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- PDB-7t29: Crystal Structure of Adenylosuccinate lyase (ASL) from Pseudomona... -

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Basic information

Entry
Database: PDB / ID: 7t29
TitleCrystal Structure of Adenylosuccinate lyase (ASL) from Pseudomonas aeruginosa complexed with AMP
ComponentsAdenylosuccinate lyase
KeywordsLYASE / SSGCID / Adenylosuccinate lyase / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
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 / cytosol
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
ADENOSINE MONOPHOSPHATE / Adenylosuccinate lyase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: to be published
Title: Crystal Structure of Adenylosuccinate lyase (ASL) from Pseudomonas aeruginosa complexed with AMP
Authors: Dranow, D.M. / Abendroth, J. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.
History
DepositionDec 3, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 15, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,0624
Polymers51,5911
Non-polymers4713
Water9,890549
1
A: Adenylosuccinate lyase
hetero molecules

A: Adenylosuccinate lyase
hetero molecules

A: Adenylosuccinate lyase
hetero molecules

A: Adenylosuccinate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)208,24816
Polymers206,3634
Non-polymers1,88512
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
crystal symmetry operation3_455-x-1,y,-z1
crystal symmetry operation4_555x,-y,-z1
Buried area34110 Å2
ΔGint-101 kcal/mol
Surface area56400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.870, 73.150, 177.790
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-323-

GLN

21A-948-

HOH

31A-974-

HOH

41A-1081-

HOH

51A-1112-

HOH

61A-1148-

HOH

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Components

#1: Protein Adenylosuccinate lyase / ASL / Adenylosuccinase / ASase


Mass: 51590.676 Da / Num. of mol.: 1 / Fragment: PsaeA.17999.a.B1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Gene: purB, PA2629 / Plasmid: PsaeA.17999.a.B1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9I0K9, adenylosuccinate lyase
#2: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP*YM
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 549 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.23 Å3/Da / Density % sol: 44.92 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: PsaeA.17999.a.B1.PW38925 at 24 mg/ml incubated with 4 mM AMP and fumarate, mixed 1:1 with MCSG1(e4): 0.2 M Lithium Sulfate, 0.1 M Tris:HCl, pH=8.5, 25% (w/v) PEG 3350. Puck: emv3-7, barcode: 320112e4.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9787 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Feb 28, 2019 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 1.5→33.82 Å / Num. obs: 74051 / % possible obs: 99.8 % / Redundancy: 6.108 % / Biso Wilson estimate: 14.54 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.053 / Rrim(I) all: 0.058 / Χ2: 0.918 / Net I/σ(I): 20.49 / Num. measured all: 452281
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.5-1.546.0880.5623.1432995542054200.8890.614100
1.54-1.586.090.483.6832180528552840.9020.525100
1.58-1.636.1130.394.5231726519251900.9380.427100
1.63-1.686.1160.3375.2730438497749770.9490.369100
1.68-1.736.1330.2796.3729935488248810.9670.305100
1.73-1.796.1340.2178.1828654467246710.9780.238100
1.79-1.866.1410.17310.3228007456145610.9850.189100
1.86-1.946.1420.14112.6326841437243700.990.154100
1.94-2.026.1550.10816.1225783419341890.9940.11899.9
2.02-2.126.1440.08220.824602400640040.9970.09100
2.12-2.246.1350.06625.2723521384038340.9970.07299.8
2.24-2.376.1340.05429.8922200363036190.9980.0699.7
2.37-2.546.1220.04435.0220865341234080.9990.04899.9
2.54-2.746.1230.03838.6119489319031830.9990.04299.8
2.74-36.1120.03343.717982295629420.9990.03699.5
3-3.356.0890.02849.3916142266326510.9990.03199.5
3.35-3.876.0620.02456.0114386238623730.9990.02699.5
3.87-4.746.030.02160.5512078202120030.9990.02399.1
4.74-6.715.960.02458.379429160315820.9990.02698.7
6.71-33.825.5310.02460.9250289429090.9990.02696.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIXdev-4274refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7T24

7t24


Resolution: 1.5→33.82 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 14.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1732 2135 2.88 %
Rwork0.1436 71905 -
obs0.1444 74040 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 70.55 Å2 / Biso mean: 21.0154 Å2 / Biso min: 6.99 Å2
Refinement stepCycle: final / Resolution: 1.5→33.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3502 0 31 558 4091
Biso mean--15.24 31.18 -
Num. residues----453
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5-1.530.19761390.181447484887100
1.53-1.570.20941550.173747514906100
1.57-1.620.17211210.162247634884100
1.62-1.660.21351570.159947344891100
1.66-1.720.2091470.15647334880100
1.72-1.780.18211650.157747524917100
1.78-1.850.17441590.153547444903100
1.85-1.930.14361360.141847854921100
1.93-2.040.18021280.141147914919100
2.04-2.160.18431320.139847994931100
2.16-2.330.16231380.134647914929100
2.33-2.560.15041780.134147784956100
2.56-2.940.15411090.14148644973100
2.94-3.70.20091420.139548665008100
3.7-33.820.15691290.13995006513599
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)
10.3432-0.02020.02830.3283-0.15450.87-0.00650.029-0.0517-0.02220.0026-0.05910.05470.0665-0.00170.06660.00560.00860.0668-0.00430.0985-21.2847-9.7102-3.9599
20.8670.7838-0.71262.7971-1.36761.6294-0.0360.37280.2517-0.24720.08620.1522-0.1384-0.0573-0.05920.2364-0.00370.03390.28820.05550.1558-18.391114.2016-40.3737
30.98950.18370.85230.85080.34851.63630.01980.0266-0.22070.00460.04070.03080.07990.0323-0.0970.09960.01940.00960.05260.01430.163-28.2517-26.06444.5856
40.7054-0.12640.53810.3702-0.0090.74490.1503-0.1526-0.51340.15470.0508-0.12520.36260.0334-0.16360.23180.0421-0.07910.14530.03950.3739-16.9328-32.204518.1877
50.295-0.53090.30241.0224-0.56180.34170.206-0.331-0.44590.21420.0672-0.14340.3953-0.0465-0.0770.27850.0474-0.11420.20140.10440.3471-17.1194-31.064824.5375
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 123 through 370 )A123 - 370
2X-RAY DIFFRACTION2chain 'A' and (resid 371 through 456 )A371 - 456
3X-RAY DIFFRACTION3chain 'A' and (resid -5 through 49 )A-5 - 49
4X-RAY DIFFRACTION4chain 'A' and (resid 50 through 91 )A50 - 91
5X-RAY DIFFRACTION5chain 'A' and (resid 92 through 122 )A92 - 122

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