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- PDB-2ptr: Crystal structure of Escherichia coli adenylosuccinate lyase muta... -

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Basic information

Entry
Database: PDB / ID: 2ptr
TitleCrystal structure of Escherichia coli adenylosuccinate lyase mutant H171A with bound adenylosuccinate substrate
ComponentsAdenylosuccinate lyase
KeywordsLYASE / adenylosuccinate lyase / mutant-substrate complex
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 / guanosine tetraphosphate binding / DNA damage response / cytosol
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 ...: / 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
Chem-2SA / Adenylosuccinate lyase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsTsai, M. / Howell, P.L.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Substrate and Product Complexes of Escherichia coli Adenylosuccinate Lyase Provide New Insights into the Enzymatic Mechanism.
Authors: Tsai, M. / Koo, J. / Yip, P. / Colman, R.F. / Segall, M.L. / Howell, P.L.
History
DepositionMay 8, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: 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
Revision 1.4Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.5Apr 3, 2024Group: Refinement description / Category: 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,6654
Polymers104,7392
Non-polymers9272
Water10,989610
1
A: Adenylosuccinate lyase
B: Adenylosuccinate lyase
hetero molecules

A: Adenylosuccinate lyase
B: Adenylosuccinate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)211,3318
Polymers209,4784
Non-polymers1,8534
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area37640 Å2
ΔGint-151 kcal/mol
Surface area53170 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)98.400, 143.190, 69.450
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsThe biological assembly is a homotetramer generated from the dimer in the asymmetric unit by the operations: -x, -y, x.

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Components

#1: Protein Adenylosuccinate lyase / Adenylosuccinate / ASL


Mass: 52369.426 Da / Num. of mol.: 2 / Mutation: H171A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: purB / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21C+ / References: UniProt: P0AB89, adenylosuccinate lyase
#2: 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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 610 / 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: 2.33 Å3/Da / Density % sol: 47.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: Tris-HCl, sodium acetate tri-hydrate, PEG-4000, glycerol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Feb 25, 2005
RadiationMonochromator: Confocal multilayer / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.85→44 Å / Num. all: 84440 / Num. obs: 84140 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.29 % / Biso Wilson estimate: 20.5 Å2 / Rsym value: 6.8 / Net I/σ(I): 19.5
Reflection shellResolution: 1.85→1.93 Å / Redundancy: 6.08 % / Mean I/σ(I) obs: 5.6 / Num. unique all: 490 / Rsym value: 30.8 / % possible all: 97.1

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Processing

Software
NameClassification
CrystalCleardata collection
CNSrefinement
d*TREKdata reduction
d*TREKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2007-May-08.deposit.rcsb.org.80.Session.24495

Resolution: 1.85→44 Å / Isotropic thermal model: overall / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.216 4220 -random
Rwork0.183 ---
all-84440 --
obs-84140 99.6 %-
Displacement parametersBiso mean: 22.91 Å2
Baniso -1Baniso -2Baniso -3
1-3.02 Å2--
2---3.54 Å2-
3---0.52 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.26 Å0.23 Å
Refinement stepCycle: LAST / Resolution: 1.85→44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7184 0 62 610 7856
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_dihedral_angle_d20
X-RAY DIFFRACTIONx_improper_angle_d0.9
LS refinement shellResolution: 1.85→1.93 Å / Rfactor Rfree error: 0.014
RfactorNum. reflection% reflection
Rfree0.313 490 -
Rwork0.282 --
obs-10160 97.1 %

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