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- PDB-3r7t: Crystal Structure of Adenylosuccinate Synthetase from Campylobact... -

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Basic information

Entry
Database: PDB / ID: 3r7t
TitleCrystal Structure of Adenylosuccinate Synthetase from Campylobacter jejuni
ComponentsAdenylosuccinate synthetaseAdenylosuccinate synthase
KeywordsLIGASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / alpha-beta fold / cytosol
Function / homology
Function and homology information


adenylosuccinate synthase / adenylosuccinate synthase activity / 'de novo' AMP biosynthetic process / GTP binding / magnesium ion binding / cytoplasm
Similarity search - Function
Adenylosuccinate Synthetase, subunit A; domain 2 / Adenylosuccinate Synthetase, subunit A, domain 2 / Adenylosuccinate Synthetase; Chain A, domain 1 / Adenylosuccinate Synthetase, subunit A, domain 1 / Adenylosuccinate Synthetase; Chain A, domain 3 / Adenylosuccinate Synthetase, subunit A, domain 3 / Adenylosuccinate synthase, active site / Adenylosuccinate synthetase active site. / Adenylosuccinate synthase, GTP-binding site / Adenylosuccinate synthetase, domain 2 ...Adenylosuccinate Synthetase, subunit A; domain 2 / Adenylosuccinate Synthetase, subunit A, domain 2 / Adenylosuccinate Synthetase; Chain A, domain 1 / Adenylosuccinate Synthetase, subunit A, domain 1 / Adenylosuccinate Synthetase; Chain A, domain 3 / Adenylosuccinate Synthetase, subunit A, domain 3 / 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 / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
CITRIC ACID / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Adenylosuccinate synthetase
Similarity search - Component
Biological speciesCampylobacter jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsKim, Y. / Gu, M. / Kwon, K. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: Crystal Structure of Adenylosuccinate Synthetase from Campylobacter jejuni
Authors: Kim, Y. / Gu, M. / Kwon, K. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionMar 23, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 20, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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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)47,7128
Polymers46,8801
Non-polymers8327
Water4,197233
1
A: Adenylosuccinate synthetase
hetero molecules

A: Adenylosuccinate synthetase
hetero molecules

A: Adenylosuccinate synthetase
hetero molecules

A: Adenylosuccinate synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)190,85032
Polymers187,5214
Non-polymers3,32928
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_655-x+1,-y,z1
crystal symmetry operation8_555x-y,-y,-z1
crystal symmetry operation11_655-x+y+1,y,-z1
Buried area14920 Å2
ΔGint-39 kcal/mol
Surface area67720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.232, 127.232, 122.250
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422
Components on special symmetry positions
IDModelComponents
11A-465-

HOH

21A-540-

HOH

31A-608-

HOH

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 46880.172 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni (Campylobacter) / Strain: jejuni NCTC 11168 / Gene: Cj1498c, purA / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 magic / References: UniProt: Q9PMG4, adenylosuccinate synthase

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Non-polymers , 6 types, 240 molecules

#2: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-CL / CHLORIDE ION / Chloride


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


Mass: 18.015 Da / Num. of mol.: 233 / 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: 3.05 Å3/Da / Density % sol: 59.63 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2 M magnesium chloride 0.1 M sodium citrate pH 5.5, 40 % (v/v) PEG400, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97903 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Nov 18, 2010 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97903 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 26582 / Num. obs: 26582 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 23.5 % / Biso Wilson estimate: 42.4 Å2 / Rsym value: 0.083 / Net I/σ(I): 13.2
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 23.2 % / Mean I/σ(I) obs: 5.75 / Num. unique all: 1295 / Rsym value: 0.779 / % possible all: 100

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
SHELXSphasing
MLPHAREphasing
BUCCANEERmodel building
PHENIX(phenix.refine: 1.7_650)refinement
HKL-3000data reduction
HKL-3000data scaling
BUCCANEERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.3→35.175 Å / SU ML: 0.29 / Isotropic thermal model: mixed / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 21.34 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.209 1320 5.04 %random
Rwork0.176 ---
all0.178 26176 --
obs0.178 26176 98.79 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 61.477 Å2 / ksol: 0.356 e/Å3
Displacement parametersBiso mean: 48 Å2
Baniso -1Baniso -2Baniso -3
1-3.4497 Å2-0 Å2-0 Å2
2--3.4497 Å20 Å2
3----6.8994 Å2
Refinement stepCycle: LAST / Resolution: 2.3→35.175 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3190 0 54 233 3477
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013428
X-RAY DIFFRACTIONf_angle_d1.414632
X-RAY DIFFRACTIONf_dihedral_angle_d16.6811312
X-RAY DIFFRACTIONf_chiral_restr0.102502
X-RAY DIFFRACTIONf_plane_restr0.009606
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.3-2.39210.29251460.23322698284499
2.3921-2.50090.26991540.21122707286199
2.5009-2.63270.25661450.19772704284999
2.6327-2.79760.26731470.20162701284898
2.7976-3.01350.26011340.20072695282998
3.0135-3.31660.21591370.19792756289399
3.3166-3.7960.19841610.17382755291699
3.796-4.78060.1751450.13952836298199
4.7806-35.17960.18221510.170130043155100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
1-0.06070.2078-0.08710.084-0.10240.0312-0.03410.06810.0655-0.16950.07640.07850.18430.024-00.31080.0009-0.00930.2219-0.04860.28787.628614.03666.6657
20.45380.0606-0.12920.18510.0271-0.01780.02910.05480.0327-0.12930.0334-0.09130.0917-0.1327-00.3058-0.03760.00010.1405-0.02070.184272.943313.00337.8617
30.3929-0.27690.13260.2523-0.07410.2624-0.0913-0.06720.0406-0.11180.09470.0364-0.0512-0.0323-00.2873-0.0355-0.03160.1609-0.01210.247361.225620.430619.7184
40.03010.12350.14970.03480.00550.07760.04090.0342-0.02570.0389-0.024-0.02730.05530.117300.24780.00020.02360.1514-0.02220.24286.28249.714515.9899
50.2406-0.15290.32320.52950.36370.5066-0.07760.0784-0.0072-0.07460.0625-0.0301-0.1130.126600.2041-0.05040.01430.2329-0.01480.201991.610729.39081.3698
60.3330.08060.15570.2616-0.34020.6183-0.15090.1899-0.0668-0.11830.1529-0.1185-0.03020.4042-00.2432-0.04520.10630.4416-0.05680.2645100.472323.0539-7.9685
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 1:41)
2X-RAY DIFFRACTION2chain 'A' and (resseq 42:117)
3X-RAY DIFFRACTION3chain 'A' and (resseq 118:196)
4X-RAY DIFFRACTION4chain 'A' and (resseq 197:224)
5X-RAY DIFFRACTION5chain 'A' and (resseq 225:356)
6X-RAY DIFFRACTION6chain 'A' and (resseq 357:416)

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