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- PDB-2vd6: Human adenylosuccinate lyase in complex with its substrate N6-(1,... -

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Basic information

Entry
Database: PDB / ID: 2vd6
TitleHuman adenylosuccinate lyase in complex with its substrate N6-(1,2- Dicarboxyethyl)-AMP, and its products AMP and fumarate.
ComponentsADENYLOSUCCINATE LYASE
KeywordsLYASE / PURINE BIOSYNTHESIS / EPILEPSY / 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
Chem-2SA / ADENOSINE MONOPHOSPHATE / FUMARIC ACID / Adenylosuccinate lyase
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsStenmark, P. / Moche, M. / Arrowsmith, C. / Berglund, H. / Busam, R. / Collins, R. / Dahlgren, L.G. / Edwards, A. / Flodin, S. / Flores, A. ...Stenmark, P. / Moche, M. / Arrowsmith, C. / Berglund, H. / Busam, R. / Collins, R. / Dahlgren, L.G. / Edwards, A. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Hallberg, B.M. / Holmberg-schiavone, L. / Johansson, I. / Kallas, A. / Karlberg, T. / Kotenyova, T. / Lehtio, L. / Nilsson, M. / Nyman, T. / Ogg, D. / Persson, C. / Sagemark, J. / Sundstrom, M. / Thorsell, A.G. / Tresaugues, L. / van den Berg, S. / Weigelt, J. / Welin, M. / Nordlund, P. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Human Adenylosuccinate Lyase in Complex with its Substrate N6-(1,2-Dicarboxyethyl)-AMP, and its Products AMP and Fumarate.
Authors: Stenmark, P. / Moche, M. / Arrowsmith, C. / Berglund, H. / Busam, R. / Collins, R. / Dahlgren, L.G. / Edwards, A. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Hallberg, B.M. ...Authors: Stenmark, P. / Moche, M. / Arrowsmith, C. / Berglund, H. / Busam, R. / Collins, R. / Dahlgren, L.G. / Edwards, A. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Hallberg, B.M. / Holmberg-Schiavone, L. / Johansson, I. / Kallas, A. / Karlberg, T. / Kotenyova, T. / Lehtio, L. / Nilsson, M. / Nyman, T. / Ogg, D. / Persson, C. / Sagemark, J. / Sundstrom, M. / Thorsell, A.G. / Tresaugues, L. / Van Den Berg, S. / Weigelt, J. / Welin, M. / Nordlund, P.
History
DepositionSep 30, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 23, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Jul 18, 2012Group: Other
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _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
Revision 2.1Dec 13, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)231,32822
Polymers228,7664
Non-polymers2,56218
Water15,853880
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area37520 Å2
ΔGint-159.7 kcal/mol
Surface area75610 Å2
MethodPQS
Unit cell
Length a, b, c (Å)87.300, 128.100, 190.500
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(-1, -0.013, -0.011), (-0.016, 0.533, 0.846), (-0.005, 0.846, -0.533)30.468, -14.447
2given(-1, -0.013, -0.011), (-0.016, 0.533, 0.846), (-0.005, 0.846, -0.533)30.468, -14.447
3given(0.392, 0.449, -0.803), (0.459, -0.852, -0.253), (-0.798, -0.269, -0.54)23.213, -3.798

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
ADENYLOSUCCINATE LYASE / / ADENYLOSUCCINASE / ASL / ASASE


Mass: 57191.512 Da / Num. of mol.: 4 / Fragment: RESIDUES 1-481
Source method: isolated from a genetically manipulated source
Details: THE CONSTRUCT CONTAINS A HEXAHISTIDINE TAIL AND A LINKER SEQUENCE IN THE N-TERMINUS (MHHHHHHSSGVDLGTENLYFQS)
Source: (gene. exp.) HOMO SAPIENS (human) / Description: MAMMALIAN GENE COLLECTION (MGC) / Plasmid: PNIC-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P30566, adenylosuccinate lyase

