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- PDB-5e3v: Truncated X-ray crystal structure of Adenylosuccinate Lyase from ... -

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Basic information

Entry
Database: PDB / ID: 5e3v
TitleTruncated X-ray crystal structure of Adenylosuccinate Lyase from Salmonella typhimurium
ComponentsAdenylosuccinate lyase
KeywordsLYASE / Adenylosuccinate / Purine Biosynthesis Folding
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
Similarity search - Function
Adenylosuccinate lyase PurB, C-terminal / Adenylosuccinate lyase C-terminal / Adenylosuccinate lyase / Fumarate lyase, conserved site / Fumarate lyases signature. / Fumarate lyase family / Fumarate lyase, N-terminal / Lyase / Fumarase/histidase, N-terminal / L-Aspartase-like
Similarity search - Domain/homology
Adenylosuccinate lyase
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.72 Å
AuthorsBanerjee, S. / Agrawal, M.J. / Murthy, M.R.N.
Funding support India, 3items
OrganizationGrant numberCountry
Department of Biotechnology India
Department of Science and Technology India
Council of Scientific and Industrial Research India
CitationJournal: To Be Published
Title: Crystallographic and kinetic studies on Adenylosuccinate Lyase from Salmonella typhimurium
Authors: Banerjee, S. / Agrawal, M.J. / Murthy, N.M. / Balaram, H. / Savithri, H.S. / Murthy, M.R.N.
History
DepositionOct 4, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 5, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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 / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Adenylosuccinate lyase


Theoretical massNumber of molelcules
Total (without water)42,7721
Polymers42,7721
Non-polymers00
Water34219
1
A: Adenylosuccinate lyase

A: Adenylosuccinate lyase

A: Adenylosuccinate lyase

A: Adenylosuccinate lyase


Theoretical massNumber of molelcules
Total (without water)171,0894
Polymers171,0894
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-11
crystal symmetry operation10_555-x,-y,z1
crystal symmetry operation15_554y,x,-z-11
Buried area12470 Å2
ΔGint-63 kcal/mol
Surface area56400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)165.360, 165.360, 79.120
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

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Components

#1: Protein Adenylosuccinate lyase / / ASL / Adenylosuccinase


Mass: 42772.348 Da / Num. of mol.: 1 / Fragment: UNP residues 1-366
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (strain 14028s / SGSC 2262) (bacteria)
Strain: 14028s / SGSC 2262 / Gene: purB, STM14_1410 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) pLysS / References: UniProt: A0A0F6B070, adenylosuccinate lyase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 19 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.16 Å3/Da / Density % sol: 56.7 %
Crystal growTemperature: 291 K / Method: evaporation / pH: 7
Details: 0.1M sodium acetate trihydrate pH 4.0 and 10% Jeffamine M-600 pH 7.0 and 0.1M EDTA, under oil microbatch method

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9537 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 16, 2012 / Details: Bent collimating mirror and toroid
RadiationMonochromator: Si(111) Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.72→54 Å / Num. obs: 15037 / % possible obs: 99.9 % / Redundancy: 12 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 10.7
Reflection shellResolution: 2.72→2.87 Å / Mean I/σ(I) obs: 3.2

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2PTS

2pts


Resolution: 2.72→52.29 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.883 / SU B: 35.94 / SU ML: 0.336 / Cross valid method: THROUGHOUT / ESU R: 0.509 / ESU R Free: 0.362 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.32581 760 5.1 %RANDOM
Rwork0.27424 ---
obs0.27681 14254 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 86.472 Å2
Baniso -1Baniso -2Baniso -3
1--1.79 Å20 Å20 Å2
2---1.79 Å20 Å2
3---3.59 Å2
Refinement stepCycle: 1 / Resolution: 2.72→52.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2262 0 0 22 2284
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0212307
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9331.9393144
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.3155304
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.05425.05297
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.25315318
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.35157
X-RAY DIFFRACTIONr_chiral_restr0.1340.2370
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211761
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7591.51538
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.39722417
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.1163769
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.3884.5727
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: 2.72→2.79 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 48 -
Rwork0.301 1042 -
obs--99.91 %
Refinement TLS params.Method: refined / Origin x: 10.645 Å / Origin y: 10.37 Å / Origin z: -24.149 Å
111213212223313233
T0.5004 Å2-0.0154 Å2-0.0833 Å2-0.3925 Å2-0.0409 Å2--0.0662 Å2
L3.404 °20.8524 °2-0.5827 °2-4.1946 °2-0.1034 °2--2.3238 °2
S0.0606 Å °-0.3512 Å °0.2402 Å °0.6304 Å °-0.0391 Å °-0.1773 Å °-0.121 Å °0.1915 Å °-0.0214 Å °

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