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

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Basic information

Entry
Database: PDB / ID: 5tle
TitleFructose-1,6-bisphosphate aldolase from rabbit muscle in complex with the inhibitor 2-phosphate-naphthalene 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
Chem-RD1 / Fructose-bisphosphate aldolase A
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.576 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)158,83110
Polymers157,0554
Non-polymers1,7776
Water39,8852214
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12360 Å2
ΔGint-40 kcal/mol
Surface area46790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.742, 103.717, 84.524
Angle α, β, γ (deg.)90.000, 98.810, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and ((resid 1 and (name O or name...
21(chain B and ((resid 1 and (name O or name...
31(chain C and ((resid 1 and (name O or name...
41(chain D and ((resid 1 and (name N or name...

NCS domain segments:

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

Dom-IDComponent-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPRO(chain A and ((resid 1 and (name O or name...AA11
12TYRTYR(chain A and ((resid 1 and (name O or name...AA1 - 3631 - 363
13TYRTYR(chain A and ((resid 1 and (name O or name...AA1 - 3631 - 363
14TYRTYR(chain A and ((resid 1 and (name O or name...AA1 - 3631 - 363
15TYRTYR(chain A and ((resid 1 and (name O or name...AA1 - 3631 - 363
16TYRTYR(chain A and ((resid 1 and (name O or name...AA1 - 3631 - 363
21PROPRO(chain B and ((resid 1 and (name O or name...BB11
22TYRTYR(chain B and ((resid 1 and (name O or name...BB1 - 3631 - 363
23TYRTYR(chain B and ((resid 1 and (name O or name...BB1 - 3631 - 363
24TYRTYR(chain B and ((resid 1 and (name O or name...BB1 - 3631 - 363
25TYRTYR(chain B and ((resid 1 and (name O or name...BB1 - 3631 - 363
26TYRTYR(chain B and ((resid 1 and (name O or name...BB1 - 3631 - 363
31PROPRO(chain C and ((resid 1 and (name O or name...CC11
32TYRTYR(chain C and ((resid 1 and (name O or name...CC1 - 3631 - 363
33TYRTYR(chain C and ((resid 1 and (name O or name...CC1 - 3631 - 363
34TYRTYR(chain C and ((resid 1 and (name O or name...CC1 - 3631 - 363
35TYRTYR(chain C and ((resid 1 and (name O or name...CC1 - 3631 - 363
36TYRTYR(chain C and ((resid 1 and (name O or name...CC1 - 3631 - 363
41PROPRO(chain D and ((resid 1 and (name N or name...DD11
42TYRTYR(chain D and ((resid 1 and (name N or name...DD1 - 3631 - 363
43TYRTYR(chain D and ((resid 1 and (name N or name...DD1 - 3631 - 363
44TYRTYR(chain D and ((resid 1 and (name N or name...DD1 - 3631 - 363
45TYRTYR(chain D and ((resid 1 and (name N or name...DD1 - 3631 - 363
46TYRTYR(chain D and ((resid 1 and (name N or name...DD1 - 3631 - 363

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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-RD1 / {[6-(phosphonooxy)naphthalen-2-yl]methylene}bis(phosphonic acid)


Mass: 398.136 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H13O10P3
#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.: 2214 / 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: 08B1-1 / Wavelength: 1.0332 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Feb 25, 2015
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.58→50 Å / Num. obs: 184916 / % possible obs: 94.4 % / Redundancy: 2.9 % / Biso Wilson estimate: 18.22 Å2 / Rmerge(I) obs: 0.038 / Rpim(I) all: 0.025 / Rrim(I) all: 0.046 / Χ2: 0.966 / Net I/av σ(I): 21.774 / Net I/σ(I): 16 / Num. measured all: 542448
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.58-1.612.40.78395140.5470.5890.9840.7897.6
1.61-1.642.40.64794440.6080.4890.8140.82596.7
1.64-1.672.40.57493660.6880.4310.720.83896.3
1.67-1.72.40.49493640.7470.370.6190.82995.5
1.7-1.742.40.39892190.8060.2970.4990.8694.6
1.74-1.782.50.33691490.8410.2490.420.89193.5
1.78-1.822.50.27790390.90.2060.3460.90892.5
1.82-1.872.60.21889360.9330.160.2720.93191.8
1.87-1.932.70.17789440.9530.1290.221.03491.6
1.93-1.992.80.14289670.9680.1020.1761.15891.5
1.99-2.062.90.11888640.9780.0830.1441.23190.6
2.06-2.1430.09186810.9870.0630.1111.16589
2.14-2.243.10.07286230.9920.0480.0871.01288.1
2.24-2.363.20.05886770.9950.0380.071.02888.6
2.36-2.513.20.04990240.9960.0310.0581.22292.3
2.51-2.73.20.04696540.9960.030.0551.47298.2
2.7-2.973.40.03598160.9970.0220.0420.82100
2.97-3.43.70.02298160.9990.0130.0260.938100
3.4-4.293.80.016985710.0090.0190.748100
4.29-503.80.015996210.0090.0170.67699.6

