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- PDB-4flc: Structural and Biochemical Characterization of Human Adenylosucci... -

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Basic information

Entry
Database: PDB / ID: 4flc
TitleStructural and Biochemical Characterization of Human Adenylosuccinate Lyase (ADSL) and the R303C ADSL Deficiency Associated Mutation
ComponentsAdenylosuccinate lyase
KeywordsLYASE / PURINE BIOSYNTHESIS / DISEASE MUTATION / PURINE METABOLISM
Function / homology
Function and homology information


AMP biosynthetic process / adenylosuccinate lyase / N6-(1,2-dicarboxyethyl)AMP AMP-lyase (fumarate-forming) activity / (S)-2-(5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamido) succinate lyase (fumarate-forming) activity / 'de novo' XMP biosynthetic process / Purine ribonucleoside monophosphate biosynthesis / 'de novo' AMP biosynthetic process / AMP salvage / GMP biosynthetic process / purine nucleotide biosynthetic process ...AMP biosynthetic process / adenylosuccinate lyase / N6-(1,2-dicarboxyethyl)AMP AMP-lyase (fumarate-forming) activity / (S)-2-(5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamido) succinate lyase (fumarate-forming) activity / 'de novo' XMP biosynthetic process / Purine ribonucleoside monophosphate biosynthesis / 'de novo' AMP biosynthetic process / AMP salvage / GMP biosynthetic process / purine nucleotide biosynthetic process / response to muscle activity / 'de novo' IMP biosynthetic process / response to starvation / aerobic respiration / response to nutrient / response to hypoxia / protein-containing complex / identical protein binding / cytosol
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1570 / Adenylosuccinate lyase C-terminus / Adenylosuccinate lyase C-terminal / Adenylosuccinate lyase C-terminus / Adenylosuccinate lyase / Fumarate lyase, conserved site / Fumarate lyases signature. / Fumarate lyase family / Fumarate lyase, N-terminal / Lyase ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1570 / Adenylosuccinate lyase C-terminus / Adenylosuccinate lyase C-terminal / Adenylosuccinate lyase C-terminus / Adenylosuccinate lyase / Fumarate lyase, conserved site / Fumarate lyases signature. / Fumarate lyase family / Fumarate lyase, N-terminal / Lyase / Fumarase/aspartase (N-terminal domain) / Fumarase/aspartase (Central domain) / Fumarase C; Chain A, domain 2 / Fumarase C; Chain B, domain 1 / L-Aspartase-like / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Adenylosuccinate lyase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 Å
AuthorsDeaton, M.K. / Ray, S.P. / Capodagli, G.C. / Calkins, L.A.F. / Sawle, L. / Ghosh, K. / Patterson, D. / Pegan, S.D.
CitationJournal: Biochemistry / Year: 2012
Title: Structural and Biochemical Characterization of Human Adenylosuccinate Lyase (ADSL) and the R303C ADSL Deficiency-Associated Mutation.
Authors: Ray, S.P. / Deaton, M.K. / Capodagli, G.C. / Calkins, L.A. / Sawle, L. / Ghosh, K. / Patterson, D. / Pegan, S.D.
History
DepositionJun 14, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 1, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 12, 2012Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Adenylosuccinate lyase
B: Adenylosuccinate lyase
C: Adenylosuccinate lyase
D: Adenylosuccinate lyase


Theoretical massNumber of molelcules
Total (without water)220,8784
Polymers220,8784
Non-polymers00
Water2,594144
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area30320 Å2
ΔGint-100 kcal/mol
Surface area66890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.799, 105.562, 217.221
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Adenylosuccinate lyase / / ASL / Adenylosuccinase / ASase


Mass: 55219.508 Da / Num. of mol.: 4 / Mutation: R303C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ADSL, AMPS / Plasmid: pET-14b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2(DE3)pLysS / References: UniProt: P30566, adenylosuccinate lyase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 144 / 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: 2.23 Å3/Da / Density % sol: 44.76 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M Tris pH 8.5, 20% PEG 8000, 12.5 mM spermine tetrahydrochloride, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.9789 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 15, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. all: 61656 / Num. obs: 58820 / % possible obs: 95.4 %
Reflection shellResolution: 2.6→2.69 Å / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 4.8 / % possible all: 97.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 42.54 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.59 Å47.47 Å
Translation2.59 Å47.47 Å

