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- PDB-6bs7: Crystal structure of Adenylosuccinate synthetase from Legionella ... -

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Basic information

Entry
Database: PDB / ID: 6bs7
TitleCrystal structure of Adenylosuccinate synthetase from Legionella pneumophila Philadelphia 1
ComponentsAdenylosuccinate synthetase
KeywordsLIGASE / SSGCID / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


adenylosuccinate synthase / adenylosuccinate synthase activity / IMP metabolic process / 'de novo' AMP biosynthetic process / GTP binding / magnesium ion binding / cytoplasm
Similarity search - Function
Adenylosuccinate Synthetase; Chain A, domain 3 / Adenylosuccinate Synthetase, subunit A, domain 3 / Adenylosuccinate Synthetase, subunit A; domain 2 / Adenylosuccinate Synthetase, subunit A, domain 2 / Adenylosuccinate synthase, active site / Adenylosuccinate synthetase active site. / Adenylosuccinate synthase, GTP-binding site / Adenylosuccinate synthetase, domain 2 / Adenylosuccinate synthetase, domain 3 / Adenylosuccinate synthetase GTP-binding site. ...Adenylosuccinate Synthetase; Chain A, domain 3 / Adenylosuccinate Synthetase, subunit A, domain 3 / Adenylosuccinate Synthetase, subunit A; domain 2 / Adenylosuccinate Synthetase, subunit A, domain 2 / Adenylosuccinate synthase, active site / Adenylosuccinate synthetase active site. / Adenylosuccinate synthase, GTP-binding site / Adenylosuccinate synthetase, domain 2 / Adenylosuccinate synthetase, domain 3 / Adenylosuccinate synthetase GTP-binding site. / Adenylosuccinate synthetase / Adenylosuccinate synthetase, domain 1 / Adenylosuccinate synthetase / Adenylosuccinate synthetase / Alpha-Beta Complex / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Adenylosuccinate synthetase
Similarity search - Component
Biological speciesLegionella pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal structure of Adenylosuccinate synthetase from Legionella pneumophila
Authors: Abendroth, J. / Conrady, D.G. / Lorimer, D.D. / Edwards, T.E.
History
DepositionDec 1, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 17, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Adenylosuccinate synthetase


Theoretical massNumber of molelcules
Total (without water)48,4691
Polymers48,4691
Non-polymers00
Water2,306128
1
A: Adenylosuccinate synthetase

A: Adenylosuccinate synthetase


Theoretical massNumber of molelcules
Total (without water)96,9392
Polymers96,9392
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
Buried area3230 Å2
ΔGint-16 kcal/mol
Surface area31200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.890, 90.370, 59.910
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Adenylosuccinate synthetase / AdSS / IMP--aspartate ligase


Mass: 48469.332 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila (bacteria) / Gene: purA / Plasmid: LepnA.00888.a.B1
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): BL21(DE3) / References: UniProt: Q8RNM2, adenylosuccinate synthase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / 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: 1.92 Å3/Da / Density % sol: 36.06 %
Crystal growTemperature: 285 K / Method: vapor diffusion, sitting drop / pH: 8
Details: Micolytic/Anatrace MCSG 1 B5: 200mM MgCl2, 25% PEG 3350, 100mM Tris Base / HCl pH 8.5: LepnA.00888.a.B1.PW38319 at 18.46mg/ml: cryo: 15% EG: tray 295118 B5: puck EMC5-10

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Nov 16, 2017
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.95→31.958 Å / Num. obs: 27874 / % possible obs: 99.7 % / Redundancy: 4.842 % / Biso Wilson estimate: 35.88 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.037 / Rrim(I) all: 0.042 / Χ2: 1.015 / Net I/σ(I): 21.73
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.95-24.8990.4853.1120340.8490.545100
2-2.064.9280.3823.8719680.8810.42999.7
2.06-2.124.9190.2925.0419320.9410.32899.9
2.12-2.184.9370.2326.5918700.9560.26100
2.18-2.254.8920.1758.4618110.9780.19699.9
2.25-2.334.8910.14410.2517700.9830.16299.8
2.33-2.424.8470.12111.9517100.9890.13599.9
2.42-2.524.880.09914.3616350.9930.11199.8
2.52-2.634.8780.08117.4515760.9940.0999.9
2.63-2.764.870.06221.4315080.9970.06999.8
2.76-2.914.8430.05125.3514380.9980.05799.8
2.91-3.084.8450.0431.7513620.9990.04599.9
3.08-3.34.8310.03437.812990.9990.03899.6
3.3-3.564.8070.02845.0711890.9990.03199.3
3.56-3.94.7890.02448.9611100.9990.02799.8
3.9-4.364.7680.02252.7110220.9990.02599.8
4.36-5.034.70.02154.599040.9990.02399.8
5.03-6.174.6340.02252.437750.9990.02499.7
6.17-8.724.4860.02153.846170.9990.02499
8.72-31.9584.0320.02354.183440.9990.02793

