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- PDB-3eh7: The structure of a putative 4-hydroxybutyrate CoA-transferase fro... -

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Basic information

Entry
Database: PDB / ID: 3eh7
TitleThe structure of a putative 4-hydroxybutyrate CoA-transferase from Porphyromonas gingivalis W83
Components4-hydroxybutyrate CoA-transferase
KeywordsTRANSFERASE / Citrate lyase / 4-hydroxybutyrate CoA-transferase / Porphyromonas gingivalis / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


acetyl-CoA hydrolase activity / propionate metabolic process, methylcitrate cycle / 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 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
4-hydroxybutyrate CoA-transferase
Similarity search - Component
Biological speciesPorphyromonas gingivalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.05 Å
AuthorsCuff, M.E. / Duggan, E. / Gu, M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: TO BE PUBLISHED
Title: The structure of a putative 4-hydroxybutyrate CoA-transferase from Porphyromonas gingivalis W83
Authors: Cuff, M.E. / Duggan, E. / Gu, M. / Joachimiak, A.
History
DepositionSep 11, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 9, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 4-hydroxybutyrate CoA-transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4143
Polymers48,3431
Non-polymers712
Water4,486249
1
A: 4-hydroxybutyrate CoA-transferase
hetero molecules

A: 4-hydroxybutyrate CoA-transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,8286
Polymers96,6862
Non-polymers1424
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555x,x-y,-z1
Buried area4110 Å2
ΔGint-43 kcal/mol
Surface area30850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.704, 72.704, 133.694
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number153
Space group name H-MP3212
Detailsauthors state that the biological assembly is unknown

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Components

#1: Protein 4-hydroxybutyrate CoA-transferase


Mass: 48343.035 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porphyromonas gingivalis (bacteria) / Strain: W83 / Gene: abfT-1, PG_0690 / Plasmid: pmcsg7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q7MWD3
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 249 / 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: 2.11 Å3/Da / Density % sol: 41.7 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2M MgCl2, 0.1M Tris pH8.5, 16% PEG 4K, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97922 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 21, 2006
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97922 Å / Relative weight: 1
ReflectionResolution: 2.05→44.56 Å / Num. obs: 25521 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 11 % / Biso Wilson estimate: 30.5 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 6.3
Reflection shellResolution: 2.052→2.105 Å / Redundancy: 7 % / Rmerge(I) obs: 0.623 / Mean I/σ(I) obs: 2.7 / % possible all: 96.83

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Phasing

PhasingMethod: SAD
Phasing MADD res high: 2 Å / D res low: 50 Å / FOM : 0.225 / FOM acentric: 0.241 / FOM centric: 0 / Reflection: 27298 / Reflection acentric: 25485 / Reflection centric: 1813
Phasing MAD setR cullis acentric: 2.11 / R cullis centric: 1 / Highest resolution: 2 Å / Lowest resolution: 50 Å / Loc acentric: 0.2 / Loc centric: 0.1 / Power acentric: 0 / Power centric: 0 / Reflection acentric: 25485 / Reflection centric: 1813
Phasing MAD set shell