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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: 1.576→32.344 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 16.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1575 2007 1.09 %
Rwork0.1311 182860 -
obs0.1314 184867 94.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 129.31 Å2 / Biso mean: 28.3784 Å2 / Biso min: 10.45 Å2
Refinement stepCycle: final / Resolution: 1.576→32.344 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10672 0 180 2238 13090
Biso mean--23.39 39.25 -
Num. residues----1397
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00811150
X-RAY DIFFRACTIONf_angle_d0.93915154
X-RAY DIFFRACTIONf_chiral_restr0.0551689
X-RAY DIFFRACTIONf_plane_restr0.0071962
X-RAY DIFFRACTIONf_dihedral_angle_d12.5146762
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A7625X-RAY DIFFRACTION4.19TORSIONAL
12B7625X-RAY DIFFRACTION4.19TORSIONAL
13C7625X-RAY DIFFRACTION4.19TORSIONAL
14D7625X-RAY DIFFRACTION4.19TORSIONAL
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 (%)
1.5761-1.61550.28711450.2726130621320795
1.6155-1.65920.28041450.2323133391348496
1.6592-1.7080.26491460.2155131701331695
1.708-1.76320.2191400.1913130021314294
1.7632-1.82620.18481480.1806128171296593
1.8262-1.89930.18921320.1569126491278192
1.8993-1.98570.17381410.1381126981283992
1.9857-2.09040.15841380.1286124731261190
2.0904-2.22130.14271300.1186122721240288
2.2213-2.39280.14611400.1137122831242389
2.3928-2.63350.1591460.1144132421338896
2.6335-3.01430.13861490.11791386914018100
3.0143-3.79680.13891490.1131394914098100
3.7968-32.35030.1321580.11471403514193100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.4681-0.1067-0.11190.32180.35160.4366-0.0023-0.00090.00130.096-0.0103-0.0568-0.00110.0469-00.1519-0.0294-0.01540.1623-0.0090.21025.5509-20.137549.7349
20.4255-0.15560.00630.69820.1910.38470.0188-0.0575-0.00610.07950.0069-0.09750.04830.061400.1320.0002-0.01790.1391-0.00510.15432.5572-25.741545.2104
30.4145-0.23270.1371.070.44640.31870.03320.05520.01060.14970.0502-0.33690.15050.05850.04780.17110.0175-0.06170.1919-0.01710.272817.4746-32.525345.0084
40.54850.03950.16910.162-0.05240.46240.01770.0450.0650.029-0.0865-0.10110.0409-0.121200.1367-0.0199-0.00130.17880.00160.1956-33.1576-19.958652.2658
50.2897-0.0288-0.12770.23890.03510.72480.0242-0.07240.03610.0113-0.03380.0162-0.038-0.10320.00050.12950.00030.0080.1518-0.01760.1453-30.8657-14.921246.8539
60.19670.1443-0.04780.5912-0.34190.24520.0207-0.00540.08360.0089-0.06460.0481-0.2302-0.4117-0.03260.17060.0717-0.00480.3182-0.04880.1978-45.7235-8.214348.0998
70.51880.1037-0.02320.2263-0.2210.52130.0897-0.0402-0.0611-0.0237-0.1144-0.13960.0224-0.03800.15870.00630.00470.15560.01070.2008-35.3735-25.28657.4222
80.4065-0.03390.10240.4043-0.12060.66490.03410.0376-0.0478-0.0352-0.00920.03360.1225-0.08250.00040.1611-0.0263-0.00520.1219-0.00740.138-31.3768-30.002112.4957
90.4642-0.2560.36650.5674-0.3970.34260.1278-0.1198-0.0976-0.0664-0.06060.12460.4745-0.2719-0.05850.3063-0.1063-0.04050.20410.00910.1953-44.7608-39.729812.899
100.28180.21160.24480.22090.24940.41130.053-0.02370.0117-0.1-0.08280.109-0.0110.1275-00.1760.0120.02140.1897-0.00950.22962.6844-17.34955.1071
110.32580.054-0.01310.2245-0.03550.63850.01120.07220.0427-0.0521-0.0249-0.0378-0.07350.108900.1564-0.02220.02140.14290.0060.1568-0.9643-12.41299.9858
120.3141-0.1543-0.1890.46350.28690.2970.0886-0.01830.1161-0.0444-0.1039-0.0855-0.42790.3616-0.04020.2808-0.09560.03470.2770.03040.248912.4035-2.78868.34
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 51 )A1 - 51
2X-RAY DIFFRACTION2chain 'A' and (resid 52 through 275 )A52 - 275
3X-RAY DIFFRACTION3chain 'A' and (resid 276 through 363 )A276 - 363
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 51 )B1 - 51
5X-RAY DIFFRACTION5chain 'B' and (resid 52 through 275 )B52 - 275
6X-RAY DIFFRACTION6chain 'B' and (resid 276 through 363 )B276 - 363
7X-RAY DIFFRACTION7chain 'C' and (resid 1 through 51 )C1 - 51
8X-RAY DIFFRACTION8chain 'C' and (resid 52 through 275 )C52 - 275
9X-RAY DIFFRACTION9chain 'C' and (resid 276 through 363 )C276 - 363
10X-RAY DIFFRACTION10chain 'D' and (resid 1 through 51 )D1 - 51
11X-RAY DIFFRACTION11chain 'D' and (resid 52 through 275 )D52 - 275
12X-RAY DIFFRACTION12chain 'D' and (resid 276 through 363 )D276 - 363

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