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

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Basic information

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


acetate CoA-transferase activity / acetate metabolic process
Similarity search - Function
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 / 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 / MOLECULAR REPLACEMENT / Resolution: 3 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
DepositionFeb 2, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 18, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Refinement description / Category: software
Revision 1.2Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)100,2522
Polymers100,2522
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)197.508, 197.508, 61.100
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

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


Mass: 50125.949 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

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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: 3.43 Å3/Da / Density % sol: 64.16 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.3
Details: 18% PEG 3350, .2M Na Citrate, .1M BisTris Propane pH 6.3 and 1mM CoA, 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: Nov 14, 2009
RadiationMonochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 27624 / % possible obs: 100 % / Redundancy: 14.6 % / Rmerge(I) obs: 0.12 / Χ2: 1.058 / Net I/σ(I): 7.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
3-3.1114.20.56327230.9251100
3.11-3.2314.40.42727460.9691100
3.23-3.3814.50.31627380.9831100
3.38-3.5614.60.21827321.0241100
3.56-3.7814.80.16827421.061100
3.78-4.07150.12227581.0761100
4.07-4.48150.09227561.1121100
4.48-5.1314.90.08827801.2491100
5.13-6.4614.50.0827751.1021100
6.46-5014.60.0428741.061100

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.7_650refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→49.716 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8447 / SU ML: 0.34 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2168 1922 7.19 %RANDOM
Rwork0.1839 ---
obs0.1864 26715 96.74 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 15.223 Å2 / ksol: 0.324 e/Å3
Displacement parametersBiso max: 121.64 Å2 / Biso mean: 52.7933 Å2 / Biso min: 24.32 Å2
Baniso -1Baniso -2Baniso -3
1--12.7867 Å2-0 Å20 Å2
2---12.7867 Å2-0 Å2
3---25.5733 Å2
Refinement stepCycle: LAST / Resolution: 3→49.716 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6660 0 0 0 6660
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0126784
X-RAY DIFFRACTIONf_angle_d1.6279203
X-RAY DIFFRACTIONf_chiral_restr0.0921056
X-RAY DIFFRACTIONf_plane_restr0.0111209
X-RAY DIFFRACTIONf_dihedral_angle_d14.0062529
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 (%)
3-3.07430.3071280.26371633176190
3.0743-3.15740.27621260.25261647177392
3.1574-3.25030.29311270.2451705183293
3.2503-3.35520.26681340.22171692182694
3.3552-3.47510.26461360.20631750188696
3.4751-3.61420.2281360.20031759189597
3.6142-3.77860.24731360.19261775191197
3.7786-3.97770.2011410.17891791193298
3.9777-4.22680.19141360.15671809194599
4.2268-4.5530.17771400.14361810195099
4.553-5.01080.18541420.148918241966100
5.0108-5.73490.23671430.182318351978100
5.7349-7.22190.20961430.178118491992100
7.2219-49.72270.1691540.17219142068100

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