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

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Basic information

Entry
Database: PDB / ID: 5tlh
TitleFructose-1,6-bisphosphate aldolase from rabbit muscle in complex with the inhibitor 2-naphthol 6-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 / 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
METHYLENEDIPHOSPHONIC ACID / Chem-RD2 / Fructose-bisphosphate aldolase A
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.204 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 11, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 25, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Nov 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 1.3Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_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)159,21614
Polymers157,0554
Non-polymers2,16110
Water15,169842
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12960 Å2
ΔGint-25 kcal/mol
Surface area47550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.569, 103.141, 84.865
Angle α, β, γ (deg.)90.000, 98.870, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
31chain C
41chain D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO

Dom-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1TYRTYRchain AAA1 - 3631 - 363
2TYRTYRchain BBB1 - 3631 - 363
3TYRTYRchain CCC1 - 3631 - 363
4PROPROchain DDD1 - 3441 - 344

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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-RD2 / [(6-hydroxynaphthalen-2-yl)methylene]bis(phosphonic acid)


Mass: 318.156 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H12O7P2
#3: Chemical
ChemComp-MDN / METHYLENEDIPHOSPHONIC ACID / Medronic acid


Mass: 176.002 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CH6O6P2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


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


Mass: 18.015 Da / Num. of mol.: 842 / 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: 46.54 %
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: 2.204→50 Å / Num. obs: 69137 / % possible obs: 96.8 % / Redundancy: 4.8 % / Biso Wilson estimate: 24.84 Å2 / Rmerge(I) obs: 0.166 / Net I/av σ(I): 9.978 / Net I/σ(I): 8.9
Reflection shell
Resolution (Å)Redundancy (%)CC1/2Diffraction-ID% possible allRmerge(I) obs
2.21-2.254.40.682194.8
2.25-2.294.50.598194.6
2.29-2.334.60.826194.20.896
2.33-2.384.70.851194.10.761
2.38-2.434.70.891194.60.635
2.43-2.494.70.91194.20.584
2.49-2.554.70.926193.90.496
2.55-2.624.70.937194.40.416
2.62-2.74.70.949194.90.35
2.7-2.784.70.964195.80.304
2.78-2.884.60.967196.50.251
2.88-34.60.972197.30.22
3-3.144.50.973198.20.182
3.14-3.34.60.979198.80.158
3.3-3.514.60.981199.50.14
3.51-3.784.80.984199.70.123
3.78-4.1650.98611000.112
4.16-4.765.40.98811000.107
4.76-65.70.99111000.108
6-505.60.988199.80.087

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Processing

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

2qut


Resolution: 2.204→43.927 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.61
RfactorNum. reflection% reflection
Rfree0.1877 2012 2.91 %
Rwork0.1502 --
obs0.1513 69057 96.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 106.44 Å2 / Biso mean: 34.8832 Å2 / Biso min: 12.61 Å2
Refinement stepCycle: final / Resolution: 2.204→43.927 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10642 0 212 842 11696
Biso mean--53.4 35.63 -
Num. residues----1394
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00511009
X-RAY DIFFRACTIONf_angle_d0.85814943
X-RAY DIFFRACTIONf_chiral_restr0.0371667
X-RAY DIFFRACTIONf_plane_restr0.0041921
X-RAY DIFFRACTIONf_dihedral_angle_d13.0384132
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A8168X-RAY DIFFRACTION4.817TORSIONAL
12B8168X-RAY DIFFRACTION4.817TORSIONAL
13C8168X-RAY DIFFRACTION4.817TORSIONAL
14D8168X-RAY DIFFRACTION4.817TORSIONAL
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 (%)
2.2037-2.25880.27711300.22254276440686
2.2588-2.31980.25691390.19574670480994
2.3198-2.38810.20151390.1774681482094
2.3881-2.46520.22831350.16534681481694
2.4652-2.55330.21661440.15784669481394
2.5533-2.65550.22811370.1524724486195
2.6555-2.77630.19481440.14774721486595
2.7763-2.92270.19331450.15114797494297
2.9227-3.10570.2011450.15194867501298
3.1057-3.34550.18881500.1524924507499
3.3455-3.6820.17961490.145549635112100
3.682-4.21440.15761510.127749835134100
4.2144-5.30820.15771500.12450275177100
5.3082-43.93620.16471540.158450625216100

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