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Processing

Software
NameVersionClassificationNB
PHASER2.1.4phasing
REFMAC5.5.0109refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2J91
Resolution: 2.6→47.47 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.875 / Occupancy max: 1 / Occupancy min: 0.13 / SU B: 30.195 / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.415 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2984 2979 5.1 %RANDOM
Rwork0.2304 ---
obs0.2339 58588 94.5 %-
all-61998 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 102.23 Å2 / Biso mean: 55.108 Å2 / Biso min: 10.05 Å2
Baniso -1Baniso -2Baniso -3
1--1.59 Å20 Å20 Å2
2---0.69 Å20 Å2
3---2.28 Å2
Refinement stepCycle: LAST / Resolution: 2.6→47.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14699 0 0 144 14843
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.02215046
X-RAY DIFFRACTIONr_angle_refined_deg1.0091.96320331
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.83151853
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.13123.51718
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.763152761
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.80115138
X-RAY DIFFRACTIONr_chiral_restr0.0740.22294
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02111276
X-RAY DIFFRACTIONr_mcbond_it0.3751.59217
X-RAY DIFFRACTIONr_mcangle_it0.726214902
X-RAY DIFFRACTIONr_scbond_it0.935829
X-RAY DIFFRACTIONr_scangle_it1.5664.55420
LS refinement shellResolution: 2.6→2.66 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 207 -
Rwork0.247 3750 -
all-3957 -
obs-3750 87.43 %
Refinement TLS params.

L11: 0 °2 / L12: 0 °2 / L13: 0 °2 / L22: 0 °2 / L23: 0 °2 / L33: 0 °2 / S11: 0 Å ° / S12: 0 Å ° / S13: 0 Å ° / S21: 0 Å ° / S22: 0 Å ° / S23: 0 Å ° / S31: 0 Å ° / S32: 0 Å ° / S33: 0 Å ° / T11: 0 Å2 / T12: 0 Å2 / T13: 0 Å2 / T22: 0 Å2 / T23: 0 Å2 / T33: 0 Å2 / Method: refined / Refine-ID: X-RAY DIFFRACTION

IDOrigin x (Å)Origin y (Å)Origin z (Å)
135.5165-18.502825.1284
246.8626-6.149834.1559
342.27664.112131.6905
431.5715-2.076716.7965
518.85220.6721-19.5196
644.210914.06982.9424
718.114631.830522.2335
817.567338.87927.4149
932.44121.142628.3286
1020.451917.494538.4988
1136.894-2.256975.5899
1243.840220.561550.1258
13-3.021619.515434.1438
14-9.017124.384847.6705
15-0.41283.491729.9866
1612.01828.817527.3894
1716.7214-11.7409-10.1567
18-3.8625-10.29147.6408
1924.2706-26.100125.5377
2023.9699-34.822710.5362
219.5755-14.04831.5169
2222.7094-8.155336.385
238.41417.477869.5003
24-1.7197-10.710852.5208
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 26
2X-RAY DIFFRACTION2A27 - 173
3X-RAY DIFFRACTION3A174 - 285
4X-RAY DIFFRACTION4A286 - 379
5X-RAY DIFFRACTION5A380 - 441
6X-RAY DIFFRACTION6A442 - 476
7X-RAY DIFFRACTION7B5 - 52
8X-RAY DIFFRACTION8B53 - 99
9X-RAY DIFFRACTION9B102 - 274
10X-RAY DIFFRACTION10B275 - 365
11X-RAY DIFFRACTION11B366 - 447
12X-RAY DIFFRACTION12B448 - 474
13X-RAY DIFFRACTION13C9 - 52
14X-RAY DIFFRACTION14C53 - 89
15X-RAY DIFFRACTION15C90 - 276
16X-RAY DIFFRACTION16C277 - 343
17X-RAY DIFFRACTION17C344 - 446
18X-RAY DIFFRACTION18C447 - 475
19X-RAY DIFFRACTION19D5 - 52
20X-RAY DIFFRACTION20D53 - 109
21X-RAY DIFFRACTION21D110 - 274
22X-RAY DIFFRACTION22D275 - 343
23X-RAY DIFFRACTION23D344 - 446
24X-RAY DIFFRACTION24D447 - 473

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