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

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Basic information

Entry
Database: PDB / ID: 3qli
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 / 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
ACETATE ION / 4-hydroxybutyrate coenzyme A transferase
Similarity search - Component
Biological speciesYersinia pestis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,3704
Polymers100,2522
Non-polymers1182
Water7,548419
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)118.586, 108.307, 84.970
Angle α, β, γ (deg.)90.000, 120.100, 90.000
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: 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
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 419 / 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: 2.35 Å3/Da / Density % sol: 47.76 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 8% tacsimate pH 5.0, 8% PEG 3350, 4% v/v 2,5-hexandiol and 1mM Succinyl coenzyme A , 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 Q315 / 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: 1.9→50 Å / Num. obs: 71782 / % possible obs: 98.1 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.053 / Χ2: 1.009 / Net I/σ(I): 19.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.9-1.9320.15931400.964186.2
1.93-1.972.40.11734770.927195.1
1.97-2.012.60.10835420.984197.5
2.01-2.052.80.10536160.963199.2
2.05-2.092.90.11236001199.2
2.09-2.143.10.09236390.987199.7
2.14-2.193.40.08836561.068199.8
2.19-2.253.70.09136441.01199.9
2.25-2.323.70.0836441.009199.9
2.32-2.393.70.06936520.9941100
2.39-2.483.80.06536400.981100
2.48-2.583.80.06136931.034199.9
2.58-2.73.70.05936351.091199.9
2.7-2.843.80.05236461.081199.8
2.84-3.023.70.04936580.928199.9
3.02-3.253.70.04536591.086199.6
3.25-3.583.60.04435961.021198.5
3.58-4.093.50.04435880.974197.3
4.09-5.163.30.04234491.048193.4
5.16-503.50.04836080.931196.4

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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: 1.9→41.23 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8784 / SU ML: 0.18 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2031 1974 2.79 %RANDOM
Rwork0.1716 ---
obs0.1725 70864 96.76 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.406 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso max: 76.66 Å2 / Biso mean: 23.2988 Å2 / Biso min: 9.79 Å2
Baniso -1Baniso -2Baniso -3
1-2.6884 Å2-0 Å20.3365 Å2
2---4.5616 Å2-0 Å2
3---1.8732 Å2
Refinement stepCycle: LAST / Resolution: 1.9→41.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6800 0 8 419 7227
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076936
X-RAY DIFFRACTIONf_angle_d1.0429408
X-RAY DIFFRACTIONf_chiral_restr0.0731074
X-RAY DIFFRACTIONf_plane_restr0.0051238
X-RAY DIFFRACTIONf_dihedral_angle_d12.8582580
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 (%)
1.9-1.94560.2361220.19054171429383
1.9456-1.99820.23151350.16764739487493
1.9982-2.0570.22581390.16474916505597
2.057-2.12340.20611390.16534917505697
2.1234-2.19930.21651440.16614996514099
2.1993-2.28730.21911450.17114980512598
2.2873-2.39140.21511440.1750535197100
2.3914-2.51750.23311450.17495066521199
2.5175-2.67520.21441430.170250375180100
2.6752-2.88170.20031460.176150645210100
2.8817-3.17160.19531450.175250655210100
3.1716-3.63030.20541450.17375045519099
3.6303-4.57290.16691400.15774878501895
4.5729-41.23990.19451420.1834963510596

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