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- PDB-4mx2: Crystal Structure of adenylosuccinate lyase from Leishmania donovani -

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Basic information

Entry
Database: PDB / ID: 4mx2
TitleCrystal Structure of adenylosuccinate lyase from Leishmania donovani
ComponentsAdenylosuccinate lyase
KeywordsLYASE / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


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' AMP biosynthetic process / 'de novo' IMP biosynthetic process / nucleotide binding
Similarity search - Function
Adenylosuccinate lyase PurB, C-terminal / Adenylosuccinate lyase C-terminal / Adenylosuccinate lyase / Fumarase/aspartase (C-terminal domain) / Fumarate lyase, conserved site / Fumarate lyases signature. / Fumarate lyase family / Fumarate lyase, N-terminal / Lyase / Ribonucleotide Reductase Protein R1; domain 1 ...Adenylosuccinate lyase PurB, C-terminal / Adenylosuccinate lyase C-terminal / Adenylosuccinate lyase / Fumarase/aspartase (C-terminal domain) / Fumarate lyase, conserved site / Fumarate lyases signature. / Fumarate lyase family / Fumarate lyase, N-terminal / Lyase / Ribonucleotide Reductase Protein R1; domain 1 / Fumarase/aspartase (N-terminal domain) / Fumarase/aspartase (Central domain) / Fumarase C; Chain A, domain 2 / Fumarase C; Chain B, domain 1 / Fumarase/histidase, N-terminal / L-Aspartase-like / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / Adenylosuccinate lyase
Similarity search - Component
Biological speciesLeishmania donovani (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsWernimont, A.K. / Loppnau, P. / Dong, A. / Krojer, T. / Bradley, A. / Bushell, S. / von Delft, F. / Robinson, D. / Gilbert, I. / Bountra, C. ...Wernimont, A.K. / Loppnau, P. / Dong, A. / Krojer, T. / Bradley, A. / Bushell, S. / von Delft, F. / Robinson, D. / Gilbert, I. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Hui, R. / Mottaghi, K. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal Structure of adenylosuccinate lyase from Leishmania donovani
Authors: Wernimont, A.K. / Loppnau, P. / Dong, A. / Krojer, T. / Bradley, A. / Bushell, S. / von Delft, F. / Robinson, D. / Gilbert, I. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Hui, R. / Mottaghi, K.
History
DepositionSep 25, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 16, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: Adenylosuccinate lyase
B: Adenylosuccinate lyase
C: Adenylosuccinate lyase
D: Adenylosuccinate lyase
E: Adenylosuccinate lyase
F: Adenylosuccinate lyase
G: Adenylosuccinate lyase
H: Adenylosuccinate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)432,53520
Polymers429,3768
Non-polymers3,15812
Water33,9041882
1
A: Adenylosuccinate lyase
B: Adenylosuccinate lyase
E: Adenylosuccinate lyase
F: Adenylosuccinate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)216,1699
Polymers214,6884
Non-polymers1,4815
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area31460 Å2
ΔGint-149 kcal/mol
Surface area54030 Å2
MethodPISA
2
C: Adenylosuccinate lyase
D: Adenylosuccinate lyase
G: Adenylosuccinate lyase
H: Adenylosuccinate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)216,36511
Polymers214,6884
Non-polymers1,6777
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area31960 Å2
ΔGint-208 kcal/mol
Surface area54080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.015, 194.697, 147.507
Angle α, β, γ (deg.)90.000, 91.310, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Adenylosuccinate lyase /


Mass: 53672.059 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania donovani (eukaryote) / Gene: ASL, LdBPK_040440.1 / Production host: Escherichia coli (E. coli) / References: UniProt: A7LBL3
#2: Chemical
ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1882 / 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: 2.07 Å3/Da / Density % sol: 40.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 25 % PEG 3350, 0.2 M LiSO4, 0.1 M BisTris pH 6.5, AMP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.97949 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 22, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.88→50 Å / Num. all: 283875 / Num. obs: 269966 / % possible obs: 95.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 19.34 Å2 / Rmerge(I) obs: 0.125 / Net I/σ(I): 5.88
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.88-1.990.6221.691218544112389.8
1.99-2.130.3972.521168443972392.4
2.13-2.30.2733.651143033745293.3
2.3-2.520.1974.861119143505295
2.52-2.810.1456.351055923260797.6
2.81-3.250.118.681030722924499.3
3.25-3.970.08811.27836552480199.3
3.97-5.60.08412.44666301923699.5
5.60.07912.14367591072898.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
BUSTER-TNTBUSTER 2.10.0refinement
PDB_EXTRACT3.11data extraction
XDSdata scaling
Aimlessdata scaling
BALBESphasing
BUSTER2.10.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→34.98 Å / Cor.coef. Fo:Fc: 0.9168 / Cor.coef. Fo:Fc free: 0.8869 / Occupancy max: 1 / Occupancy min: 0.07 / SU R Cruickshank DPI: 0.189 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2534 13161 5.02 %RANDOM
Rwork0.2177 ---
obs0.2195 261938 95.68 %-
all-273764 --
Displacement parametersBiso max: 119.68 Å2 / Biso mean: 20.6767 Å2 / Biso min: 3 Å2
Baniso -1Baniso -2Baniso -3
1--0.0561 Å20 Å20.1019 Å2
2---1.1639 Å20 Å2
3---1.22 Å2
Refine analyzeLuzzati coordinate error obs: 0.246 Å
Refinement stepCycle: LAST / Resolution: 1.9→34.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26918 0 205 1882 29005
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d9743SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes663HARMONIC2
X-RAY DIFFRACTIONt_gen_planes4289HARMONIC5
X-RAY DIFFRACTIONt_it28243HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion3775SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact36541SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d28243HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg38524HARMONIC20.96
X-RAY DIFFRACTIONt_omega_torsion2.97
X-RAY DIFFRACTIONt_other_torsion17.03
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2545 902 4.86 %
Rwork0.2262 17672 -
all0.2275 18574 -
obs--95.68 %

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