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

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Basic information

Entry
Database: PDB / ID: 5tlz
TitleFructose-1,6-bisphosphate aldolase from rabbit muscle in complex with the inhibitor naphthalene 2,6-bisphosphate
ComponentsFructose-bisphosphate aldolase A
KeywordsLYASE/INHIBITOR / INHIBITOR / 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
naphthalene-2,6-diyl bis[dihydrogen (phosphate)] / Fructose-bisphosphate aldolase A
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 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 1.1Jan 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 / 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)158,51910
Polymers157,0554
Non-polymers1,4656
Water26,9141494
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9900 Å2
ΔGint-23 kcal/mol
Surface area48170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.254, 103.638, 84.518
Angle α, β, γ (deg.)90.000, 98.670, 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-N26 / naphthalene-2,6-diyl bis[dihydrogen (phosphate)]


Mass: 320.129 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H10O8P2
#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.: 1494 / 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: 46.41 %
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: 0.9795 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: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 87928 / % possible obs: 78.5 % / Redundancy: 3.2 % / Biso Wilson estimate: 21.79 Å2 / Rmerge(I) obs: 0.052 / Χ2: 1.145 / Net I/av σ(I): 20.071 / Net I/σ(I): 15 / Num. measured all: 283537
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.9-1.971.20.27510780.629.7
1.97-2.051.50.23133350.69429.9
2.05-2.1420.1968280.70361.2
2.14-2.252.60.17597070.72786.7
2.25-2.393.20.154109380.77798
2.39-2.583.50.109111330.83699.8
2.58-2.843.70.08111750.9699.8
2.84-3.253.70.053111951.14299.8
3.25-4.093.70.039111971.799.8
4.09-503.60.029113421.72299.6

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Processing

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

2qut


Resolution: 1.97→48.345 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 16.28
RfactorNum. reflection% reflection
Rfree0.1661 2004 2.31 %
Rwork0.1285 --
obs0.1294 86695 86.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 112.91 Å2 / Biso mean: 31.2429 Å2 / Biso min: 9.85 Å2
Refinement stepCycle: final / Resolution: 1.97→48.345 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10580 0 264 1494 12338
Biso mean--33.64 39.33 -
Num. residues----1385
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00611041
X-RAY DIFFRACTIONf_angle_d0.7114993
X-RAY DIFFRACTIONf_chiral_restr0.0451664
X-RAY DIFFRACTIONf_plane_restr0.0051927
X-RAY DIFFRACTIONf_dihedral_angle_d12.9026637
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 (%)
1.97-2.01930.2739450.21021848189327
2.0193-2.07390.2223770.19233145322245
2.0739-2.13490.18991130.16314588470166
2.1349-2.20380.19911340.15335795592983
2.2038-2.28260.20861610.14246551671293
2.2826-2.3740.18521590.13326843700298
2.374-2.4820.16191670.129469537120100
2.482-2.61290.16171670.124269547121100
2.6129-2.77660.18911540.125669847138100
2.7766-2.99090.1571650.129969487113100
2.9909-3.29180.15931610.129369937154100
3.2918-3.7680.16871650.120770127177100
3.768-4.74660.12011640.10570057169100
4.7466-48.35960.17691720.13277072724499
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)
11.09-0.63220.31210.6563-0.02410.9356-0.0106-0.06540.04670.04960.07830.00560.04210.0143-0.04260.1992-0.0461-0.02670.2137-0.03160.22156.8689-21.194350.974
20.7331-0.27280.03151.10530.10950.8890.0349-0.0695-0.01880.09520.0166-0.17160.06850.1207-0.04560.1211-0.0094-0.01730.1203-0.0010.15852.9731-25.699845.2472
31.2132-0.42590.7161.6925-0.29513.01120.09490.09380.04220.157-0.0047-0.33880.22730.1934-0.07120.17390.0154-0.05750.2307-0.02170.323817.8489-32.535345.2614
40.9603-0.00140.1792.25230.97941.80020.0972-0.05520.05160.0762-0.0901-0.1440.0029-0.1682-0.01420.1452-0.06510.01960.22340.02970.1827-33.6744-19.270653.5424
50.5289-0.0177-0.09270.3489-0.01351.18150.0297-0.09940.05590.013-0.01830.0418-0.0627-0.1465-0.01160.1165-0.01160.00810.1428-0.01630.1417-30.5096-15.077147.1407
60.3085-0.3338-0.25161.35710.87774.10970.03190.04630.12160.0042-0.0728-0.0302-0.4298-0.42510.07430.17360.0508-0.00580.3031-0.02690.2299-43.0885-8.430447.1276
71.20750.4104-0.31081.08830.11612.4797-0.02380.03180.1747-0.0284-0.09850.1234-0.2926-0.57620.05810.22820.0964-0.01120.4132-0.04530.2866-47.8883-7.908250.4113
81.15140.0390.05881.6750.45131.80930.12390.022-0.0553-0.1203-0.0937-0.17060.14180.0312-0.05740.20490.0198-0.0150.19270.0390.193-35.96-26.47396.4907
90.6802-0.00540.14870.6491-0.14691.14110.0730.0349-0.1021-0.027-0.01710.03840.1908-0.0994-0.05070.1695-0.0269-0.01010.1127-0.00730.1387-31.1487-29.983512.5756
100.9810.06250.40261.22930.31222.32530.1348-0.1104-0.1595-0.1068-0.08050.13310.5687-0.3249-0.04370.3478-0.1204-0.05690.25720.02880.2659-44.5051-39.779912.7335
110.9943-0.45790.62252.5539-0.78472.18490.14760.1480.0773-0.124-0.10280.0926-0.18790.0653-0.04530.22260.05850.08380.3018-0.00720.22973.3813-16.09773.8151
120.76830.0460.06740.6661-0.00320.83710.0510.14230.1167-0.0934-0.0539-0.0798-0.14990.1605-0.0040.1806-0.02090.03890.14850.02870.154-0.6351-12.294210.1771
130.86970.027-0.22931.2171-0.58832.36610.1180.0720.2305-0.1873-0.0873-0.1524-0.56670.49830.02310.3865-0.13350.08840.33960.04890.324512.4823-2.70458.0352
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 51 )A4 - 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 4 through 51 )B4 - 51
5X-RAY DIFFRACTION5chain 'B' and (resid 52 through 275 )B52 - 275
6X-RAY DIFFRACTION6chain 'B' and (resid 276 through 316 )B276 - 316
7X-RAY DIFFRACTION7chain 'B' and (resid 317 through 363 )B317 - 363
8X-RAY DIFFRACTION8chain 'C' and (resid 4 through 51 )C4 - 51
9X-RAY DIFFRACTION9chain 'C' and (resid 52 through 275 )C52 - 275
10X-RAY DIFFRACTION10chain 'C' and (resid 276 through 363 )C276 - 363
11X-RAY DIFFRACTION11chain 'D' and (resid 4 through 51 )D4 - 51
12X-RAY DIFFRACTION12chain 'D' and (resid 52 through 275 )D52 - 275
13X-RAY DIFFRACTION13chain 'D' and (resid 276 through 363 )D276 - 363

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