[English] 日本語
Yorodumi
- PDB-5vje: Class II fructose-1,6-bisphosphate aldolase of Escherichia coli w... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5vje
TitleClass II fructose-1,6-bisphosphate aldolase of Escherichia coli with D-glucitol 1,6-bisphosphate
ComponentsFructose-bisphosphate aldolase class 2
KeywordsLYASE / Glycolysis
Function / homology
Function and homology information


fructose-bisphosphate aldolase / fructose-bisphosphate aldolase activity / gluconeogenesis / glycolytic process / zinc ion binding / identical protein binding / cytosol
Similarity search - Function
Fructose-bisphosphate aldolase, class II, yeast/E. coli subtype / Fructose-bisphosphate aldolase class-II signature 1. / Fructose-bisphosphate aldolase class-II signature 2. / Fructose-bisphosphate aldolase class-II / Fructose-bisphosphate aldolase, class-II / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
D-Glucitol-1,6-bisphosphate / Fructose-bisphosphate aldolase class 2
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsCoincon, M. / Sygusch, J.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada) Canada
CitationJournal: J. Biol. Chem. / Year: 2018
Title: Active site remodeling during the catalytic cycle in metal-dependent fructose-1,6-bisphosphate aldolases.
Authors: Jacques, B. / Coincon, M. / Sygusch, J.
History
DepositionApr 19, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 11, 2018Provider: repository / Type: Initial release
Revision 1.1May 30, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Fructose-bisphosphate aldolase class 2
B: Fructose-bisphosphate aldolase class 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,8968
Polymers78,1202
Non-polymers7766
Water19,4021077
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5530 Å2
ΔGint-52 kcal/mol
Surface area25480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.250, 71.869, 88.983
Angle α, β, γ (deg.)90.00, 108.43, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Fructose-bisphosphate aldolase class 2 / FBPA / Fructose-1 / 6-bisphosphate aldolase / Fructose-bisphosphate aldolase class II


Mass: 39059.957 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (unknown)
Strain: K12 / Gene: fbaA, fba, fda, b2925, JW2892 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AB71, fructose-bisphosphate aldolase
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-GOS / D-Glucitol-1,6-bisphosphate / 1,6-di-O-phosphono-D-glucitol


Mass: 342.132 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H16O12P2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1077 / 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: 2.33 Å3/Da / Density % sol: 47.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: PEG 4000, MgCl2, Hepes buffer

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 0.99 Å
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Mar 1, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 1.65→29.011 Å / Num. obs: 81148 / % possible obs: 98.3 % / Redundancy: 5.7 % / Biso Wilson estimate: 16.1 Å2 / Rsym value: 0.09 / Net I/σ(I): 28.2

