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- PDB-4nle: Crystal structure of apo Adenylosuccinate Lyase from Mycobacteriu... -

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Basic information

Entry
Database: PDB / ID: 4nle
TitleCrystal structure of apo Adenylosuccinate Lyase from Mycobacterium smegmatis
ComponentsAdenylosuccinate lyase
KeywordsLYASE / Purine biosynthesis / purine salvage pathway / homotetramer / catalysis / aspartase/fumarase superfamily
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
Fumarase C; Chain B, domain 1 - #60 / Adenylosuccinate lyase C-terminus / Adenylosuccinate lyase C-terminal / Adenylosuccinate lyase C-terminus / Adenylosuccinate lyase / Fumarase/aspartase (C-terminal domain) / Fumarate lyase, conserved site / Fumarate lyases signature. / Fumarate lyase family / Fumarate lyase, N-terminal ...Fumarase C; Chain B, domain 1 - #60 / Adenylosuccinate lyase C-terminus / Adenylosuccinate lyase C-terminal / Adenylosuccinate lyase C-terminus / 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 (Central domain) / Fumarase C; Chain A, domain 2 / Fumarase C; Chain B, domain 1 / L-Aspartase-like / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Adenylosuccinate lyase
Similarity search - Component
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.16 Å
AuthorsBanerjee, S. / Murthy, M.R.N.
CitationJournal: Febs J. / Year: 2014
Title: Structural and kinetic studies on adenylosuccinate lyase from Mycobacterium smegmatis and Mycobacterium tuberculosis provide new insights on the catalytic residues of the enzyme.
Authors: Banerjee, S. / Agrawal, M.J. / Mishra, D. / Sharan, S. / Balaram, H. / Savithri, H.S. / Murthy, M.R.
History
DepositionNov 14, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 5, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: Database references
Category: citation / citation_author ...citation / citation_author / database_2 / struct_ref_seq_dif
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.2Nov 8, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Adenylosuccinate lyase
B: Adenylosuccinate lyase


Theoretical massNumber of molelcules
Total (without water)106,5492
Polymers106,5492
Non-polymers00
Water9,044502
1
A: Adenylosuccinate lyase
B: Adenylosuccinate lyase

A: Adenylosuccinate lyase
B: Adenylosuccinate lyase


Theoretical massNumber of molelcules
Total (without water)213,0984
Polymers213,0984
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area25340 Å2
ΔGint-126 kcal/mol
Surface area61040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.600, 176.830, 73.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-723-

HOH

21B-645-

HOH

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Components

#1: Protein Adenylosuccinate lyase


Mass: 53274.609 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (bacteria) / Strain: MC2 155 / Gene: MSMEG_5847, purB / Plasmid: pRSET C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) pLysS / References: UniProt: A0R4I6, adenylosuccinate lyase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 502 / 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: 2.27 Å3/Da / Density % sol: 45.78 %
Crystal growTemperature: 291 K / Method: under oil, microbatch method / pH: 7.5
Details: 0.1M Na HEPES pH 7.5, 1.4M sodium citrate, 0.1M betaine hydrochloride, Under Oil, Microbatch Method, temperature 291.0K

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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: Nov 23, 2011 / 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: 2.16→37.86 Å / Num. all: 52292 / Num. obs: 49552 / Redundancy: 4.85 % / Biso Wilson estimate: 26.371 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 11.3
Reflection shellResolution: 2.16→2.28 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 14.2 / Num. unique all: 7312

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.7.0032refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2VD6

2vd6


Resolution: 2.16→37.86 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.914 / SU B: 9.925 / SU ML: 0.136 / Cross valid method: THROUGHOUT / ESU R: 0.279 / ESU R Free: 0.204 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.23829 2661 5.1 %RANDOM
Rwork0.20475 ---
obs0.20642 49552 98.64 %-
all-52292 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.547 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20 Å2-0 Å2
2---0.17 Å2-0 Å2
3---0.09 Å2
Refinement stepCycle: LAST / Resolution: 2.16→37.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6912 0 0 502 7414
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0197081
X-RAY DIFFRACTIONr_bond_other_d0.0010.026808
X-RAY DIFFRACTIONr_angle_refined_deg0.7591.9589609
X-RAY DIFFRACTIONr_angle_other_deg0.686315535
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.3495920
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.46823.385325
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.596151145
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.3961569
X-RAY DIFFRACTIONr_chiral_restr0.0390.21112
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.028186
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021620
X-RAY DIFFRACTIONr_mcbond_it0.4922.5493683
X-RAY DIFFRACTIONr_mcbond_other0.4922.5493682
X-RAY DIFFRACTIONr_mcangle_it0.9223.8154602
X-RAY DIFFRACTIONr_mcangle_other0.9213.8154603
X-RAY DIFFRACTIONr_scbond_it0.2942.5363398
X-RAY DIFFRACTIONr_scbond_other0.2942.5363399
X-RAY DIFFRACTIONr_scangle_other0.5763.7955008
X-RAY DIFFRACTIONr_long_range_B_refined3.43320.1158747
X-RAY DIFFRACTIONr_long_range_B_other3.22619.8678500
LS refinement shellResolution: 2.159→2.215 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 171 -
Rwork0.242 3402 -
obs--93.07 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.0485-0.0519-0.02720.90910.18880.17450.0025-0.0027-0.010.1116-0.0563-0.05620.01680.04640.05380.01870.0027-0.01720.07360.0080.047615.0802-8.444927.2027
20.0871-0.0944-0.00070.83650.19310.15770.02940.02280.0374-0.132-0.0805-0.0607-0.01390.03510.05120.03380.00180.02960.07530.02030.052613.919610.375610.0187
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 471
2X-RAY DIFFRACTION2B4 - 471

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