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- PDB-7t24: Crystal Structure of Adenylosuccinate lyase (ASL) from Pseudomona... -

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Basic information

Entry
Database: PDB / ID: 7t24
TitleCrystal Structure of Adenylosuccinate lyase (ASL) from Pseudomonas aeruginosa
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
IMIDAZOLE / ISOPROPYL ALCOHOL / Adenylosuccinate lyase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / molecular replacement / Resolution: 1.45 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
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 1.1Feb 28, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)51,8405
Polymers51,5911
Non-polymers2494
Water8,485471
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)207,36020
Polymers206,3634
Non-polymers99716
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-x-1,-y-1,z1
crystal symmetry operation3_455-x-1,y,-z1
crystal symmetry operation4_545x,-y-1,-z1
Buried area30370 Å2
ΔGint-51 kcal/mol
Surface area54510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.560, 96.550, 137.580
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-871-

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-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#3: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 471 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.14 Å3/Da / Density % sol: 42.58 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: PsaeA.17999.a.B1.PW38913 at 19 mg/ml, Native data: mixed 1:1 with Morpheus(d4): 12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD, 0.1 M MES/imidazole pH 6.5, 0.02 M each of 1,6- ...Details: PsaeA.17999.a.B1.PW38913 at 19 mg/ml, Native data: mixed 1:1 with Morpheus(d4): 12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD, 0.1 M MES/imidazole pH 6.5, 0.02 M each of 1,6-hexanediol, 1-butanol, (RS)-1,2-propanediol, 2-propanol, 1,4-butanediol, 0.2 M 1,3-propanediol. Puck: qog3-8, barcode: 319675d4. Anomalous data: mixed 1:1 with Morpheus(H12): 12.5% (w/v) PEG-1000, 12.5% (w/v) PEG-3350, 12.5% (v/v) MPD, 0.1 M bicine/Trizma base, pH=8.5, 0.02 M each sodium L-glutamate, DL-alanine, glycine, DL-lysine HCl, DL-serine. Preformed crystal then soaked 20 sec with 500 mM sodium iodide and 10% ethylene glycol. Puck: kdy1-11, barcode: 319672h12.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.1271 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 17, 2021
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1271 Å / Relative weight: 1
ReflectionResolution: 1.45→33.28 Å / Num. obs: 77812 / % possible obs: 98.9 % / Redundancy: 6.216 % / Biso Wilson estimate: 15.39 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.09 / Rrim(I) all: 0.098 / Χ2: 0.936 / Net I/σ(I): 11.55 / Num. measured all: 483651 / Scaling rejects: 8
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
1.45-1.493.1290.5372.216129575051550.7660.64889.7
1.49-1.533.8480.4592.9321006562654590.8540.53197
1.53-1.575.0850.402427588544854250.9230.44999.6
1.57-1.626.7880.3625.3836121532253210.9560.393100
1.62-1.676.9630.3016.3836012517251720.9710.326100
1.67-1.736.9460.2517.4534430495849570.9790.272100
1.73-1.86.9180.2138.6933318481748160.9820.23100
1.8-1.876.8350.1799.9731450460546010.9860.19499.9
1.87-1.966.7320.14911.430239449444920.990.162100
1.96-2.056.3870.12212.9227166425842530.9910.13399.9
2.05-2.166.3120.10514.8325475404040360.9920.11499.9
2.16-2.297.0970.09817.0427337385338520.9930.105100
2.29-2.457.0750.0918.625662362936270.9940.09799.9
2.45-2.656.9850.08419.8623637338533840.9940.09100
2.65-2.96.9230.07920.7921608312331210.9950.08699.9
2.9-3.246.6870.07521.7418910283028280.9930.08299.9
3.24-3.746.0540.0721.8715141251325010.9940.07699.5
3.74-4.596.5760.06823.8414079214421410.9930.07499.9
4.59-6.487.0690.06824.5912010169916990.9950.074100
6.48-33.286.5150.06623.9763339849720.9940.07298.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIX1.20rc3-4406refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: SAD / Resolution: 1.45→33.28 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 16.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.182 2045 2.63 %
Rwork0.1511 75752 -
obs0.1519 77797 98.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 69.92 Å2 / Biso mean: 21.1204 Å2 / Biso min: 7.56 Å2
Refinement stepCycle: final / Resolution: 1.45→33.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3311 0 21 478 3810
Biso mean--31.24 29.36 -
Num. residues----432
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 (%)
1.45-1.480.26951220.22964523464589
1.48-1.520.2261060.19414872497897
1.52-1.560.20251440.17044999514399
1.56-1.610.18531630.159550485211100
1.61-1.660.18951390.160550355174100
1.66-1.720.17861210.157250855206100
1.72-1.790.1691390.149750685207100
1.79-1.870.16651370.14550545191100
1.87-1.970.17071440.148551145258100
1.97-2.090.20961530.15150465199100
2.09-2.250.17051340.14251225256100
2.25-2.480.16851380.142250975235100
2.48-2.840.1931290.148351615290100
2.84-3.570.17561350.148851805315100
3.57-33.280.17671410.148253485489100
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)
14.1526-1.84840.55921.8747-1.152.3640.05890.36040.0044-0.09090.0173-0.0029-0.0093-0.0598-0.07890.1418-0.00020.00760.1487-0.00590.0586-31.5092-45.2407-25.8436
21.6584-0.8182-0.10211.2907-0.01120.61560.05080.2127-0.0205-0.1658-0.0558-0.07430.04160.0303-0.00270.15470.00060.0230.194-0.0720.1148-13.3101-64.7616-29.6803
31.3697-0.8797-1.35210.64520.66972.95570.04670.3521-0.3648-0.2299-0.17230.08210.08870.07750.10990.21970.00940.00510.2725-0.1230.2334-14.2293-72.1695-30.9076
40.5124-0.2183-0.04791.37540.33130.35650.00140.0729-0.0031-0.05290.0042-0.07650.00860.0471-0.01330.0822-0.01050.00550.1149-0.01180.083-13.0437-48.6554-9.2222
51.0568-0.5914-0.11141.97150.55250.4612-0.00960.0890.175-0.09660.02920.0302-0.09250.01210.01280.0964-0.01560.00260.08050.01330.0932-24.4455-30.8453-7.3534
60.4719-0.2251-0.08964.3968-0.49650.51790.01740.07080.0084-0.0437-0.0339-0.086-0.03270.02490.01130.0602-0.0081-0.01080.0953-0.00460.0665-26.8369-45.5347-11.3549
70.65250.01090.12990.4521-0.81711.4998-0.2311-0.41610.62130.31470.1605-0.0947-0.6713-0.0090.05440.39340.0334-0.0840.2386-0.16730.5013-15.0481-8.907212.0467
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 28 )A0 - 28
2X-RAY DIFFRACTION2chain 'A' and (resid 29 through 91 )A29 - 91
3X-RAY DIFFRACTION3chain 'A' and (resid 92 through 122 )A92 - 122
4X-RAY DIFFRACTION4chain 'A' and (resid 123 through 252 )A123 - 252
5X-RAY DIFFRACTION5chain 'A' and (resid 253 through 304 )A253 - 304
6X-RAY DIFFRACTION6chain 'A' and (resid 305 through 370 )A305 - 370
7X-RAY DIFFRACTION7chain 'A' and (resid 371 through 456 )A371 - 456

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