[English] 日本語
Yorodumi
- PDB-3t2b: Fructose-1,6-bisphosphate aldolase/phosphatase from Thermoproteus... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3t2b
TitleFructose-1,6-bisphosphate aldolase/phosphatase from Thermoproteus neutrophilus, ligand free
ComponentsFructose-1,6-bisphosphate aldolase/phosphatase
KeywordsLYASE / HYDROLASE / (beta/alpha)8 TIM barrel / FBP / F6P / DHAP / GAP / phosphorylation
Function / homology
Function and homology information


fructose-bisphosphate aldolase / fructose-bisphosphate aldolase activity / fructose-bisphosphatase / fructose 1,6-bisphosphate 1-phosphatase activity / gluconeogenesis / magnesium ion binding
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1180 / Fructose-1,6-bisphosphatase, class V / Fructose-1,6-bisphosphatase, class V superfamily / Fructose-1,6-bisphosphatase / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special
Similarity search - Domain/homology
Fructose-1,6-bisphosphate aldolase/phosphatase
Similarity search - Component
Biological speciesThermoproteus neutrophilus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.52 Å
AuthorsDu, J. / Say, R. / Lue, W. / Fuchs, G. / Einsle, O.
CitationJournal: Nature / Year: 2011
Title: Active-site remodelling in the bifunctional fructose-1,6-bisphosphate aldolase/phosphatase.
Authors: Du, J. / Say, R.F. / Lu, W. / Fuchs, G. / Einsle, O.
History
DepositionJul 22, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 26, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 9, 2011Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Fructose-1,6-bisphosphate aldolase/phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,5103
Polymers45,4611
Non-polymers492
Water5,765320
1
A: Fructose-1,6-bisphosphate aldolase/phosphatase
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)364,07724
Polymers363,6888
Non-polymers38916
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_465-x-1,-y+1,z1
crystal symmetry operation3_565-y,x+1,z1
crystal symmetry operation4_455y-1,-x,z1
crystal symmetry operation5_455-x-1,y,-z1
crystal symmetry operation6_565x,-y+1,-z1
crystal symmetry operation7_465y-1,x+1,-z1
crystal symmetry operation8_555-y,-x,-z1
Buried area60540 Å2
ΔGint-516 kcal/mol
Surface area80620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.532, 112.532, 151.126
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-581-

HOH

21A-606-

HOH

31A-611-

HOH

-
Components

#1: Protein Fructose-1,6-bisphosphate aldolase/phosphatase


Mass: 45461.031 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoproteus neutrophilus (archaea) / Strain: DSM 2338 / JCM 9278 / V24Sta / Gene: Tneu_0133 / Plasmid: pET23b / Production host: Escherichia coli (E. coli)
References: UniProt: B1YAL1, fructose-bisphosphate aldolase, fructose-bisphosphatase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 320 / 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: 2.63 Å3/Da / Density % sol: 53.25 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 8% PEG3350, 0.1 M HEPES/NaOH, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K

-
Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Aug 1, 2010
RadiationMonochromator: Fixed-exit LN2 cooled Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
211
ReflectionResolution: 1.52→54.794 Å / Num. all: 74360 / Num. obs: 74283 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 10 % / Rmerge(I) obs: 0.064 / Rsym value: 0.064 / Net I/σ(I): 22.4
Reflection shellResolution: 1.52→1.62 Å / Redundancy: 10.3 % / Rmerge(I) obs: 0.363 / Mean I/σ(I) obs: 6 / Rsym value: 0.363 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
MAR345dtbdata collection
MOLREPphasing
REFMAC5.5.0109refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1UMG

1umg


Resolution: 1.52→54.79 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.958 / SU B: 1.085 / SU ML: 0.04 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.062 / ESU R Free: 0.064 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.18818 3740 5 %RANDOM
Rwork0.16454 ---
obs0.16573 70543 99.9 %-
all-70543 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.389 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2---0.01 Å2-0 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.52→54.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2976 0 2 320 3298
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0330.0223124
X-RAY DIFFRACTIONr_angle_refined_deg2.5741.9724245
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5165396
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.92823.31142
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.25615528
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1981522
X-RAY DIFFRACTIONr_chiral_restr0.1870.2454
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.0212411
X-RAY DIFFRACTIONr_mcbond_it1.5741.51917
X-RAY DIFFRACTIONr_mcangle_it2.5223097
X-RAY DIFFRACTIONr_scbond_it3.58431207
X-RAY DIFFRACTIONr_scangle_it5.6484.51138
LS refinement shellResolution: 1.52→1.559 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.259 254 -
Rwork0.236 5162 -
obs--99.91 %

+
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