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Non-polymers , 6 types, 898 molecules

#2: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#3: Chemical ChemComp-FUM / FUMARIC ACID / Fumaric acid


Mass: 116.072 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H4O4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-2SA / 2-[9-(3,4-DIHYDROXY-5-PHOSPHONOOXYMETHYL-TETRAHYDRO-FURAN-2-YL)-9H-PURIN-6-YLAMINO]-SUCCINIC ACID / ADENYLOSUCCINIC ACID


Type: RNA linking / Mass: 463.293 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H18N5O11P
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 880 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsOUR CONSTRUCT HAS INITIALLY AN N-TERMINAL HEXAHISTIDINE TAIL AND LINKER SEQUENCE ...OUR CONSTRUCT HAS INITIALLY AN N-TERMINAL HEXAHISTIDINE TAIL AND LINKER SEQUENCE (MHHHHHHSSGVDLGTENLYFQS-) AND THEN P30566 RESIDUE 1-481 AND FINALLY OUR CONSTRUCT MISSES THE FINAL THREE AA OF P30466 (482-484, -LCL).

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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: 2.41 Å3/Da / Density % sol: 48.46 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.0723
DetectorType: ADSC CCD / Detector: CCD / Date: May 23, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0723 Å / Relative weight: 1
ReflectionResolution: 2→25 Å / Num. obs: 144136 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 21.3
Reflection shellResolution: 2→2.2 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 5.5 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.3.0040refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2J91

2j91


Resolution: 2→50 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.932 / SU B: 8.973 / SU ML: 0.13 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.181 / ESU R Free: 0.159 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.229 7207 5 %RANDOM
Rwork0.192 ---
obs0.194 136929 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.83 Å2
Baniso -1Baniso -2Baniso -3
1-1.79 Å20 Å20 Å2
2--0.08 Å20 Å2
3----1.87 Å2
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14706 0 161 880 15747
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.02215216
X-RAY DIFFRACTIONr_bond_other_d0.0010.0210549
X-RAY DIFFRACTIONr_angle_refined_deg1.0881.97320568
X-RAY DIFFRACTIONr_angle_other_deg0.877325626
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.26351856
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.10823.556720
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.61152752
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.45715136
X-RAY DIFFRACTIONr_chiral_restr0.0580.22305
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0216760
X-RAY DIFFRACTIONr_gen_planes_other0.0020.023118
X-RAY DIFFRACTIONr_nbd_refined0.1990.23611
X-RAY DIFFRACTIONr_nbd_other0.1810.211340
X-RAY DIFFRACTIONr_nbtor_refined0.1710.27399
X-RAY DIFFRACTIONr_nbtor_other0.0830.27558
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1360.2849
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.30.214
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2470.228
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1360.216
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5671.512133
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.648214923
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.16536821
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.7174.55640
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.283 526
Rwork0.239 10005
Refinement TLS params.Method: refined / Origin x: 15.1723 Å / Origin y: -0.6615 Å / Origin z: 17.0699 Å
111213212223313233
T-0.0888 Å2-0.0347 Å20.0537 Å2--0.1647 Å20.0068 Å2---0.1528 Å2
L0.5061 °20.0393 °2-0.2367 °2-0.5698 °20.1958 °2--1.286 °2
S0.1189 Å °-0.0066 Å °0.0442 Å °-0.0003 Å °-0.0007 Å °0.0045 Å °-0.5291 Å °0.0909 Å °-0.1182 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 474
2X-RAY DIFFRACTION1A1000 - 2002
3X-RAY DIFFRACTION1B5 - 476
4X-RAY DIFFRACTION1B1002 - 2002
5X-RAY DIFFRACTION1C5 - 472
6X-RAY DIFFRACTION1C1000 - 2002
7X-RAY DIFFRACTION1D5 - 476
8X-RAY DIFFRACTION1D1002 - 2002

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