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- PDB-2oas: Crystal Structure of 4-hydroxybutyrate coenzyme A transferase (At... -

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Basic information

Entry
Database: PDB / ID: 2oas
TitleCrystal Structure of 4-hydroxybutyrate coenzyme A transferase (AtoA) in complex with CoA from Shewanella oneidensis, Northeast Structural Genomics Target SoR119.
Components4-hydroxybutyrate coenzyme A transferase
KeywordsTRANSFERASE / alpha beta protein / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


4-hydroxybutyrate CoA-transferase activity / propionate metabolic process, methylcitrate cycle / acetyl-CoA hydrolase activity / acetate CoA-transferase activity / acetate metabolic process / anaerobic respiration
Similarity search - Function
4-hydroxybutyrate coenzyme like domains / Acetyl-CoA hydrolase/transferase C-terminal domain / Glutaconate Coenzyme A-transferase / Glutaconate Coenzyme A-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 / Transcription Regulator spoIIAA ...4-hydroxybutyrate coenzyme like domains / Acetyl-CoA hydrolase/transferase C-terminal domain / Glutaconate Coenzyme A-transferase / Glutaconate Coenzyme A-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 / Transcription Regulator spoIIAA / NagB/RpiA transferase-like / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
COENZYME A / Acetyl-CoA hydrolase/transferase
Similarity search - Component
Biological speciesShewanella oneidensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsForouhar, F. / Neely, H. / Hussain, M. / Benach, J. / Seetharaman, J. / Cunningham, K. / Ma, L.C. / Owen, L. / Fang, Y. / Xiao, R. ...Forouhar, F. / Neely, H. / Hussain, M. / Benach, J. / Seetharaman, J. / Cunningham, K. / Ma, L.C. / Owen, L. / Fang, Y. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal Structure of 4-hydroxybutyrate coenzyme A transferase (AtoA) from Shewanella oneidensis in complex with CoA, Northeast Structural Genomics Target SoR119.
Authors: Forouhar, F. / Neely, H. / Hussain, M. / Benach, J. / Seetharaman, J. / Cunningham, K. / Ma, L.C. / Owen, L. / Fang, Y. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L.
History
DepositionDec 17, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 23, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / 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_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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

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Assembly

Deposited unit
A: 4-hydroxybutyrate coenzyme A transferase
B: 4-hydroxybutyrate coenzyme A transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,9664
Polymers94,4312
Non-polymers1,5352
Water2,720151
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6310 Å2
ΔGint8 kcal/mol
Surface area28690 Å2
MethodPISA
2
A: 4-hydroxybutyrate coenzyme A transferase
B: 4-hydroxybutyrate coenzyme A transferase
hetero molecules

A: 4-hydroxybutyrate coenzyme A transferase
B: 4-hydroxybutyrate coenzyme A transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)191,9338
Polymers188,8624
Non-polymers3,0704
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area14890 Å2
ΔGint11 kcal/mol
Surface area55110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.157, 111.337, 179.430
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein 4-hydroxybutyrate coenzyme A transferase / AtoA


Mass: 47215.594 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella oneidensis (bacteria) / Strain: MR-1 / Gene: cat2, SO_1708 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: Q8EG98
#2: Chemical ChemComp-COA / COENZYME A / Coenzyme A


Mass: 767.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 151 / 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: 2.12 Å3/Da / Density % sol: 41.95 %
Description: The structure factor file contains Friedel pairs
Crystal growTemperature: 277 K / pH: 7
Details: 100mM HEPES, 20% PEG 6000, 1M Lithium chloride, 5mM DTT, 5mM acetyl-CoA, pH 7.0, microbatch under oil, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 12, 2006 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.4→29.89 Å / Num. all: 59902 / Num. obs: 59902 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Biso Wilson estimate: 23.7 Å2 / Rmerge(I) obs: 0.125 / Rsym value: 0.103 / Net I/σ(I): 23.06
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.482 / Mean I/σ(I) obs: 2.86 / Num. unique all: 5729 / Rsym value: 0.441 / % possible all: 95.5

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Processing

Software
NameVersionClassification
CNS1.1refinement
ADSCQUANTUMdata collection
HKL-2000data reduction
HKL-2000data scaling
SnBphasing
SOLVEphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.4→19.92 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 170270.8 / Data cutoff low absF: 0 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 1.5 / σ(I): 1.5 / Stereochemistry target values: Engh & Huber
Details: XtalView has also been used in refinement. The Friedel pairs were used for phasing
RfactorNum. reflection% reflectionSelection details
Rfree0.266 5094 9.9 %RANDOM
Rwork0.225 ---
all0.226 59902 --
obs0.225 51468 85.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 21.6149 Å2 / ksol: 0.309488 e/Å3
Displacement parametersBiso mean: 39.1 Å2
Baniso -1Baniso -2Baniso -3
1--17.26 Å20 Å20 Å2
2--1.73 Å20 Å2
3---15.53 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.42 Å0.36 Å
Refinement stepCycle: LAST / Resolution: 2.4→19.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6408 0 96 151 6655
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d24.5
X-RAY DIFFRACTIONc_improper_angle_d0.77
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 2.4→2.49 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.346 286 9.2 %
Rwork0.314 2832 -
obs-2832 51.6 %

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