[English] 日本語
Yorodumi
- PDB-2yce: Structure of an Archaeal fructose-1,6-bisphosphate aldolase with ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2yce
TitleStructure of an Archaeal fructose-1,6-bisphosphate aldolase with the catalytic Lys covalently bound to the carbinolamine intermediate of the substrate.
ComponentsFRUCTOSE-BISPHOSPHATE ALDOLASE CLASS 1
KeywordsLYASE / GLYCOLYSIS
Function / homology
Function and homology information


fructose-bisphosphate aldolase / fructose-bisphosphate aldolase activity / glycolytic process / cytoplasm
Similarity search - Function
Aldolase FbaB-like, archaeal-type / : / DeoC/LacD family aldolase / DeoC/FbaB/LacD aldolase / DeoC/LacD family aldolase / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
D-MANNITOL-1,6-DIPHOSPHATE / Fructose-bisphosphate aldolase class 1
Similarity search - Component
Biological speciesTHERMOPROTEUS TENAX (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsLorentzen, E. / Siebers, B. / Hensel, R. / Pohl, E.
CitationJournal: Biochemistry / Year: 2005
Title: Mechanism of the Schiff Base Forming Fructose-1,6-Bisphosphate Aldolase: Structural Analysis of Reaction Intermediates.
Authors: Lorentzen, E. / Siebers, B. / Hensel, R. / Pohl, E.
History
DepositionMar 14, 2011Deposition site: PDBE / Processing site: PDBE
SupersessionApr 27, 2011ID: 1W8R
Revision 1.0Apr 27, 2011Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 17, 2019Group: Data collection / Derived calculations / Category: diffrn_source / struct_conn
Item: _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: FRUCTOSE-BISPHOSPHATE ALDOLASE CLASS 1
B: FRUCTOSE-BISPHOSPHATE ALDOLASE CLASS 1
C: FRUCTOSE-BISPHOSPHATE ALDOLASE CLASS 1
D: FRUCTOSE-BISPHOSPHATE ALDOLASE CLASS 1
E: FRUCTOSE-BISPHOSPHATE ALDOLASE CLASS 1
F: FRUCTOSE-BISPHOSPHATE ALDOLASE CLASS 1
G: FRUCTOSE-BISPHOSPHATE ALDOLASE CLASS 1
H: FRUCTOSE-BISPHOSPHATE ALDOLASE CLASS 1
I: FRUCTOSE-BISPHOSPHATE ALDOLASE CLASS 1
J: FRUCTOSE-BISPHOSPHATE ALDOLASE CLASS 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)290,83220
Polymers287,41110
Non-polymers3,42110
Water27,3471518
1
A: FRUCTOSE-BISPHOSPHATE ALDOLASE CLASS 1
B: FRUCTOSE-BISPHOSPHATE ALDOLASE CLASS 1
C: FRUCTOSE-BISPHOSPHATE ALDOLASE CLASS 1
D: FRUCTOSE-BISPHOSPHATE ALDOLASE CLASS 1
E: FRUCTOSE-BISPHOSPHATE ALDOLASE CLASS 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,41610
Polymers143,7055
Non-polymers1,7115
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18030 Å2
ΔGint-59.1 kcal/mol
Surface area40360 Å2
MethodPISA
2
F: FRUCTOSE-BISPHOSPHATE ALDOLASE CLASS 1
G: FRUCTOSE-BISPHOSPHATE ALDOLASE CLASS 1
H: FRUCTOSE-BISPHOSPHATE ALDOLASE CLASS 1
I: FRUCTOSE-BISPHOSPHATE ALDOLASE CLASS 1
J: FRUCTOSE-BISPHOSPHATE ALDOLASE CLASS 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,41610
Polymers143,7055
Non-polymers1,7115
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18060 Å2
ΔGint-58.2 kcal/mol
Surface area39880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.900, 159.200, 101.400
Angle α, β, γ (deg.)90.00, 107.80, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
FRUCTOSE-BISPHOSPHATE ALDOLASE CLASS 1 / FRUCTOSE-BIPHOSPHATE ALDOLASE CLASS I / FBP ALDOLASE


Mass: 28741.064 Da / Num. of mol.: 10 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: K177 COVALENTLY LINKED TO THE CARBINOLAMINE FORM OF THE SUBSTRATE FBP
Source: (gene. exp.) THERMOPROTEUS TENAX (archaea) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P58315, fructose-bisphosphate aldolase
#2: Chemical
ChemComp-M2P / D-MANNITOL-1,6-DIPHOSPHATE / 1,6-DI-O-PHOSPHONO-D-MANNITOL


