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- PDB-2qdh: Fructose-1,6-bisphosphate aldolase from Leishmania mexicana in co... -

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Basic information

Entry
Database: PDB / ID: 2qdh
TitleFructose-1,6-bisphosphate aldolase from Leishmania mexicana in complex with mannitol-1,6-bisphosphate, a competitive inhibitor
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
D-MANNITOL-1,6-DIPHOSPHATE / Fructose-bisphosphate aldolase
Similarity search - Component
Biological speciesLeishmania mexicana (unknown)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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

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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)173,6018
Polymers172,2324
Non-polymers1,3694
Water31,1661730
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16420 Å2
ΔGint-46 kcal/mol
Surface area47680 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)85.053, 115.946, 161.657
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 (unknown) / Gene: ald / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 pLysS / References: UniProt: Q9U5N6, fructose-bisphosphate aldolase
#2: Chemical
ChemComp-M2P / D-MANNITOL-1,6-DIPHOSPHATE / 1,6-DI-O-PHOSPHONO-D-MANNITOL


Mass: 342.132 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H16O12P2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1730 / 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: 2.44 Å3/Da / Density % sol: 49.5 %
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: 5.9 % / Av σ(I) over netI: 12.6 / Number: 588554 / Rmerge(I) obs: 0.08 / Χ2: 0.9 / D res high: 1.9 Å / D res low: 50 Å / Num. obs: 99258 / % possible obs: 78.8
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.095099.910.0480.4737
3.254.0910010.0530.8477.3
2.843.2510010.090.9567.3
2.582.8410010.1551.027.1
2.392.5899.710.2431.0376.7
2.252.3997.710.3481.0285.6
2.142.2583.910.4251.0963.9
2.052.1456.410.5051.0562.8
1.972.0534.410.6011.0021.9
1.91.971410.7680.9381.4
ReflectionResolution: 1.9→50 Å / Num. all: 125938 / Num. obs: 99258 / % possible obs: 78.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.9 % / Rmerge(I) obs: 0.08 / Χ2: 0.902 / Net I/σ(I): 12.6
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.768 / Num. unique all: 1745 / Χ2: 0.938 / % possible all: 14

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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
Resolution: 1.9→20 Å / FOM work R set: 0.84 / σ(F): 38460 / σ(I): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.235 4427 3.5 %RANDOM
Rwork0.19 ---
all-126118 --
obs-87658 69.5 %-
Solvent computationBsol: 53.589 Å2
Displacement parametersBiso mean: 35.431 Å2
Baniso -1Baniso -2Baniso -3
1--4.379 Å20 Å20 Å2
2---0.835 Å20 Å2
3---5.214 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.24 Å
Luzzati d res low-2.2 Å
Luzzati sigma a0.29 Å0.24 Å
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11184 0 80 1730 12994
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.253
X-RAY DIFFRACTIONc_mcbond_it1.1711.5
X-RAY DIFFRACTIONc_scbond_it1.9792
X-RAY DIFFRACTIONc_mcangle_it1.7932
X-RAY DIFFRACTIONc_scangle_it2.7442.5
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
1.9-1.91110.2942930
1.91-1.930.24770.32110117
1.93-1.940.25460.323152158
1.94-1.950.16720.287206208
1.95-1.970.26110.315262273
1.97-1.980.398230.366325348
1.98-20.371160.302387403
2-2.010.347280.328448476
2.01-2.030.37260.326509535
2.03-2.050.313310.315621652
2.05-2.060.314370.303671708
2.06-2.080.343530.281815868
2.08-2.10.299450.277865910
2.1-2.120.292630.2679841047
2.12-2.140.305570.26610601117
2.14-2.160.342640.27611931257
2.16-2.180.301720.26913681440
2.18-2.20.256730.2414731546
2.2-2.230.293900.2616781768
2.23-2.250.312860.25817531839
2.25-2.280.2771040.24918201924
2.28-2.30.295970.24318981995
2.3-2.330.2531160.22719782094
2.33-2.360.283970.22420882185
2.36-2.390.2941150.23720232138
2.39-2.430.2751100.22921432253
2.43-2.460.261960.21621662262
2.46-2.50.3251220.22821992321
2.5-2.540.2861260.22321882314
2.54-2.580.2791500.21522392389
2.58-2.620.2661210.20722422363
2.62-2.670.2781310.21622732404
2.67-2.720.2541090.20823132422
2.72-2.780.2711100.21423232433
2.78-2.840.2561260.19723142440
2.84-2.90.2471340.20422982432
2.9-2.970.291320.21323362468
2.97-3.050.2251470.19423312478
3.05-3.140.2381100.19623662476
3.14-3.250.2331270.19323482475
3.25-3.360.211220.17823842506
3.36-3.490.2391300.17724002530
3.49-3.650.2271120.17124192531
3.65-3.840.2111350.16524182553
3.84-4.080.1931260.15524172543
4.08-4.40.171280.14224182546
4.4-4.830.1721350.1424402575
4.83-5.520.2031210.15524712592
5.52-6.90.241190.18924952614
6.9-200.1691280.15625742702
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 DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5HBP.parHBP.top

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