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- PDB-1w8s: The mechanism of the Schiff Base Forming Fructose-1,6-bisphosphat... -

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Basic information

Entry
Database: PDB / ID: 1w8s
TitleThe mechanism of the Schiff Base Forming Fructose-1,6-bisphosphate Aldolase: Structural analysis of reaction intermediates
ComponentsFRUCTOSE-BISPHOSPHATE ALDOLASE CLASS I
KeywordsLYASE / ALDOLASE / FRUCTOSE 1 / 6-BISPHOSPHATE / TIM BARREL / GLYCOLYTIC / ARCHAEAL / CATALYTIC MECHANISM / REACTION INTERMEDIATE
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
1,6-di-O-phosphono-beta-D-fructofuranose / Fructose-bisphosphate aldolase class 1
Similarity search - Component
Biological speciesTHERMOPROTEUS TENAX (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsLorentzen, E. / Hensel, R. / Siebers, B. / 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
DepositionSep 27, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 23, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 28, 2018Group: Data collection / Database references ...Data collection / Database references / Refinement description / Source and taxonomy
Category: citation / diffrn_source ...citation / diffrn_source / entity_src_gen / refine / reflns / reflns_shell
Item: _citation.page_last / _citation.pdbx_database_id_DOI ..._citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant / _refine.ls_percent_reflns_obs / _reflns.percent_possible_obs / _reflns_shell.percent_possible_all
Revision 1.4Jul 10, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.5Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.6Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.7Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA, BA, CA" IN EACH CHAIN ON SHEET ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA, BA, CA" IN EACH CHAIN ON SHEET RECORDS BELOW ARE ACTUALLY 9-STRANDED BARRELS WHICH ARE REPRESENTED BY 10-STRANDED SHEETS IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "DA, EA, FA, GA, HA, IA, JA" IN EACH CHAIN ON SHEET RECORDS BELOW ARE ACTUALLY 7-STRANDED BARRELS REPRESENTED BY 8-STRANDED SHEETS IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)290,08120
Polymers286,68010
Non-polymers3,40110
Water24,5361362
1
A: FRUCTOSE-BISPHOSPHATE ALDOLASE CLASS I
B: FRUCTOSE-BISPHOSPHATE ALDOLASE CLASS I
C: FRUCTOSE-BISPHOSPHATE ALDOLASE CLASS I
D: FRUCTOSE-BISPHOSPHATE ALDOLASE CLASS I
E: FRUCTOSE-BISPHOSPHATE ALDOLASE CLASS I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,04010
Polymers143,3405
Non-polymers1,7015
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
F: FRUCTOSE-BISPHOSPHATE ALDOLASE CLASS I
G: FRUCTOSE-BISPHOSPHATE ALDOLASE CLASS I
H: FRUCTOSE-BISPHOSPHATE ALDOLASE CLASS I
I: FRUCTOSE-BISPHOSPHATE ALDOLASE CLASS I
J: FRUCTOSE-BISPHOSPHATE ALDOLASE CLASS I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,04010
Polymers143,3405
Non-polymers1,7015
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)82.500, 157.300, 101.200
Angle α, β, γ (deg.)90.00, 107.90, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.96895, -0.16745, -0.18194), (-0.11733, 0.33637, -0.93439), (0.21767, 0.92672, 0.30628)
Vector: 21.34281, 90.45076, -70.82803)

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Components

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


Mass: 28667.971 Da / Num. of mol.: 10 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: CYCLIC FBP BOUND / Source: (gene. exp.) THERMOPROTEUS TENAX (archaea) / Plasmid: PET15B / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P58315, fructose-bisphosphate aldolase
#2: Sugar
ChemComp-FBP / 1,6-di-O-phosphono-beta-D-fructofuranose / BETA-FRUCTOSE-1,6-DIPHOSPHATE / FRUCTOSE-1,6-BISPHOSPHATE / 1,6-di-O-phosphono-beta-D-fructose / 1,6-di-O-phosphono-D-fructose / 1,6-di-O-phosphono-fructose


Type: D-saccharide, beta linking / Mass: 340.116 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Formula: C6H14O12P2
IdentifierTypeProgram
b-D-Fruf1PO36PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1362 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUES TYR 146 PHE, TRP 144 GLU CHAINS: A, B, C, D, E, F, G, H, I, J

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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: 45 %
Crystal growpH: 5
Details: 9% (W/V) PEG 4000, 0.1 M NAACETATE PH 5.0, 1-8% GLYCEROL, 100 MM FBP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.842
DetectorDate: Nov 15, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.842 Å / Relative weight: 1
ReflectionResolution: 1.85→40 Å / Num. obs: 199708 / % possible obs: 100 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 22.2
Reflection shellResolution: 1.85→1.86 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.328 / Mean I/σ(I) obs: 2.2 / % possible all: 60

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OJX

1ojx


Resolution: 1.85→40 Å / SU B: 2.759 / SU ML: 0.081 / Cross valid method: THROUGHOUT / ESU R: 0.12 / ESU R Free: 0.115
Details: DEFAULT REFMAC5 BULK SOLVENT MODELLING. RESIDUES 1-2 AND 153-263 DISORDERED AND NOT MODELLED.
RfactorNum. reflection% reflectionSelection details
Rfree0.187 2012 1 %RANDOM
Rwork0.149 ---
obs0.149 197604 97.3 %-
Displacement parametersBiso mean: 14.875 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.85→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19298 0 200 1362 20860

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