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- PDB-3lax: The crystal structure of a domain of phenylacetate-coenzyme A lig... -

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Basic information

Entry
Database: PDB / ID: 3lax
TitleThe crystal structure of a domain of phenylacetate-coenzyme A ligase from Bacteroides vulgatus ATCC 8482
ComponentsPhenylacetate-coenzyme A ligase
KeywordsLIGASE / structural genomics / PSI-2 / protein structure initiative / midwest center for structural genomics / MCSG
Function / homology
Function and homology information


phenylacetate-CoA ligase / phenylacetate-CoA ligase activity / phenylacetate catabolic process / nucleotide binding
Similarity search - Function
Phenylacetate-CoA ligase / AMP-dependent ligase, C-terminal / AMP-binding enzyme C-terminal domain / ANL, C-terminal domain / ANL, N-terminal domain / GMP Synthetase; Chain A, domain 3 / AMP-dependent synthetase/ligase / AMP-binding enzyme / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Phenylacetate-coenzyme A ligase
Similarity search - Component
Biological speciesBacteroides vulgatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.428 Å
AuthorsTan, K. / Wu, R. / Cobb, G. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of a domain of phenylacetate-coenzyme A ligase from Bacteroides vulgatus ATCC 8482
Authors: Tan, K. / Wu, R. / Cobb, G. / Joachimiak, A.
History
DepositionJan 7, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 19, 2010Provider: repository / Type: Initial release
SupersessionFeb 2, 2010ID: 3GXS
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phenylacetate-coenzyme A ligase


Theoretical massNumber of molelcules
Total (without water)12,4731
Polymers12,4731
Non-polymers00
Water1,62190
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)33.737, 44.334, 67.601
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsExperimentally unknown. The domain is likely a monomer.

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Components

#1: Protein Phenylacetate-coenzyme A ligase


Mass: 12473.078 Da / Num. of mol.: 1 / Fragment: residues 327-432
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides vulgatus (bacteria) / Strain: ATCC 8482 / Gene: Bacteroides vulgatus, BVU_1668 / Plasmid: pMCSG19 / Production host: Escherichia coli (E. coli) / Strain (production host): pPK1037 / References: UniProt: A6L0Y5
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 90 / 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: 2.03 Å3/Da / Density % sol: 39.31 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2M Ammonium acetate, 0.1M HEPES, 45% w/v MPD, pH 8.5, 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: 0.97926 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 21, 2008 / Details: mirror
RadiationMonochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 1.428→37 Å / Num. all: 19292 / Num. obs: 19292 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.3 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 39.7
Reflection shellResolution: 1.43→1.45 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.709 / Mean I/σ(I) obs: 1.96 / Num. unique all: 914 / % possible all: 96

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
SHELXDphasing
MLPHAREphasing
DMmodel building
ARPmodel building
WARPmodel building
HKL-3000phasing
PHENIX(phenix.refine: 1.5_2)refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RefinementMethod to determine structure: SAD / Resolution: 1.428→30.187 Å / SU ML: 0.17 / σ(F): 1.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2253 986 5.14 %random
Rwork0.1743 ---
all0.1767 19197 --
obs0.1767 19197 98.65 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.164 Å2 / ksol: 0.392 e/Å3
Refinement stepCycle: LAST / Resolution: 1.428→30.187 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms923 0 0 90 1013
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007945
X-RAY DIFFRACTIONf_angle_d1.091295
X-RAY DIFFRACTIONf_dihedral_angle_d16.925397
X-RAY DIFFRACTIONf_chiral_restr0.072163
X-RAY DIFFRACTIONf_plane_restr0.004163
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4281-1.50340.26971350.19922499X-RAY DIFFRACTION96
1.5034-1.59760.22851410.16262572X-RAY DIFFRACTION99
1.5976-1.72090.25411540.1512576X-RAY DIFFRACTION100
1.7209-1.89410.21121500.13412594X-RAY DIFFRACTION100
1.8941-2.16810.18891400.13182624X-RAY DIFFRACTION100
2.1681-2.73130.22121450.14452663X-RAY DIFFRACTION100
2.7313-30.19340.2181210.20082683X-RAY DIFFRACTION95

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