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX(dev_2947)refinement
PDB_EXTRACT3.24data extraction
MoRDaphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3hid via MORDA

3hid


Resolution: 1.95→31.958 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.17
RfactorNum. reflection% reflectionSelection details
Rfree0.2315 1995 7.16 %0
Rwork0.1855 ---
obs0.1888 27866 99.74 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 142.99 Å2 / Biso mean: 50.6482 Å2 / Biso min: 18.99 Å2
Refinement stepCycle: final / Resolution: 1.95→31.958 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2867 0 0 129 2996
Biso mean---50.4 -
Num. residues----390
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.95-1.99880.31021420.245418201962100
1.9988-2.05280.29411360.23217981934100
2.0528-2.11320.28291420.227918331975100
2.1132-2.18140.22241340.20718221956100
2.1814-2.25940.27721500.17818301980100
2.2594-2.34980.21181450.19318171962100
2.3498-2.45670.2761460.194518371983100
2.4567-2.58620.24781390.205718351974100
2.5862-2.74810.30311470.204718421989100
2.7481-2.96020.28111470.205918291976100
2.9602-3.25780.25611410.196118612002100
3.2578-3.72860.22171350.169618782013100
3.7286-4.69520.16321400.152319032043100
4.6952-31.96250.2231510.18611966211799
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)
16.8955-1.3853-1.34478.03441.45543.35280.23240.25470.6238-0.182-0.0995-0.3619-0.38520.5005-0.08060.2557-0.08450.03460.281-0.02790.2569-25.447314.6297-9.2259
22.9633-1.1615-2.32094.63891.64842.42630.19780.14990.8407-0.14470.1948-0.8087-0.55560.7206-0.14160.3564-0.04470.0610.39050.05790.5277-17.74888.4427-16.6033
34.0782-1.1008-1.9552.8396-0.22194.81650.64151.32680.5848-0.3609-0.2616-0.3274-0.5054-0.00460.04850.38850.14370.15490.68120.20140.4255-19.45831.5967-32.3796
40.92460.7205-0.93421.23720.27662.44631.03581.74730.8309-0.22220.0172-0.47-0.8571-0.80381.29330.74020.40310.40011.34420.4990.5362-17.22713.2624-44.2031
54.6677-1.1378-2.57232.54290.31026.3745-0.03770.232-0.02760.0155-0.0003-0.3880.11940.1792-0.12780.176-0.0142-0.02550.27980.02740.3619-18.2075-1.131-14.8275
61.4954-0.0008-0.42843.8575-0.73621.06170.08120.12270.2742-0.10560.03680.0686-0.19360.0194-0.06030.2827-0.01770.01790.2525-0.00410.2752-34.496222.7857-13.1727
73.60490.3248-0.17214.6619-0.1642.8220.0082-0.16280.48010.2796-0.02270.1587-0.2883-0.1163-0.02990.29030.0020.07690.1887-0.0390.2571-38.452425.0071-5.6392
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 26 )A1 - 26
2X-RAY DIFFRACTION2chain 'A' and (resid 27 through 76 )A27 - 76
3X-RAY DIFFRACTION3chain 'A' and (resid 77 through 175 )A77 - 175
4X-RAY DIFFRACTION4chain 'A' and (resid 176 through 193 )A176 - 193
5X-RAY DIFFRACTION5chain 'A' and (resid 194 through 253 )A194 - 253
6X-RAY DIFFRACTION6chain 'A' and (resid 254 through 340 )A254 - 340
7X-RAY DIFFRACTION7chain 'A' and (resid 341 through 431 )A341 - 431

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