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- PDB-5u2a: Crystal structure of Brucella canis Acyl-CoA Synthetase -

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Basic information

Entry
Database: PDB / ID: 5u2a
TitleCrystal structure of Brucella canis Acyl-CoA Synthetase
ComponentsAMP-dependent synthetase and ligase
KeywordsLIGASE / SSGCID / NIH / NIAID / SBRI / UW / BERYLLIUM / SYNTHETASE / ACYL-COA / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


ANL, C-terminal domain / ANL, N-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-binding enzyme C-terminal domain / GMP Synthetase; Chain A, domain 3 / AMP-dependent synthetase/ligase / AMP-binding enzyme / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
AMP-dependent synthetase and ligase
Similarity search - Component
Biological speciesBrucella canis
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID) / Fox III, D. / Abendroth, J.
CitationJournal: To Be Published
Title: Crystal structure of Brucella canis Acyl-CoA Synthetase
Authors: Seattle Structural Genomics Center for Infectious Disease (SSGCID) / Fox III, D. / Abendroth, J.
History
DepositionNov 30, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 21, 2016Provider: 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: AMP-dependent synthetase and ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,7002
Polymers60,6651
Non-polymers351
Water73941
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.600, 92.200, 141.190
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein AMP-dependent synthetase and ligase


Mass: 60664.629 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brucella canis (strain ATCC 23365 / NCTC 10854) (bacteria)
Strain: ATCC 23365 / NCTC 10854 / Gene: BCAN_B0452 / Plasmid: BG1861 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A9MB96
#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.: 41 / 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: 3.45 Å3/Da / Density % sol: 64.32 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: ACETYL COA SYNTHETASE FROM BRUCELLA CANIS ATCC 23365 (BRCAA.00629.A.B1.PW37891) AT 26MG/ML (25 MM TRIS PH 8.0, 200 MM NACL, 1% GLYCEROL, 1 MM TCEP) WAS SET UP IN SPARSE CRYSTALLIZATION ...Details: ACETYL COA SYNTHETASE FROM BRUCELLA CANIS ATCC 23365 (BRCAA.00629.A.B1.PW37891) AT 26MG/ML (25 MM TRIS PH 8.0, 200 MM NACL, 1% GLYCEROL, 1 MM TCEP) WAS SET UP IN SPARSE CRYSTALLIZATION TRIALS AT 16C. CRYSTALS WERE PRODUCED BY SITTING DROP VAPOR DIFFUSION WITH AN EQUAL VOLUME OF PROTEIN AND SPARSE SCREEN MORPHEUS CONDITION A9 (0.1M TRIS(BASE), 0.1M BICINE, PH8.5, 0.06M MAGNESIUM CHLORIDE HEXAHYDRATE, 0.06M CALCIUM CHLORIDE DIHYDRATE, 20% PEG500 MME, 10% PEG20,000) AND DIRECTLY CRYO-PROTECTED. CRYSTAL ID 273132A9,RDJ0-10, CLSI-08ID, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 289K
PH range: 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: May 27, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 28526 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 4.8 % / Biso Wilson estimate: 70.73 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.047 / Net I/σ(I): 20.27
Reflection shellResolution: 2.5→2.56 Å / Redundancy: 5 % / Rmerge(I) obs: 0.512 / Mean I/σ(I) obs: 3.36 / Num. unique all: 10440 / CC1/2: 0.944 / % possible all: 99.9

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX(1.11.1_2575: 000)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1pg4

1pg4


Resolution: 2.5→41.918 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.95
RfactorNum. reflection% reflection
Rfree0.2283 1421 5 %
Rwork0.1906 --
obs0.1926 28442 99.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 70.73 Å2
Refinement stepCycle: LAST / Resolution: 2.5→41.918 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3965 0 1 41 4007
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074080
X-RAY DIFFRACTIONf_angle_d0.8525577
X-RAY DIFFRACTIONf_dihedral_angle_d14.7482431
X-RAY DIFFRACTIONf_chiral_restr0.051638
X-RAY DIFFRACTIONf_plane_restr0.007741
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.58930.35031390.27192652X-RAY DIFFRACTION100
2.5893-2.6930.31651390.27582651X-RAY DIFFRACTION99
2.693-2.81550.25181400.25422669X-RAY DIFFRACTION100
2.8155-2.96390.34551410.25122678X-RAY DIFFRACTION100
2.9639-3.14960.34691400.25162668X-RAY DIFFRACTION100
3.1496-3.39270.28821420.24222678X-RAY DIFFRACTION100
3.3927-3.73390.24361420.20142696X-RAY DIFFRACTION99
3.7339-4.27370.20861420.16342713X-RAY DIFFRACTION100
4.2737-5.38270.16741450.14852741X-RAY DIFFRACTION100
5.3827-41.9240.17781510.15872875X-RAY DIFFRACTION99
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)
12.21670.4579-0.21612.26380.40374.08550.00110.16480.16480.05360.10920.2637-0.6583-0.3222-0.07220.63840.06150.19970.4611-0.01510.447130.84462.25667.1787
24.73060.46230.49194.5362.77325.45840.2418-0.26640.4474-0.0998-0.37560.9501-0.8736-1.38250.12370.76160.32130.17630.84030.04860.682716.0858.56877.1367
32.1565-0.098-0.27060.59880.46014.04490.0166-0.26-0.08550.36950.05220.0641-0.4415-0.2109-0.06260.64690.00610.15430.3856-0.03750.431535.8795-1.480920.8505
43.0110.39261.59382.3533-0.07323.9786-0.1158-0.0890.15320.26180.0859-0.2128-1.08380.59120.00750.9713-0.14790.16940.5656-0.03750.429848.87328.410425.7769
51.52140.1384-1.24282.04440.51756.83650.00080.1028-0.045-1.29970.2499-0.0156-1.02270.4389-0.29350.909-0.11920.0740.5304-0.04630.528548.401417.112539.7541
63.70140.4934-2.12455.4806-0.30883.30240.4377-0.2156-0.08690.3925-0.2470.1888-0.17950.1664-0.17370.5493-0.0049-0.11460.5291-0.0060.394743.2869.53554.7384
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 18 through 134 )
2X-RAY DIFFRACTION2chain 'A' and (resid 135 through 192 )
3X-RAY DIFFRACTION3chain 'A' and (resid 193 through 325 )
4X-RAY DIFFRACTION4chain 'A' and (resid 326 through 423 )
5X-RAY DIFFRACTION5chain 'A' and (resid 424 through 461 )
6X-RAY DIFFRACTION6chain 'A' and (resid 462 through 553 )

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