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- PDB-5tlw: Fructose-1,6-bisphosphate aldolase from rabbit muscle in complex ... -

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Basic information

Entry
Database: PDB / ID: 5tlw
TitleFructose-1,6-bisphosphate aldolase from rabbit muscle in complex with the inhibitor 1-phosphate-benzene 4-bisphosphonate
ComponentsFructose-bisphosphate aldolase A
KeywordsLYASE/INHIBITOR / INHIBITOR / BISPHOSPHONATE / COMPLEX / ALDOLASE / LYASE / LYASE-INHIBITOR 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 / fructose 1,6-bisphosphate metabolic process / glycolytic process / protein homotetramerization / positive regulation of cell migration / cytosol
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
Chem-RD3 / Fructose-bisphosphate aldolase A
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 Å
AuthorsHeron, P.W. / Sygusch, J.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada) Canada
CitationJournal: J.Med.Chem. / Year: 2018
Title: Bisphosphonate Inhibitors of Mammalian Glycolytic Aldolase.
Authors: Heron, P.W. / Abellan-Flos, M. / Salmon, L. / Sygusch, J.
History
DepositionOct 12, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 25, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Nov 9, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / 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-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)158,63110
Polymers157,0554
Non-polymers1,5776
Water11,548641
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12080 Å2
ΔGint-40 kcal/mol
Surface area48450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.857, 102.707, 84.905
Angle α, β, γ (deg.)90.000, 98.540, 90.000
Int Tables number4
Space group name H-MP1211

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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): BL21(SI) / References: UniProt: P00883, fructose-bisphosphate aldolase
#2: Chemical
ChemComp-RD3 / {[4-(phosphonooxy)phenyl]methylene}bis(phosphonic acid)


Mass: 348.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C7H11O10P3
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 641 / 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: 2.3 Å3/Da / Density % sol: 46.57 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1M Sodium HEPES, 17.5% PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Sep 14, 2012
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.29→50 Å / Num. obs: 59195 / % possible obs: 93.1 % / Redundancy: 3.2 % / Biso Wilson estimate: 28.73 Å2 / Rmerge(I) obs: 0.152 / Rpim(I) all: 0.095 / Rrim(I) all: 0.176 / Χ2: 1.105 / Net I/av σ(I): 7.626 / Net I/σ(I): 11.5 / Num. measured all: 191921
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
2.29-2.332.60.8270.558185.7
2.33-2.372.70.7410.583185.8
2.37-2.422.70.6460.688185.7
2.42-2.472.80.6150.773185.5
2.47-2.522.90.5670.79185.7
2.52-2.582.90.4650.836185.7
2.58-2.6430.420.858186.8
2.64-2.7230.3690.883187.9
2.72-2.793.10.3230.888188.6
2.79-2.893.10.2790.922192.2
2.89-2.993.10.2470.945195.8
2.99-3.113.20.1970.955197.8
3.11-3.253.30.1710.964199.2
3.25-3.423.40.1580.964199.9
3.42-3.633.60.1470.9631100
3.63-3.923.70.1290.975199.9
3.92-4.313.80.1160.9761100
4.31-4.933.80.1040.9851100
4.93-6.213.80.1030.9791100
6.21-503.70.0730.992199.6

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Processing

Software
NameVersionClassification
PHENIXrefinement
Blu-Icedata collection
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2QUT

2qut


Resolution: 2.29→43.809 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 21.66
RfactorNum. reflection% reflection
Rfree0.1911 1985 3.38 %
Rwork0.152 --
obs0.1533 58707 91.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 115.76 Å2 / Biso mean: 41.4156 Å2 / Biso min: 15.71 Å2
Refinement stepCycle: final / Resolution: 2.29→43.809 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10654 0 156 644 11454
Biso mean--60.03 37.37 -
Num. residues----1394
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00310962
X-RAY DIFFRACTIONf_angle_d0.57414869
X-RAY DIFFRACTIONf_chiral_restr0.0411670
X-RAY DIFFRACTIONf_plane_restr0.0041917
X-RAY DIFFRACTIONf_dihedral_angle_d15.2856639
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.29-2.34730.29281000.23072953305367
2.3473-2.41080.2741300.20163792392286
2.4108-2.48170.2441310.18853734386585
2.4817-2.56180.22611340.18533785391985
2.5618-2.65330.24551260.18453795392186
2.6533-2.75960.22271390.17833828396787
2.7596-2.88510.21651370.18144023416091
2.8851-3.03720.23081530.17444226437996
3.0372-3.22740.23141480.16794360450899
3.2274-3.47650.19971550.157743984553100
3.4765-3.82620.18561550.134644504605100
3.8262-4.37940.14561590.114544114570100
4.3794-5.51590.1441520.117444684620100
5.5159-43.81710.1551660.146144994665100

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