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- PDB-6c25: Crystal structure of Adenylosuccinate synthetase from Legionella ... -

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Basic information

Entry
Database: PDB / ID: 6c25
TitleCrystal structure of Adenylosuccinate synthetase from Legionella pneumophila Philadelphia 1 in complex with GDP
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
GUANOSINE-5'-DIPHOSPHATE / Adenylosuccinate synthetase
Similarity search - Component
Biological speciesLegionella pneumophila (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal structure of Adenylosuccinate synthetase from Legionella pneumophila Philadelphia 1 in complex with GDP
Authors: Abendroth, J. / Conrady, D.G. / Lorimer, D.D. / Edwards, T.E.
History
DepositionJan 6, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 14, 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

Downloads & links

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Assembly

Deposited unit
A: Adenylosuccinate synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,9724
Polymers48,4691
Non-polymers5033
Water3,837213
1
A: Adenylosuccinate synthetase
hetero molecules

A: Adenylosuccinate synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,9458
Polymers96,9392
Non-polymers1,0066
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
Buried area5240 Å2
ΔGint-73 kcal/mol
Surface area31260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.810, 90.260, 60.010
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: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: GDP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 213 / 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 %
Crystal growTemperature: 285 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Molecular Dimensions Morpheus screen B4: 12.5% w/V PEG 1000, 12.5% w/V PEG 3350, 12.5% V/V MPD: 30mM of each NaF, NaBr, NaI: 100mM MES/imidazole pH 6.5: LepnA.00888.a.B1.PW38319 at 18.4mg/ml ...Details: Molecular Dimensions Morpheus screen B4: 12.5% w/V PEG 1000, 12.5% w/V PEG 3350, 12.5% V/V MPD: 30mM of each NaF, NaBr, NaI: 100mM MES/imidazole pH 6.5: LepnA.00888.a.B1.PW38319 at 18.4mg/ml + 2mM MgCl2 + 2mM GDP: cryo: direct: tray 297195 b4: puck esb5-10

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Dec 29, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→40.435 Å / Num. obs: 30104 / % possible obs: 99.9 % / Redundancy: 5.835 % / Biso Wilson estimate: 25.45 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.066 / Rrim(I) all: 0.072 / Χ2: 1.014 / Net I/σ(I): 16.09
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.9-1.952.7330.5342.0821680.7130.66599
1.95-23.5550.4243.1821320.7930.50199.8
2-2.064.1730.3434.4120790.890.394100
2.06-2.124.6610.2975.5820190.9420.335100
2.12-2.195.1720.2337.6819610.9630.26100
2.19-2.275.5140.29.1819080.980.221100
2.27-2.365.9770.18310.318310.9850.20199.9
2.36-2.456.860.16212.2517700.9890.175100
2.45-2.567.1340.1413.8316970.9930.151100
2.56-2.697.1140.12815.0916420.9950.138100
2.69-2.837.130.10317.4715560.9960.111100
2.83-37.1020.08220.714940.9970.089100
3-3.217.1240.06525.213650.9970.07100
3.21-3.477.0750.05230.8713120.9980.056100
3.47-3.87.0660.04635.512070.9980.0599.9
3.8-4.257.050.0438.2710840.9990.043100
4.25-4.917.0260.03741.159800.9990.04100
4.91-6.016.9620.04137.168470.9990.044100
6.01-8.56.80.04137.916590.9990.045100
8.5-40.4356.0970.03243.853930.9990.03598.2

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX(1.13_2998)refinement
PDB_EXTRACT3.24data extraction
PHENIXphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: native structure, PDB entry 6bs7

6bs7


Resolution: 1.9→40.435 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.09
RfactorNum. reflection% reflectionSelection details
Rfree0.2136 2002 6.65 %0
Rwork0.1739 ---
obs0.1765 30102 99.89 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 111.93 Å2 / Biso mean: 36.6687 Å2 / Biso min: 10.77 Å2
Refinement stepCycle: final / Resolution: 1.9→40.435 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2962 0 30 218 3210
Biso mean--30.22 39.97 -
Num. residues----394
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 (%)
1.9001-1.94760.27771530.24271939209299
1.9476-2.00030.25271530.219119572110100
2.0003-2.05910.2571450.204919632108100
2.0591-2.12560.251590.191319662125100
2.1256-2.20160.23431270.180619862113100
2.2016-2.28970.21661380.179620112149100
2.2897-2.39390.23891510.177719722123100
2.3939-2.52010.23391510.183819852136100
2.5201-2.6780.22821300.18320092139100
2.678-2.88470.23651380.185720172155100
2.8847-3.17490.19691360.174520262162100
3.1749-3.6340.20021520.155920182170100
3.634-4.57750.16631320.142720792211100
4.5775-40.44390.21071370.176721722309100
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)
11.46390.1395-0.28553.124-0.58081.01040.03510.15810.2655-0.17640.08030.0437-0.1407-0.038-0.10080.16760.0010.01150.12770.00490.1659-34.498522.9671-13.2686
23.21750.267-0.05163.5562-0.11532.0423-0.0506-0.04980.40810.00330.04560.158-0.06320.01970.01440.17430.02030.04240.1326-0.02190.1732-38.169424.9698-5.6395
33.7635-1.6707-0.81134.99871.29370.41130.08770.05930.2038-0.17810.0339-0.4083-0.05410.0799-0.11860.176-0.01120.00820.14190.00190.1576-23.792412.4354-11.6961
43.3998-1.5514-1.67941.75190.89172.92640.49570.69150.4518-0.4023-0.1896-0.4998-0.4898-0.19390.0070.2730.04630.12110.29180.0980.2463-18.12332.8662-27.0507
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 254 through 340 )A254 - 340
2X-RAY DIFFRACTION2chain 'A' and (resid 341 through 431 )A341 - 431
3X-RAY DIFFRACTION3chain 'A' and (resid 1 through 41 )A1 - 41
4X-RAY DIFFRACTION4chain 'A' and (resid 42 through 253 )A42 - 253

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