORM)


Type: saccharideCarbohydrate / Mass: 340.116 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O12P2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2408 / 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: 2.27 Å3/Da / Density % sol: 45.9 %
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: Jun 1, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.63→50 Å / Num. all: 174626 / Num. obs: 154432 / % possible obs: 88.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.068 / Χ2: 1.021
Reflection shellResolution: 1.63→1.69 Å / % possible obs: 48.1 % / Rmerge(I) obs: 0.65 / Num. measured obs: 8362 / Χ2: 0.722 / % possible all: 48.1

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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: 1.76→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.19 11870 7.3 %RANDOM
Rwork0.155 ---
all-134970 --
obs-119216 85.9 %-
Solvent computationBsol: 82.354 Å2
Displacement parametersBiso mean: 26.408 Å2
Baniso -1Baniso -2Baniso -3
1--0.447 Å20 Å21.619 Å2
2---3.843 Å20 Å2
3---4.29 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.16 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 1.76→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11032 0 76 2408 13516
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetWeight
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.270
X-RAY DIFFRACTIONc_mcbond_it1.09801.5
X-RAY DIFFRACTIONc_mcangle_it1.64302
X-RAY DIFFRACTIONc_scbond_it1.788
X-RAY DIFFRACTIONc_scangle_it2.567
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 DIFFRACTION5fpi.parfpi.top

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