Mass: 342.132 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C6H16O12P2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1518 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, TYR 146 TO PHE ENGINEERED RESIDUE IN CHAIN A, ALA 173 TO SER ...ENGINEERED RESIDUE IN CHAIN A, TYR 146 TO PHE ENGINEERED RESIDUE IN CHAIN A, ALA 173 TO SER ENGINEERED RESIDUE IN CHAIN B, TYR 146 TO PHE ENGINEERED RESIDUE IN CHAIN B, ALA 173 TO SER ENGINEERED RESIDUE IN CHAIN C, TYR 146 TO PHE ENGINEERED RESIDUE IN CHAIN C, ALA 173 TO SER ENGINEERED RESIDUE IN CHAIN D, TYR 146 TO PHE ENGINEERED RESIDUE IN CHAIN D, ALA 173 TO SER ENGINEERED RESIDUE IN CHAIN E, TYR 146 TO PHE ENGINEERED RESIDUE IN CHAIN E, ALA 173 TO SER ENGINEERED RESIDUE IN CHAIN F, TYR 146 TO PHE ENGINEERED RESIDUE IN CHAIN F, ALA 173 TO SER ENGINEERED RESIDUE IN CHAIN G, TYR 146 TO PHE ENGINEERED RESIDUE IN CHAIN G, ALA 173 TO SER ENGINEERED RESIDUE IN CHAIN H, TYR 146 TO PHE ENGINEERED RESIDUE IN CHAIN H, ALA 173 TO SER ENGINEERED RESIDUE IN CHAIN I, TYR 146 TO PHE ENGINEERED RESIDUE IN CHAIN I, ALA 173 TO SER ENGINEERED RESIDUE IN CHAIN J, TYR 146 TO PHE ENGINEERED RESIDUE IN CHAIN J, ALA 173 TO SER
Has protein modificationY
Nonpolymer detailsM2P: THE SUBSTRATE FRUCTOSE 1,6-BISPHOSPHATE IS COVALENTLY LINKED TO THE CATALYTIC LYSINE AS A ...M2P: THE SUBSTRATE FRUCTOSE 1,6-BISPHOSPHATE IS COVALENTLY LINKED TO THE CATALYTIC LYSINE AS A CARBINOLAMINE FORM.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2 Å3/Da / Density % sol: 40 % / Description: SOLVED BY RIGID BODY REFINEMENT OF 1OJX.
Crystal growpH: 5
Details: 9% (W/V) PEG 4000, 0.1 M NAACETATE PH 5.0, 1-8% GLYCEROL, 100 MM FBP

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.812
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 15, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.812 Å / Relative weight: 1
ReflectionResolution: 1.93→40 Å / Num. obs: 179009 / % possible obs: 97.3 % / Observed criterion σ(I): -3 / Redundancy: 4.2 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 16.2
Reflection shellResolution: 1.93→2.02 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 2.2 / % possible all: 77.6

-
Processing

Software
NameVersionClassification
REFMAC5.5.0110refinement
DENZOdata reduction
SCALEPACKdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OJX

1ojx


Resolution: 1.93→39.8 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.945 / SU B: 6.061 / SU ML: 0.091 / Cross valid method: THROUGHOUT / ESU R: 0.144 / ESU R Free: 0.132 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED.
RfactorNum. reflection% reflectionSelection details
Rfree0.19811 2723 1.5 %RANDOM
Rwork0.15592 ---
obs0.15654 179009 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 22.83 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å2-0.06 Å2
2--0.06 Å20 Å2
3----0.07 Å2
Refinement stepCycle: LAST / Resolution: 1.93→39.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19381 0 200 1518 21099
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.02220162
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4851.9827292
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.72252522
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.89223.161851
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.504153382
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.85515151
X-RAY DIFFRACTIONr_chiral_restr0.1090.23017
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02115111
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6571.512444
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.125219925
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.15837708
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.3954.57354
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.931→1.981 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.272 148 -
Rwork0.223 9800 -
obs--100 %
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)
11.1916-0.2965-0.13510.84820.02581.6116-0.00270.04520.2759-0.02620.0111-0.1402-0.24240.101-0.00840.0547-0.0284-0.00820.01770.01120.0956-2.6703126.281917.3401
21.07130.1988-0.13261.1141-0.01171.07420.0246-0.22840.09170.1219-0.0188-0.0487-0.06440.0867-0.00580.0304-0.0003-0.02010.0733-0.03320.0341-5.3635116.90850.2377
31.65490.32380.05871.21520.6171.39820.011-0.3197-0.32110.2256-0.0284-0.08910.29350.02630.01740.10770.01390.00050.09260.08990.0918-12.382483.370251.1022
41.34880.09670.11571.0372-0.2111.7099-0.01130.0567-0.3585-0.04490.0104-0.04930.27570.05360.0010.07820.00380.02420.005-0.02220.159-14.301571.981318.8387
51.2293-0.16640.10851.51960.12410.78650.02130.2972-0.0253-0.2231-0.0215-0.0728-0.02310.0820.00020.0399-0.01050.01480.1068-0.02130.0137-8.246598.3651-2.2534
61.3260.05440.01391.01070.37871.5317-0.02220.11960.3662-0.10570.00240.0287-0.324-0.10560.01980.10190.0303-0.02320.03550.03840.1565-43.0245134.178615.2551
71.26450.1467-0.15671.0620.00771.34310.0436-0.22290.27120.0644-0.04860.0876-0.1651-0.06880.00490.04070.02010.00270.095-0.08950.0987-45.0514126.362548.525
81.41870.29720.44561.33680.09510.94110.0659-0.3559-0.08210.185-0.06260.05020.0675-0.1949-0.00330.0508-0.03510.0190.14410.01640.0171-52.049192.961951.3163
91.361-0.21470.16080.8055-0.17641.57140.03240.0285-0.2659-0.04590.02980.10770.2273-0.1132-0.06230.0562-0.0364-0.00220.0272-0.01150.0753-54.368780.013419.6841
100.9807-0.1611-0.12021.3213-0.23841.03620.00840.2102-0.0112-0.1757-0.02810.06860.0428-0.11490.01970.0303-0.004-0.00810.10370.01370.0201-48.7818105.4234-2.5236
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 252
2X-RAY DIFFRACTION2B2 - 253
3X-RAY DIFFRACTION3C3 - 252
4X-RAY DIFFRACTION4D3 - 252
5X-RAY DIFFRACTION5E3 - 257
6X-RAY DIFFRACTION6F3 - 252
7X-RAY DIFFRACTION7G3 - 252
8X-RAY DIFFRACTION8H3 - 252
9X-RAY DIFFRACTION9I3 - 252
10X-RAY DIFFRACTION10J3 - 252

+
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