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- PDB-2ahv: Crystal Structure of Acyl-CoA transferase from E. coli O157:H7 (Y... -

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Basic information

Entry
Database: PDB / ID: 2ahv
TitleCrystal Structure of Acyl-CoA transferase from E. coli O157:H7 (YdiF)-thioester complex with CoA- 1
Componentsputative enzyme YdiF
KeywordsTRANSFERASE / YdiF / CoA transferase / Glutamyl thioester / Structural Genomics / Montreal-Kingston Bacterial Structural Genomics Initiative / BSGI
Function / homology
Function and homology information


acetate CoA-transferase / ketone body catabolic process / short-chain fatty acid metabolic process / acetate CoA-transferase activity / protein homotetramerization
Similarity search - Function
3-oxoacid CoA-transferase / Glutaconate Coenzyme A-transferase / Glutaconate Coenzyme A-transferase / Coenzyme A transferase family I / Coenzyme A transferase / Coenzyme A transferase / NagB/RpiA transferase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
COENZYME A / Acetate CoA-transferase YdiF
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsRangarajan, E.S. / Li, Y. / Ajamian, E. / Iannuzzi, P. / Kernaghan, S.D. / Fraser, M.E. / Cygler, M. / Matte, A. / Montreal-Kingston Bacterial Structural Genomics Initiative (BSGI)
CitationJournal: J.Biol.Chem. / Year: 2005
Title: Crystallographic trapping of the glutamyl-CoA thioester intermediate of family I CoA transferases.
Authors: Rangarajan, E.S. / Li, Y. / Ajamian, E. / Iannuzzi, P. / Kernaghan, S.D. / Fraser, M.E. / Cygler, M. / Matte, A.
History
DepositionJul 28, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 1, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: putative enzyme YdiF
B: putative enzyme YdiF
C: putative enzyme YdiF
D: putative enzyme YdiF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)233,3388
Polymers230,2684
Non-polymers3,0704
Water26,5541474
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17920 Å2
ΔGint-25 kcal/mol
Surface area68820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.085, 140.240, 112.682
Angle α, β, γ (deg.)90.00, 108.22, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
putative enzyme YdiF


Mass: 57566.914 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: O157:H7 / Gene: YdiF / Plasmid: pFO1 / Production host: Escherichia coli (E. coli) / Strain (production host): E. coli. BL21
References: UniProt: Q8X5X6, Transferases; Transferring sulfur-containing groups; CoA-transferases
#2: Chemical
ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1474 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.43 Å3/Da / Density % sol: 48 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 7.5
Details: 16% (w/v) PEG 3350, 80 mM Na K tartarate, pH 7.5, Microbatch, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 25, 2005
RadiationMonochromator: silicone / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 159093 / Num. obs: 159093 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 25.8 Å2 / Rsym value: 0.079 / Net I/σ(I): 9
Reflection shellResolution: 2→2.07 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 2 / Num. unique all: 14536 / Rsym value: 0.454 / % possible all: 90.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 2AHU

2ahu


Resolution: 2→50 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.932 / SU B: 4.028 / SU ML: 0.112 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.185 / ESU R Free: 0.163 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.22437 14361 9.2 %RANDOM
Rwork0.18232 ---
all0.207 156370 --
obs0.1862 142009 97.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 25.933 Å2
Baniso -1Baniso -2Baniso -3
1-1.17 Å20 Å20.93 Å2
2---1.3 Å20 Å2
3---0.71 Å2
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15618 0 192 1474 17284
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.02216084
X-RAY DIFFRACTIONr_angle_refined_deg1.1831.97521805
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.75252036
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.99724.619669
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.114152742
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.8761592
X-RAY DIFFRACTIONr_chiral_restr0.0780.22508
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211924
X-RAY DIFFRACTIONr_nbd_refined0.1870.27806
X-RAY DIFFRACTIONr_nbtor_refined0.3050.211104
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1260.21473
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2240.242
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1360.214
X-RAY DIFFRACTIONr_mcbond_it0.5761.510494
X-RAY DIFFRACTIONr_mcangle_it0.957216279
X-RAY DIFFRACTIONr_scbond_it1.47636325
X-RAY DIFFRACTIONr_scangle_it2.3724.55526
LS refinement shellResolution: 2.001→2.053 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 869 -
Rwork0.256 8344 -
obs--77.58 %

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