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- PDB-1ojx: Crystal structure of an Archaeal fructose 1,6-bisphosphate aldolase -

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Basic information

Entry
Database: PDB / ID: 1ojx
TitleCrystal structure of an Archaeal fructose 1,6-bisphosphate aldolase
ComponentsFRUCTOSE-BISPHOSPHATE ALDOLASE CLASS I
KeywordsLYASE / ALDOLASE / FRUCTOSE 1 / 6-BISPHOSPHATE / TIM BARREL / GLYCOLYTIC / ARCHAEAL
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
Fructose-bisphosphate aldolase class 1
Similarity search - Component
Biological speciesTHERMOPROTEUS TENAX (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsLorentzen, E. / Zwart, P. / Stark, A. / Hensel, R. / Siebers, B. / Pohl, E.
CitationJournal: J. Biol. Chem. / Year: 2003
Title: Crystal structure of an archaeal class I aldolase and the evolution of (betaalpha)8 barrel proteins.
Authors: Lorentzen, E. / Pohl, E. / Zwart, P. / Stark, A. / Russell, R.B. / Knura, T. / Hensel, R. / Siebers, B.
History
DepositionJul 16, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 4, 2003Provider: 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 / citation_author ...citation / citation_author / diffrn_source / entity_src_gen / refine
Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name / _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 / _refine.pdbx_method_to_determine_struct
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 1.6May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA, BA, CA, DA, EA, FA, GA, HA, IA, JA" ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA, BA, CA, DA, EA, FA, GA, HA, IA, JA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 9-STRANDED BARREL THIS IS REPRESENTED BY A 10-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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


Theoretical massNumber of molelcules
Total (without water)287,41110
Polymers287,41110
Non-polymers00
Water37,9402106
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


Theoretical massNumber of molelcules
Total (without water)143,7055
Polymers143,7055
Non-polymers00
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


Theoretical massNumber of molelcules
Total (without water)143,7055
Polymers143,7055
Non-polymers00
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)83.300, 158.974, 102.986
Angle α, β, γ (deg.)90.00, 108.11, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.96895, -0.16745, -0.18194), (-0.11733, 0.33637, -0.93439), (0.21767, 0.92672, 0.30628)21.34281, 90.45076, -70.82803
2given(0.92192, -0.3777, -0.0861), (-0.35326, -0.72845, -0.58699), (0.15899, 0.57158, -0.805)39.05897, 184.53218, -5.74984
3given(0.9205, -0.35735, 0.15806), (-0.3807, -0.72908, 0.56877), (-0.08801, -0.58373, -0.80717)30.49924, 152.8273, 106.73904
4given(0.96985, -0.11956, 0.21238), (-0.16213, 0.33412, 0.92848), (-0.18197, -0.93492, 0.30467)5.85791, 39.4264, 110.14107
5given(-0.92178, 0.35817, -0.14844), (0.36395, 0.66736, -0.64975), (-0.13366, -0.65295, -0.74551)-89.1777, 62.50253, 110.70587
6given(-0.92237, 0.37369, 0.09797), (0.37066, 0.78457, 0.49706), (0.10888, 0.49478, -0.86217)-97.69477, 19.63104, 2.258
7given(-0.97291, 0.15211, 0.17411), (0.13571, -0.23397, 0.96273), (0.18718, 0.96027, 0.20698)-78.26493, 105.88753, -72.33798
8given(-0.9999, 0.00263, -0.014), (-0.00406, -0.99466, 0.10315), (-0.01365, 0.10319, 0.99457)-58.32344, 203.79181, -10.68643
9given(-0.96826, 0.13111, -0.21278), (0.13546, -0.44014, -0.88765), (-0.21003, -0.8883, 0.40842)-65.2347, 177.11978, 101.75456

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Components

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


Mass: 28741.064 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMOPROTEUS TENAX (archaea) / Plasmid: PET15B / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P58315, fructose-bisphosphate aldolase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2106 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

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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
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
13 mg/mlprotein1drop
210 mMHEPES-NaOH1droppH7.5
3100 mM1dropKCl
41 mMdithiothreitol1drop
59 %(w/v)PEG40001reservoir
60.1 Msodium acetate1reservoirpH5.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.845
DetectorDate: Feb 15, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.845 Å / Relative weight: 1
ReflectionResolution: 1.9→40 Å / Num. obs: 188245 / % possible obs: 94.5 % / Redundancy: 4 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 14.5
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.365 / Mean I/σ(I) obs: 2.4 / % possible all: 87
Reflection
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 40 Å / Rmerge(I) obs: 0.085
Reflection shell
*PLUS
% possible obs: 87 % / Rmerge(I) obs: 0.365 / Mean I/σ(I) obs: 2.4

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXDphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→40 Å / SU B: 2.776 / SU ML: 0.08 / Cross valid method: THROUGHOUT / ESU R: 0.134 / ESU R Free: 0.118 / Details: DEFAULT REFMAC5 BULK SOLVENT MODELLING
RfactorNum. reflection% reflectionSelection details
Rfree0.179 4723 2.5 %RANDOM
Rwork0.149 ---
obs0.15 188243 94.5 %-
Displacement parametersBiso mean: 13.234 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20 Å20.11 Å2
2--0.85 Å20 Å2
3----0.82 Å2
Refinement stepCycle: LAST / Resolution: 1.9→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19368 0 0 2106 21474
Refinement
*PLUS
Highest resolution: 1.9 Å / Num. reflection obs: 183520
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONbond_d0.012
X-RAY DIFFRACTIONangle_d
X-RAY DIFFRACTIONangle_deg1.3

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