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- PDB-4gs5: The crystal structure of acyl-CoA synthetase (AMP-forming)/AMP-ac... -

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Basic information

Entry
Database: PDB / ID: 4gs5
TitleThe crystal structure of acyl-CoA synthetase (AMP-forming)/AMP-acid ligase II-like protein from Dyadobacter fermentans DSM 18053
ComponentsAcyl-CoA synthetase (AMP-forming)/AMP-acid ligase II-like protein
KeywordsLIGASE / structural genomics / PSI-Biology / protein structure initiative / MCSG / Midwest Center for Structural Genomics
Function / homology
Function and homology information


ANL, C-terminal domain / ANL, N-terminal domain / ANL, N-terminal domain / AMP-binding, conserved site / Putative AMP-binding domain signature. / GMP Synthetase; Chain A, domain 3 / AMP-dependent synthetase/ligase / AMP-binding enzyme / Rossmann fold / 2-Layer Sandwich ...ANL, C-terminal domain / ANL, N-terminal domain / ANL, N-terminal domain / AMP-binding, conserved site / Putative AMP-binding domain signature. / GMP Synthetase; Chain A, domain 3 / AMP-dependent synthetase/ligase / AMP-binding enzyme / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
IODIDE ION / Acyl-CoA synthetase (AMP-forming)/AMP-acid ligase II-like protein
Similarity search - Component
Biological speciesDyadobacter fermentans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.018 Å
AuthorsTan, K. / Holowicki, J. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of acyl-CoA synthetase (AMP-forming)/AMP-acid ligase II-like protein from Dyadobacter fermentans DSM 18053
Authors: Tan, K. / Holowicki, J. / Clancy, S. / Joachimiak, A.
History
DepositionAug 27, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 12, 2012Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Acyl-CoA synthetase (AMP-forming)/AMP-acid ligase II-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,93325
Polymers39,6651
Non-polymers2,26824
Water2,792155
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.148, 67.148, 176.257
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322
DetailsExperimentally unknown. The molecule is predicted to be a monomer.

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Components

#1: Protein Acyl-CoA synthetase (AMP-forming)/AMP-acid ligase II-like protein


Mass: 39665.277 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dyadobacter fermentans (bacteria) / Strain: DSM 18053 / Gene: Dfer_1215 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: C6W5A4
#2: Chemical
ChemComp-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: I
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 155 / 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: 2.5 Å3/Da / Density % sol: 50.89 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2M Ammonium Iodine, 20% (w/v) PEG3350, 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: 0.97937 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 23, 2012 / Details: mirror
RadiationMonochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97937 Å / Relative weight: 1
ReflectionResolution: 2.018→33 Å / Num. all: 27429 / Num. obs: 27429 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 31.2
Reflection shellResolution: 2.02→2.05 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.602 / Mean I/σ(I) obs: 3.6 / Num. unique all: 1340 / % possible all: 99.9

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
SHELXDphasing
MLPHAREphasing
DMmodel building
RESOLVEmodel building
HKL-3000phasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.018→32.981 Å / SU ML: 0.53 / σ(F): 1.34 / Phase error: 23.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2545 1373 5.02 %Random
Rwork0.1956 ---
all0.1984 27373 --
obs0.1984 27373 99.68 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 33.609 Å2 / ksol: 0.322 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.3829 Å20 Å2-0 Å2
2--3.3829 Å20 Å2
3----6.7658 Å2
Refinement stepCycle: LAST / Resolution: 2.018→32.981 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2681 0 60 155 2896
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072790
X-RAY DIFFRACTIONf_angle_d1.0153768
X-RAY DIFFRACTIONf_dihedral_angle_d15.0121009
X-RAY DIFFRACTIONf_chiral_restr0.069427
X-RAY DIFFRACTIONf_plane_restr0.004483
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0179-2.090.2841200.22762561X-RAY DIFFRACTION100
2.09-2.17370.29091290.21412556X-RAY DIFFRACTION100
2.1737-2.27260.26071320.20932551X-RAY DIFFRACTION100
2.2726-2.39230.2881470.21382549X-RAY DIFFRACTION100
2.3923-2.54220.30821440.22562555X-RAY DIFFRACTION100
2.5422-2.73840.30081430.22242573X-RAY DIFFRACTION100
2.7384-3.01380.28411510.22092586X-RAY DIFFRACTION100
3.0138-3.44950.26451470.2112614X-RAY DIFFRACTION100
3.4495-4.34440.24011390.16752659X-RAY DIFFRACTION100
4.3444-32.98540.19371210.17412796X-RAY DIFFRACTION98
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)
11.26420.3414-0.16961.4320.20476.0224-0.10810.74750.1378-0.4679-0.25690.0528-0.051-0.09330.06020.48370.4504-0.02311.51660.3434-0.196314.817731.2517-18.7229
21.9787-0.8238-0.3180.51330.11880.06510.23931.28610.1043-0.4569-0.35460.0511-0.0686-0.65520.09730.2416-0.0221-0.04230.717-0.11830.150218.864716.8786-10.7174
35.97150.4941-0.55041.33930.28512.86560.25041.12860.6037-0.2995-0.1709-0.09030.02720.0799-0.05590.1880.12540.01780.50160.11350.209417.468629.9914-5.1629
42.9284-0.1727-0.93586.2648-0.24082.68080.12960.14750.5890.1768-0.0185-0.3872-0.24260.1471-0.09410.1040.01010.02450.30160.00110.302124.903233.64447.3907
53.1915-1.3139-1.54164.35064.42834.5756-0.13620.2867-0.16450.1530.03320.09460.3491-0.2450.10180.218-0.01990.02210.2752-0.02630.155919.731519.90639.9259
65.8416-0.22441.28352.8147-0.48114.03490.02320.2828-0.5757-0.2077-0.03460.10411.0239-0.4769-0.03320.391-0.11130.07870.2329-0.07450.285818.67486.89388.9969
74.4267-0.98014.8191.9904-2.57356.52880.0581-0.0196-0.07670.1187-0.212-0.13860.68510.17160.14330.2842-0.00550.03170.1517-0.01120.203826.70519.933419.5539
86.11840.9652-0.72683.00070.58743.20030.1167-0.06850.18190.2106-0.1477-0.32730.2580.5940.03710.33330.10490.01390.19050.11340.273447.83267.267929.0315
93.828-1.8107-2.1751.6073-0.38334.3519-0.41890.2794-0.3098-0.0229-0.24740.04970.95030.56850.52130.48390.16330.09620.34830.0750.394947.16551.408523.7686
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 1:18)
2X-RAY DIFFRACTION2chain 'A' and (resseq 19:69)
3X-RAY DIFFRACTION3chain 'A' and (resseq 70:127)
4X-RAY DIFFRACTION4chain 'A' and (resseq 128:177)
5X-RAY DIFFRACTION5chain 'A' and (resseq 178:198)
6X-RAY DIFFRACTION6chain 'A' and (resseq 199:230)
7X-RAY DIFFRACTION7chain 'A' and (resseq 231:254)
8X-RAY DIFFRACTION8chain 'A' and (resseq 255:314)
9X-RAY DIFFRACTION9chain 'A' and (resseq 315:350)

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