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- PDB-1ok6: Orthorhombic crystal form of an Archaeal fructose 1,6-bisphosphat... -

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Basic information

Entry
Database: PDB / ID: 1ok6
TitleOrthorhombic crystal form of an Archaeal fructose 1,6-bisphosphate aldolase
ComponentsFRUCTOSE-BISPHOSPHATE ALDOLASE CLASS I
KeywordsLYASE / ALDOLASE / FRUCTOSE 1 / 6-BISPHOSPHATE / TIM BARREL / GLYCOLYTIC / ARCHAEAL / ORTHORHOMBIC / SCHIFF BASE
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: 2.4 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 18, 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
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 1.6Dec 13, 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
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" 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. THE SHEETS PRESENTED AS "BA" 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. THE SHEETS PRESENTED AS "CA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "DA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "EA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "FA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "GA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "HA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "IA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "JA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)287,50311
Polymers287,41110
Non-polymers921
Water16,502916
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)143,7976
Polymers143,7055
Non-polymers921
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)89.900, 176.500, 185.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.99996, 0.0083, -0.0044), (-0.00675, 0.30944, -0.9509), (-0.00653, 0.95088, 0.30948)-1.42472, 136.44199, -157.13022
2given(0.99982, 0.00695, -0.01748), (-0.00459, -0.8109, -0.58517), (-0.01824, 0.58514, -0.81073)-1.12122, 328.66281, -75.10992
3given(0.99994, 0.00513, -0.01002), (0.01003, -0.81018, 0.5861), (-0.00512, -0.58616, -0.81018)-0.7657, 309.84802, 130.17494
4given(0.99998, -0.00142, -0.00584), (0.00599, 0.31012, 0.95068), (0.00046, -0.9507, 0.31012)0.32694, 107.33363, 177.75323
5given(-0.99996, -0.00441, 0.00756), (0.00801, -0.80889, 0.5879), (0.00352, 0.58794, 0.8089)180.4019, 309.78061, -101.24377
6given(-0.99992, -0.00391, 0.01194), (-0.0038, -0.81136, -0.58454), (0.01197, -0.58454, 0.81128)180.30048, 328.57874, 104.70187
7given(-0.99989, -0.00759, 0.01306), (-0.01475, 0.30512, -0.9522), (0.00324, -0.95228, -0.3052)180.96823, 138.06003, 186.75951
8given(-0.99999, -0.00299, 0.00134), (-0.003, 0.99999, -0.00376), (-0.00133, -0.00376, -0.99999)180.22672, 0.32156, 29.85572
9given(-0.99997, -0.00428, 0.00572), (0.00412, 0.30773, 0.95146), (-0.00583, 0.95146, -0.3077)180.42378, 107.92429, -148.1765

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Components

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


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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 916 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCATALYTIC ACTIVITY: D-FRUCTOSE 1,6-BISPHOSPHATE = GLYCERONE PHOSPHATE + D-GLYCERALDEHYDE 3-PHOSPHATE.

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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: 2.6 Å3/Da / Density % sol: 53 %
Crystal growpH: 5 / Details: 9% (W/V) PEG 4000, 0.1 M NA ACETATE PH 5.0
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: BW7B / 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: 2.39→20 Å / Num. obs: 106518 / % possible obs: 93.6 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.121 / Net I/σ(I): 13.3
Reflection shellResolution: 2.39→2.47 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.372 / Mean I/σ(I) obs: 2.7 / % possible all: 69
Reflection
*PLUS
Highest resolution: 2.39 Å / Lowest resolution: 20 Å / Rmerge(I) obs: 0.121
Reflection shell
*PLUS
% possible obs: 69 % / Rmerge(I) obs: 0.372 / Mean I/σ(I) obs: 2.7

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Processing

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

1ojx


Resolution: 2.4→20 Å / SU B: 7.96 / SU ML: 0.178 / Cross valid method: THROUGHOUT / ESU R: 0.494 / ESU R Free: 0.277
RfactorNum. reflection% reflectionSelection details
Rfree0.263 2725 2.5 %RANDOM
Rwork0.232 ---
obs0.233 106518 93.6 %-
Displacement parametersBiso mean: 32.7 Å2
Baniso -1Baniso -2Baniso -3
1-0.63 Å20 Å20 Å2
2---0.32 Å20 Å2
3----0.32 Å2
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19204 0 6 916 20126
Refinement
*PLUS
Highest resolution: 2.39 Å / Num. reflection Rfree: 2735
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONbond_d0.013
X-RAY DIFFRACTIONangle_d
X-RAY DIFFRACTIONangle_deg1.3

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