[English] 日本語
Yorodumi
- PDB-5tle: Fructose-1,6-bisphosphate aldolase from rabbit muscle in complex ... -

+
Open data


ID or keywords:

Loading...

-
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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 / Glycerol


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


Mass: 18.015 Da / Num. of mol.: 2214 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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: 0

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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more