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- PDB-2qap: Fructose-1,6-bisphosphate aldolase from Leishmania mexicana -

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Basic information

Entry
Database: PDB / ID: 2qap
TitleFructose-1,6-bisphosphate 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
PHOSPHATE ION / Fructose-bisphosphate aldolase
Similarity search - Component
Biological speciesLeishmania mexicana (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.59 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 15, 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
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)173,27715
Polymers172,2324
Non-polymers1,04511
Water36,6062032
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16740 Å2
ΔGint-134 kcal/mol
Surface area48090 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)85.777, 117.309, 160.195
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 / Phosphate


Mass: 94.971 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2032 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.46 Å3/Da / Density % sol: 50.06 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 15% polyethylene glycol 5000 MME in 20mM sodium phosphate pH 4.0, 11mg/mL of protein, 1:4 protein:precipitant ratio, pH 4.5, 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: 12.6 / Number: 1147834 / Rmerge(I) obs: 0.08 / Χ2: 1.53 / D res high: 1.59 Å / D res low: 50 Å / Num. obs: 186782 / % possible obs: 86.8
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
3.435099.910.0462.7877
2.723.4310010.0622.1687.3
2.382.7210010.0871.5177.4
2.162.3810010.1341.3047.4
22.1610010.2031.147.2
1.89210010.2960.9836.8
1.791.8998.410.3930.8865.6
1.711.7981.710.4590.8523.4
1.651.7155.110.5250.7942.3
1.591.6531.610.5090.7741.6
ReflectionResolution: 1.59→50 Å / Num. all: 215234 / Num. obs: 186782 / % possible obs: 86.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Rmerge(I) obs: 0.08 / Χ2: 1.526 / Net I/σ(I): 12.6
Reflection shellResolution: 1.59→1.65 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.509 / Num. unique all: 6757 / Χ2: 0.774 / % possible all: 31.6

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
PDB_EXTRACT2data extraction
HKL-2000data collection
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1epx

1epx


Resolution: 1.59→20 Å / FOM work R set: 0.894 / σ(F): 52421 / σ(I): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.203 8213 3.8 %RANDOM
Rwork0.173 ---
all-216361 --
obs-163940 75.8 %-
Solvent computationBsol: 50.271 Å2
Displacement parametersBiso mean: 25.026 Å2
Baniso -1Baniso -2Baniso -3
1-2.43 Å20 Å20 Å2
2---7.538 Å20 Å2
3---5.108 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.18 Å
Luzzati d res low-1.71 Å
Luzzati sigma a0.14 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 1.59→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11072 0 55 2032 13159
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.372
X-RAY DIFFRACTIONc_mcbond_it1.0961.5
X-RAY DIFFRACTIONc_scbond_it2.1322
X-RAY DIFFRACTIONc_mcangle_it1.5982
X-RAY DIFFRACTIONc_scangle_it3.1482.5
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
1.59-1.60.427120.256339351
1.6-1.610.288310.291547578
1.61-1.620.241220.275648670
1.62-1.630.279420.271771813
1.63-1.650.249400.237894934
1.65-1.660.292560.26610021058
1.66-1.670.255680.26111651233
1.67-1.690.316670.26612851352
1.69-1.70.299770.25813751452
1.7-1.710.212790.26315981677
1.71-1.730.258860.25417831869
1.73-1.740.2611190.25220052124
1.74-1.760.31070.2422002307
1.76-1.770.2211260.23623702496
1.77-1.790.2661340.2425722706
1.79-1.810.2631300.22828202950
1.81-1.830.2461710.21831053276
1.83-1.840.2272180.20331213339
1.84-1.860.2351600.20133613521
1.86-1.880.2271810.19733703551
1.88-1.910.2131780.19434823660
1.91-1.930.2341990.19435173716
1.93-1.950.2291810.18836193800
1.95-1.980.2221890.18236403829
1.98-20.2131730.17437843957
2-2.030.2161920.17937523944
2.03-2.060.212130.18238724085
2.06-2.090.2111970.17638594056
2.09-2.120.1962020.17138784080
2.12-2.160.2092200.17239484168
2.16-2.190.2062150.17539654180
2.19-2.230.2062280.17239474175
2.23-2.280.2282100.18339934203
2.28-2.320.2382290.17640024231
2.32-2.370.1982220.16939984220
2.37-2.430.2092080.17240294237
2.43-2.490.2062230.17140204243
2.49-2.560.1932160.16940674283
2.56-2.630.212030.17740774280
2.63-2.720.2012240.16841024326
2.72-2.810.1982060.16840954301
2.81-2.930.2072180.17441254343
2.93-3.060.212020.17241174319
3.06-3.220.1932130.16241424355
3.22-3.420.1831980.15341944392
3.42-3.680.1782290.15441304359
3.68-4.050.1592480.14441814429
4.05-4.630.1852140.14341894403
4.63-5.810.1912080.16442784486
5.81-200.212290.18343944623
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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