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- PDB-2qdg: Fructose-1,6-bisphosphate Schiff base intermediate in FBP aldolas... -

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Basic information

Entry
Database: PDB / ID: 2qdg
TitleFructose-1,6-bisphosphate Schiff base intermediate in FBP aldolase from Leishmania mexicana
ComponentsFructose-1,6-bisphosphate aldolase
KeywordsLYASE / beta barrel / aldolase / leishmania / fructose-1 / 6-bisphosphate / c-teminal tail
Function / homology
Function and homology information


fructose-bisphosphate aldolase / fructose-bisphosphate aldolase activity / glycolytic process / cytoplasm
Similarity search - Function
Fructose-bisphosphate aldolase class-I active site / Fructose-bisphosphate aldolase class-I active site. / Fructose-bisphosphate aldolase, class-I / Fructose-bisphosphate aldolase class-I / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
1,6-FRUCTOSE DIPHOSPHATE (LINEAR FORM) / PHOSPHATE ION / Fructose-bisphosphate aldolase
Similarity search - Component
Biological speciesLeishmania mexicana (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsLafrance-Vanasse, J. / Sygusch, J.
CitationJournal: Biochemistry / Year: 2007
Title: Carboxy-Terminus Recruitment Induced by Substrate Binding in Eukaryotic Fructose Bis-phosphate Aldolases
Authors: Lafrance-Vanasse, J. / Sygusch, J.
History
DepositionJun 20, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software
Revision 1.3Aug 30, 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 / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fructose-1,6-bisphosphate aldolase
B: Fructose-1,6-bisphosphate aldolase
C: Fructose-1,6-bisphosphate aldolase
D: Fructose-1,6-bisphosphate aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,35216
Polymers172,2324
Non-polymers2,12012
Water30,8781714
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18570 Å2
ΔGint-117 kcal/mol
Surface area47260 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)85.109, 117.090, 161.798
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 43058.062 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania mexicana (eukaryote) / Gene: ald / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 pLysS / References: UniProt: Q9U5N6, fructose-bisphosphate aldolase
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: PO4
#3: Sugar
ChemComp-2FP / 1,6-FRUCTOSE DIPHOSPHATE (LINEAR FORM)


Type: saccharide / Mass: 340.116 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O12P2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1714 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.46 Å3/Da / Density % sol: 50.07 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 15% polyethylene glycol 5000 MME in 20mM sodium phosphate pH 4.0, 11mg/mL of protein, 1:4 protein:precipitant ratio, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 14, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionRedundancy: 6.1 % / Av σ(I) over netI: 10.1 / Number: 545258 / Rmerge(I) obs: 0.081 / Χ2: 0.96 / D res high: 1.95 Å / D res low: 50 Å / Num. obs: 89616 / % possible obs: 75.7
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.25099.810.0410.8827.1
3.334.210010.0591.1657.3
2.913.3310010.1061.1077.4
2.652.9110010.1991.0187.2
2.462.6599.610.2790.8946.3
2.312.4690.910.3390.7925.1
2.22.3171.610.3920.7264.4
2.12.250.910.4910.6593.6
2.022.128.910.5710.6222.4
1.952.0212.810.7120.6251.7
ReflectionResolution: 1.95→50 Å / Num. all: 118409 / Num. obs: 89616 / % possible obs: 75.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Rmerge(I) obs: 0.081 / Χ2: 0.96 / Net I/σ(I): 10.1
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.712 / Num. unique all: 1493 / Χ2: 0.625 / % possible all: 12.8

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Phasing

Phasing MRMethod rotation: fast direct / Method translation: &STRIP%trans_method

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT2data extraction
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1epx

1epx


Resolution: 2.2→20 Å / FOM work R set: 0.85 / σ(F): 13530 / σ(I): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.238 3511 4.3 %RANDOM
Rwork0.185 ---
all-82576 --
obs-69046 83.6 %-
Solvent computationBsol: 57.117 Å2
Displacement parametersBiso mean: 41.839 Å2
Baniso -1Baniso -2Baniso -3
1-1.715 Å20 Å20 Å2
2---11.711 Å20 Å2
3---9.996 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.26 Å
Luzzati d res low-2.2 Å
Luzzati sigma a0.3 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11184 0 116 1714 13014
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.367
X-RAY DIFFRACTIONc_mcbond_it1.2941.5
X-RAY DIFFRACTIONc_scbond_it2.0172
X-RAY DIFFRACTIONc_mcangle_it2.0462
X-RAY DIFFRACTIONc_scangle_it2.8482.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 50

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs
2.2-2.210.259360.241672708
2.21-2.230.261410.229744785
2.23-2.250.303380.245769807
2.25-2.260.312360.246793829
2.26-2.280.292290.281826855
2.28-2.30.316340.246833867
2.3-2.310.321610.264894955
2.31-2.330.343490.28924973
2.33-2.350.324530.269901043
2.35-2.370.28630.24710191082
2.37-2.390.284520.24910261078
2.39-2.410.277700.23110491119
2.41-2.430.292730.26711121185
2.43-2.450.27660.23411491215
2.45-2.480.258720.22911661238
2.48-2.50.306630.2312121275
2.5-2.530.329500.24712341284
2.53-2.550.305650.24712511316
2.55-2.580.296660.22412771343
2.58-2.610.285670.21612971364
2.61-2.640.298680.22613301398
2.64-2.670.278840.22313401424
2.67-2.70.289860.2213371423
2.7-2.730.323850.23713841469
2.73-2.770.302620.22213991461
2.77-2.810.292840.21914121496
2.81-2.850.263760.21314471523
2.85-2.890.282770.21114371514
2.89-2.940.255810.1914621543
2.94-2.980.24740.21314471521
2.98-3.040.324730.21614901563
3.04-3.090.306690.21615061575
3.09-3.150.229770.18615281605
3.15-3.210.258870.19414961583
3.21-3.280.24820.18815571639
3.28-3.360.267820.19814921574
3.36-3.440.2531030.19415401643
3.44-3.540.22760.18615331609
3.54-3.640.23790.17615511630
3.64-3.760.205990.17715661665
3.76-3.890.251830.16515711654
3.89-4.040.223780.16315841662
4.04-4.230.2930.14815491642
4.23-4.450.207860.14515961682
4.45-4.720.154770.12115851662
4.72-5.080.149960.12515761672
5.08-5.580.21750.15816201695
5.58-6.370.221670.18116091676
6.37-7.940.219760.16716501726
7.94-200.19920.15517041796
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ALL.parALL.top

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