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- PDB-3d3u: Crystal structure of 4-hydroxybutyrate CoA-transferase (abfT-2) f... -

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Basic information

Entry
Database: PDB / ID: 3d3u
TitleCrystal structure of 4-hydroxybutyrate CoA-transferase (abfT-2) from Porphyromonas gingivalis. Northeast Structural Genomics Consortium target PgR26
Components4-hydroxybutyrate CoA-transferase
KeywordsTRANSFERASE / alpha-beta protein / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


acetate CoA-transferase activity / acetate metabolic process
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 / Acetyl-CoA hydrolase/transferase N-terminal domain / Acetyl-CoA hydrolase/transferase C-terminal domain ...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 / 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
4-hydroxybutyrate CoA-transferase
Similarity search - Component
Biological speciesPorphyromonas gingivalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å
AuthorsForouhar, F. / Neely, H. / Zhang, X.-Z. / Price II, W.N. / Hussain, M. / Seetharaman, J. / Xiao, R. / Conover, K. / Cunningham, K. / Ma, L.-C. ...Forouhar, F. / Neely, H. / Zhang, X.-Z. / Price II, W.N. / Hussain, M. / Seetharaman, J. / Xiao, R. / Conover, K. / Cunningham, K. / Ma, L.-C. / Ho, C.K. / Everett, J.K. / 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 CoA-transferase (abfT-2) from Porphyromonas gingivalis.
Authors: Forouhar, F. / Neely, H. / Zhang, X.-Z. / Price II, W.N. / Hussain, M. / Seetharaman, J. / Xiao, R. / Conover, K. / Cunningham, K. / Ma, L.-C. / Ho, C.K. / Everett, J.K. / Acton, T.B. / ...Authors: Forouhar, F. / Neely, H. / Zhang, X.-Z. / Price II, W.N. / Hussain, M. / Seetharaman, J. / Xiao, R. / Conover, K. / Cunningham, K. / Ma, L.-C. / Ho, C.K. / Everett, J.K. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L.
History
DepositionMay 12, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Jan 24, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.4Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / struct_conn / struct_ref_seq_dif
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_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 4-hydroxybutyrate CoA-transferase


Theoretical massNumber of molelcules
Total (without water)48,8371
Polymers48,8371
Non-polymers00
Water36020
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.684, 87.279, 93.504
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein 4-hydroxybutyrate CoA-transferase


Mass: 48836.629 Da / Num. of mol.: 1 / Mutation: I192G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porphyromonas gingivalis (bacteria) / Strain: W83 / Gene: abfT-2, PG_1956 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: Q7MTJ6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.26 Å3/Da / Density % sol: 45.48 %
Description: The structure factor file contains Friedel pairs
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop
Details: Protein solution: 20 mM Tris-HCl pH 7.5, 100 mM NaCl, 5 mM Acetyl-CoA. Reservoir solution: 200 mM Ammonium citrate pH 5.0, 20% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.979 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Apr 30, 2008 / 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: 2.8→29.35 Å / Num. all: 21251 / Num. obs: 21251 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 28.5 Å2 / Rmerge(I) obs: 0.112 / Rsym value: 0.097 / Net I/σ(I): 12.43
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.354 / Mean I/σ(I) obs: 2.25 / Rsym value: 0.324 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0003refinement
ADSCQuantumdata collection
DENZOdata reduction
SCALEPACKdata scaling
SnBphasing
SOLVEphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.8→29.35 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.88 / SU B: 34.071 / SU ML: 0.302 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.406 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: The Friedel pairs were used in phasing. Program CNS 1.2 has also been used in refinement
RfactorNum. reflection% reflectionSelection details
Rfree0.25967 505 4.8 %RANDOM
Rwork0.19863 ---
obs0.20172 10089 100 %-
all-21251 --
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: 24.309 Å2
Baniso -1Baniso -2Baniso -3
1-1.43 Å20 Å20 Å2
2---1.98 Å20 Å2
3---0.55 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.47 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.56 Å0.33 Å
Refinement stepCycle: LAST / Resolution: 2.8→29.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3018 0 0 20 3038
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0330.0223077
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.8061.9484157
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9755382
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.74523.688141
X-RAY DIFFRACTIONr_dihedral_angle_3_deg25.2215534
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7661524
X-RAY DIFFRACTIONr_chiral_restr0.1770.2465
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022327
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2990.21633
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.350.22105
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1980.2104
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.340.217
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1210.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2191.51973
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.07523104
X-RAY DIFFRACTIONr_scbond_it3.57531229
X-RAY DIFFRACTIONr_scangle_it5.5994.51053
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 34 -
Rwork0.234 648 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 13.3542 Å / Origin y: 5.1715 Å / Origin z: 15.1827 Å
111213212223313233
T-0.0329 Å20.0121 Å20.0016 Å2-0.0237 Å2-0.0304 Å2---0.0019 Å2
L0.6884 °20.3462 °2-0.1697 °2-1.3709 °2-1.1791 °2--1.4346 °2
S-0.0297 Å °0.0584 Å °-0.1483 Å °-0.081 Å °0.0072 Å °-0.0954 Å °0.1341 Å °-0.0506 Å °0.0225 Å °

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