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- PDB-3s8d: Crystal Structure of RipA from Yersinia pestis -

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Basic information

Entry
Database: PDB / ID: 3s8d
TitleCrystal Structure of RipA from Yersinia pestis
ComponentsCoenzyme A transferase
KeywordsTRANSFERASE / 4-HYDROXYBUTYRYL COA TRANSFERASE / COA TRANSFERASE
Function / homology
Function and homology information


acetate CoA-transferase activity / acetate metabolic process
Similarity search - Function
Acetyl-CoA hydrolase/transferase / Acetyl-CoA hydrolase/transferase, N-terminal / Acetyl-CoA hydrolase/transferase C-terminal domain / Acetyl-CoA hydrolase/transferase, C-terminal domain superfamily / Acetyl-CoA hydrolase/transferase N-terminal domain / Acetyl-CoA hydrolase/transferase C-terminal domain / NagB/RpiA transferase-like
Similarity search - Domain/homology
4-hydroxybutyrate coenzyme A transferase
Similarity search - Component
Biological speciesYersinia pestis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.31 Å
AuthorsTorres, R. / Goulding, C.W.
CitationJournal: Plos One / Year: 2011
Title: Biochemical, structural and molecular dynamics analyses of the potential virulence factor RipA from Yersinia pestis.
Authors: Torres, R. / Swift, R.V. / Chim, N. / Wheatley, N. / Lan, B. / Atwood, B.R. / Pujol, C. / Sankaran, B. / Bliska, J.B. / Amaro, R.E. / Goulding, C.W.
History
DepositionMay 27, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 18, 2012Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Coenzyme A transferase
B: Coenzyme A transferase


Theoretical massNumber of molelcules
Total (without water)101,4712
Polymers101,4712
Non-polymers00
Water1,910106
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)117.533, 109.306, 85.303
Angle α, β, γ (deg.)90.00, 120.20, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Coenzyme A transferase / Similar to 4-hydroxybutyrate CoA transferase


Mass: 50735.578 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis (bacteria) / Gene: aCH1, y2385, YPO1926, YP_1668 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9ZC36
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / 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: 2.36 Å3/Da / Density % sol: 47.92 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.7
Details: 18% PEG 3350, 0.2M sodium citrate, 0.1M Bis-tris propane, 1mM acetyl CoA, pH 5.7, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 21, 2009
RadiationProtocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 38932 / % possible obs: 94.7 % / Biso Wilson estimate: 32.05 Å2

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Processing

Software
NameVersionClassificationNB
PHENIX1.7.1_741refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.31→26.701 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7908 / SU ML: 0.6 / Cross valid method: FREE R / σ(F): 1 / Phase error: 28.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.263 1947 5.03 %RANDOM
Rwork0.2013 ---
obs0.2044 38671 94.65 %-
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 23.502 Å2 / ksol: 0.33 e/Å3
Displacement parametersBiso max: 94.95 Å2 / Biso mean: 39.5409 Å2 / Biso min: 17.47 Å2
Baniso -1Baniso -2Baniso -3
1--6.1127 Å2-0 Å24.6653 Å2
2--2.7527 Å2-0 Å2
3---3.3599 Å2
Refinement stepCycle: LAST / Resolution: 2.31→26.701 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6672 0 0 106 6778
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096754
X-RAY DIFFRACTIONf_angle_d1.1479168
X-RAY DIFFRACTIONf_chiral_restr0.0731060
X-RAY DIFFRACTIONf_plane_restr0.0051202
X-RAY DIFFRACTIONf_dihedral_angle_d15.6972506
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.31-2.36780.35721210.28292413253487
2.3678-2.43170.3641250.27242450257588
2.4317-2.50320.32821260.25522434256089
2.5032-2.5840.30491400.24742527266791
2.584-2.67630.34831330.25252550268392
2.6763-2.78330.32061430.24242555269894
2.7833-2.90980.31871340.23552618275294
2.9098-3.0630.28421240.23232691281597
3.063-3.25460.29321470.21282703285098
3.2546-3.50540.28131500.19952732288299
3.5054-3.85720.25251520.18552744289699
3.8572-4.41320.21591490.16142747289699
4.4132-5.5520.19231510.16212733288498
5.552-26.70250.22491520.172828272979100

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