-
Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1B57
Resolution: 1.65→29.011 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 15.96
RfactorNum. reflection% reflection
Rfree0.1642 6493 8 %
Rwork0.1377 --
obs0.1398 81148 98.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.65→29.011 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5252 0 44 1077 6373
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065430
X-RAY DIFFRACTIONf_angle_d0.8247372
X-RAY DIFFRACTIONf_dihedral_angle_d14.0023220
X-RAY DIFFRACTIONf_chiral_restr0.05819
X-RAY DIFFRACTIONf_plane_restr0.006950
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6499-1.66870.29031930.24262104X-RAY DIFFRACTION84
1.6687-1.68830.23011980.22482225X-RAY DIFFRACTION89
1.6883-1.70890.25441980.21912314X-RAY DIFFRACTION92
1.7089-1.73050.232060.20492393X-RAY DIFFRACTION95
1.7305-1.75330.23362090.19722437X-RAY DIFFRACTION97
1.7533-1.77730.21322180.18662521X-RAY DIFFRACTION100
1.7773-1.80270.20242180.16912529X-RAY DIFFRACTION100
1.8027-1.82960.19552140.1622483X-RAY DIFFRACTION100
1.8296-1.85820.18522220.15392521X-RAY DIFFRACTION100
1.8582-1.88860.17792220.14792510X-RAY DIFFRACTION100
1.8886-1.92120.17062180.14612502X-RAY DIFFRACTION100
1.9212-1.95610.20132130.14342542X-RAY DIFFRACTION100
1.9561-1.99370.18572210.13552524X-RAY DIFFRACTION100
1.9937-2.03440.1592190.1412532X-RAY DIFFRACTION100
2.0344-2.07860.17992140.13822508X-RAY DIFFRACTION100
2.0786-2.1270.1552210.12882523X-RAY DIFFRACTION100
2.127-2.18010.14952190.12452524X-RAY DIFFRACTION100
2.1801-2.23910.13952200.12312522X-RAY DIFFRACTION100
2.2391-2.30490.14592230.11522507X-RAY DIFFRACTION100
2.3049-2.37930.13392300.11622530X-RAY DIFFRACTION100
2.3793-2.46430.15822170.11792505X-RAY DIFFRACTION100
2.4643-2.56290.17032170.12132533X-RAY DIFFRACTION100
2.5629-2.67950.16032250.12862520X-RAY DIFFRACTION100
2.6795-2.82060.15962150.13282533X-RAY DIFFRACTION100
2.8206-2.99720.17852170.13342547X-RAY DIFFRACTION100
2.9972-3.22830.16792150.13572525X-RAY DIFFRACTION100
3.2283-3.55270.14112220.1312563X-RAY DIFFRACTION100
3.5527-4.06550.14732200.12472550X-RAY DIFFRACTION100
4.0655-5.11760.14522220.11312552X-RAY DIFFRACTION100
5.1176-29.01560.15532270.1652576X-RAY DIFFRACTION99
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.12440.00510.11590.31090.00040.26270.03970.0357-0.0330.0692-0.0576-0.0916-0.03330.0955-0.01120.0961-0.0042-0.02240.14310.02360.162631.2948-12.706554.7868
20.7550.6495-0.11840.4411-0.17180.26810.1157-0.08320.03630.1407-0.11140.0317-0.03890.02480.00670.1339-0.02060.00010.1167-0.00560.110417.4037-12.447865.4209
30.39380.2034-0.16680.1048-0.09110.41540.1544-0.16240.07710.1514-0.1147-0.0187-0.15830.10980.0540.2102-0.0808-0.00340.1718-0.02460.165529.71382.324767.0819
40.15320.1686-0.28310.4151-0.03130.42640.13160.08390.20960.0186-0.03040.1441-0.1238-0.05430.00010.1316-0.00710.00910.14390.04790.205527.77484.414650.2445
50.2316-0.09160.12460.13930.12890.1356-0.0010.1102-0.0552-0.0125-0.004-0.0294-0.0049-0.0179-0.00030.1041-0.0008-0.0050.15450.00980.1204-5.3977-19.121746.2583
60.1522-0.00050.10710.0223-0.05860.0518-0.03220.1936-0.0224-0.02940.0335-0.03920.0207-0.0301-00.1096-0.01020.01550.16240.00070.134915.1134-15.030846.6896
70.4240.1608-0.19130.6689-0.43090.48120.0381-0.0556-0.02580.0067-0.0426-0.06910.00840.0179-0.00030.124-0.0071-0.00830.09790.00570.09464.0609-30.446471.0945
80.08840.0432-0.10650.1683-0.06940.1471-0.042-0.1003-0.1421-0.1286-0.0694-0.0970.0934-0.0204-0.0040.2086-0.00040.00150.10690.01250.16721.689-47.250270.3397
90.67630.2062-0.45120.6053-0.08080.37990.00240.087-0.0303-0.131-0.00460.07970.1075-0.1733-0.01980.1737-0.0457-0.02630.1640.01150.1161-12.0596-42.437471.8159
100.505-0.13960.20290.18370.08130.22140.17770.20390.24480.1134-0.19650.1571-0.0721-0.0228-0.03520.1030.05640.00960.13270.09680.1708-4.0549-6.289150.4687
110.1462-0.05950.11350.0706-0.15780.10170.053-0.03840.08280.0910.01290.057-0.1053-0.0585-00.14450.00680.02510.1240.00650.1222-8.2535-17.84467.541
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 38 )
2X-RAY DIFFRACTION2chain 'A' and (resid 39 through 133 )
3X-RAY DIFFRACTION3chain 'A' and (resid 134 through 220 )
4X-RAY DIFFRACTION4chain 'A' and (resid 221 through 288 )
5X-RAY DIFFRACTION5chain 'A' and (resid 289 through 329 )
6X-RAY DIFFRACTION6chain 'A' and (resid 330 through 358 )
7X-RAY DIFFRACTION7chain 'B' and (resid 1 through 149 )
8X-RAY DIFFRACTION8chain 'B' and (resid 150 through 198 )
9X-RAY DIFFRACTION9chain 'B' and (resid 199 through 288 )
10X-RAY DIFFRACTION10chain 'B' and (resid 289 through 329 )
11X-RAY DIFFRACTION11chain 'B' and (resid 330 through 358 )

+
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