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- PDB-4m0g: The crystal structure of an adenylosuccinate synthetase from Baci... -

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Basic information

Entry
Database: PDB / ID: 4m0g
TitleThe crystal structure of an adenylosuccinate synthetase from Bacillus anthracis str. Ames Ancestor.
ComponentsAdenylosuccinate synthetaseAdenylosuccinate synthase
KeywordsLIGASE / structural genomics / The Center for Structural Genomics of Infectious Diseases / CSGID
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
Adenylosuccinate synthetase
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.152 Å
AuthorsTan, K. / Zhou, M. / Zhang, R. / Kwon, K. / Anderson, W.F. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: The crystal structure of an adenylosuccinate synthetase from Bacillus anthracis str. Ames Ancestor.
Authors: Tan, K. / Zhou, M. / Zhang, R. / Kwon, K. / Anderson, W.F. / Joachimiak, A.
History
DepositionAug 1, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2013Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Adenylosuccinate synthetase
B: Adenylosuccinate synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,9903
Polymers95,9542
Non-polymers351
Water4,918273
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5910 Å2
ΔGint-33 kcal/mol
Surface area30000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.498, 76.498, 342.797
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
DetailsExperimentally unknown. It is predicted that chains A and B form a dimer.

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Components

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


Mass: 47977.211 Da / Num. of mol.: 2 / Mutation: Y370C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: Ames Ancestor / Gene: BAS5320, BA_5716, GBAA_5716, purA / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: Q81JI9, adenylosuccinate synthase
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


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


Mass: 18.015 Da / Num. of mol.: 273 / 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: 2.61 Å3/Da / Density % sol: 52.93 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 25% (w/v) PEG1500, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97940, 0.97957
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 6, 2009 / Details: mirror
RadiationMonochromator: Si 111 crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97941
20.979571
ReflectionResolution: 2.15→46 Å / Num. all: 55297 / Num. obs: 55297 / % possible obs: 97.3 % / Observed criterion σ(F): -5 / Observed criterion σ(I): 0 / Redundancy: 9.1 % / Rmerge(I) obs: 0.099 / Net I/σ(I): 40.2
Reflection shellResolution: 2.15→2.19 Å / Redundancy: 8.8 % / Rmerge(I) obs: 0.643 / Mean I/σ(I) obs: 4.3 / Num. unique all: 2781 / % possible all: 99.2

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
SHELXDphasing
MLPHAREphasing
DMmodel building
ARPmodel building
WARPmodel building
HKL-3000phasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RefinementMethod to determine structure: MAD / Resolution: 2.152→45.742 Å / SU ML: 0.25 / σ(F): 1.33 / Phase error: 26.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.243 2804 5.1 %random
Rwork0.1915 ---
all0.1942 54941 --
obs0.1942 54941 96.89 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.152→45.742 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6403 0 1 273 6677
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086517
X-RAY DIFFRACTIONf_angle_d1.0378837
X-RAY DIFFRACTIONf_dihedral_angle_d13.0872370
X-RAY DIFFRACTIONf_chiral_restr0.071010
X-RAY DIFFRACTIONf_plane_restr0.0041152
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1519-2.1890.30711290.23712611X-RAY DIFFRACTION98
2.189-2.22880.29641400.22952568X-RAY DIFFRACTION99
2.2288-2.27170.32861590.22162593X-RAY DIFFRACTION99
2.2717-2.3180.34031380.2232646X-RAY DIFFRACTION99
2.318-2.36840.28221340.21412580X-RAY DIFFRACTION99
2.3684-2.42350.24921240.21132623X-RAY DIFFRACTION99
2.4235-2.48410.27781360.20852647X-RAY DIFFRACTION99
2.4841-2.55130.28311400.20352624X-RAY DIFFRACTION99
2.5513-2.62630.27111150.21392636X-RAY DIFFRACTION99
2.6263-2.71110.29751480.21872594X-RAY DIFFRACTION99
2.7111-2.8080.261480.21532627X-RAY DIFFRACTION99
2.808-2.92040.27611400.21272638X-RAY DIFFRACTION99
2.9204-3.05330.32461420.21752647X-RAY DIFFRACTION98
3.0533-3.21420.27951310.21452644X-RAY DIFFRACTION98
3.2142-3.41550.23461420.19712643X-RAY DIFFRACTION98
3.4155-3.67910.21591360.1722665X-RAY DIFFRACTION98
3.6791-4.04920.21041350.15372541X-RAY DIFFRACTION93
4.0492-4.63460.17871490.15392399X-RAY DIFFRACTION88
4.6346-5.83730.20081570.17452488X-RAY DIFFRACTION89
5.8373-45.75280.26031610.20282723X-RAY DIFFRACTION91
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)
12.7027-0.15030.09931.7782-0.23161.30090.09680.078-0.564-0.2841-0.0541-0.02470.5956-0.1255-0.04940.55480.00070.03160.2911-0.00820.36912.3403-2.983519.3254
21.7221-0.85260.55812.47361.56794.3355-0.005-0.1072-0.12410.1592-0.0503-0.10880.25080.07310.0940.3467-0.00060.05870.25770.05360.31626.46378.171734.4789
31.91950.3458-0.49151.7251-0.7232.0330.03350.0401-0.2284-0.16420.17270.45240.4988-0.4793-0.16980.4651-0.0951-0.02340.33880.03110.4536-7.3606-2.880428.0093
44.5708-0.6315-1.34982.85550.36442.77660.1894-0.01630.43330.0037-0.03120.1793-0.6467-0.3202-0.15520.50340.05960.04890.41980.07760.4560.466231.2219.1725
51.391-0.6973-0.10742.66191.15673.3346-0.03070.07270.5374-0.02170.0627-0.0636-0.4463-0.0853-0.07960.48840.03930.11290.4723-0.00850.5256-2.758932.743834.3607
63.2555-0.88870.81521.4179-0.44851.42570.0282-0.25980.08950.4392-0.01030.084-0.045-0.18140.00570.5751-0.00970.12280.3752-0.03580.35946.786620.554747.1745
71.20480.0759-0.34410.8856-0.1861.7670.02970.01310.15020.02730.02660.1392-0.2982-0.0947-0.07350.4120.0350.02130.2626-0.01940.310510.166731.038214.0003
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 106 )
2X-RAY DIFFRACTION2chain 'A' and (resid 107 through 199 )
3X-RAY DIFFRACTION3chain 'A' and (resid 200 through 429 )
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 26 )
5X-RAY DIFFRACTION5chain 'B' and (resid 27 through 89 )
6X-RAY DIFFRACTION6chain 'B' and (resid 90 through 199 )
7X-RAY DIFFRACTION7chain 'B' and (resid 200 through 428 )

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