ID: 1 / R cullis centric: 1 / Power acentric: 0 / Power centric: 0

Resolution (Å)R cullis acentricLoc acentricLoc centricReflection acentricReflection centric
12.5-501.2310.68835
7.14-12.51.5110.642498
5-7.142.230.90.31051152
3.85-51.290.50.31946201
3.12-3.851.610.30.23121261
2.63-3.123.050.20.14555309
2.27-2.6310.770.106278359
2-2.273.010.108022398
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Se34.69711-0.391-0.885-0.010
2Se47.64196-0.762-0.879-0.0680
3Se67.8178-0.524-1.0430.0650
4Se39.51631-0.008-0.6240.0710
5Se39.110250.021-0.5690.1680
6Se39.95364-0.553-0.8970.1110
7Se50.42597-0.623-0.972-0.0140
8Se48.11994-0.348-1.0210.050
9Se31.95347-0.569-1.0840.110
10Se58.574630.011-0.6640.0990
11Se23.29985-0.915-1.108-0.0630
12Se63.61886-0.528-0.7480.1130
13Se52.61732-0.612-1.10.1410
Phasing MAD shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
12.5-500.3820.53401238835
7.14-12.50.4560.561052242498
5-7.140.4840.554012031051152
3.85-50.4420.488021471946201
3.12-3.850.3990.433033823121261
2.63-3.120.2860.305048644555309
2.27-2.630.1570.166066376278359
2-2.270.0660.069084208022398
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 27298
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
7.78-10061.60.784503
6.14-7.7854.20.887505
5.34-6.1453.70.879513
4.79-5.3458.50.877568
4.38-4.7954.90.918629
4.06-4.3852.50.918675
3.81-4.0654.40.9726
3.59-3.8157.10.891769
3.41-3.59580.888822
3.25-3.4158.50.875864
3.11-3.2557.80.842871
2.99-3.11600.84923
2.89-2.9962.30.847961
2.79-2.8960.90.864975
2.7-2.7967.70.8381043
2.62-2.767.40.8121053
2.55-2.6272.40.8181099
2.48-2.55710.8181113
2.42-2.4871.90.8111124
2.36-2.4274.50.8131196
2.31-2.3676.40.8331192
2.25-2.3179.90.8091241
2.21-2.2578.90.8171229
2.16-2.2181.20.8061283
2.12-2.1683.30.7851313
2.08-2.1280.80.7881286
2.04-2.0886.50.7661327
2-2.0485.80.7411495

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
DM5phasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
SHELXDphasing
SHELXEmodel building
SOLVEphasing
RESOLVEphasing
ARP/wARPmodel building
CCP4phasing
Omodel building
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.05→44.56 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.945 / WRfactor Rfree: 0.198 / WRfactor Rwork: 0.165 / Occupancy max: 1 / Occupancy min: 0.4 / FOM work R set: 0.877 / SU B: 9.881 / SU ML: 0.12 / SU R Cruickshank DPI: 0.202 / SU Rfree: 0.163 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.2 / ESU R Free: 0.162
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.208 1299 5.1 %RANDOM
Rwork0.171 ---
all0.173 25521 --
obs0.173 25521 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 78.73 Å2 / Biso mean: 26.712 Å2 / Biso min: 2.18 Å2
Baniso -1Baniso -2Baniso -3
1--1.85 Å2-0.92 Å20 Å2
2---1.85 Å20 Å2
3---2.77 Å2
Refinement stepCycle: LAST / Resolution: 2.05→44.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3060 0 2 249 3311
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0223174
X-RAY DIFFRACTIONr_bond_other_d0.0010.022131
X-RAY DIFFRACTIONr_angle_refined_deg1.4131.9674306
X-RAY DIFFRACTIONr_angle_other_deg0.9083.0015229
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.875414
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.86224.453137
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.06715556
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.1121518
X-RAY DIFFRACTIONr_chiral_restr0.0860.2493
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213550
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02611
X-RAY DIFFRACTIONr_mcbond_it0.7021.52011
X-RAY DIFFRACTIONr_mcbond_other0.1721.5824
X-RAY DIFFRACTIONr_mcangle_it1.28723244
X-RAY DIFFRACTIONr_scbond_it2.18731163
X-RAY DIFFRACTIONr_scangle_it3.5334.51054
LS refinement shellResolution: 2.052→2.105 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.263 95 -
Rwork0.228 1709 -
all-1804 -
obs--96.83 %
Refinement TLS params.Method: refined / Origin x: 33.1235 Å / Origin y: 1.6164 Å / Origin z: 9.1852 Å
111213212223313233
T0.073 Å2-0.0107 Å2-0.0101 Å2-0.0174 Å20.0042 Å2--0.1073 Å2
L1.1646 °20.2656 °20.5011 °2-0.7448 °20.2282 °2--1.3607 °2
S0.1114 Å °-0.1039 Å °-0.1917 Å °0.0591 Å °-0.025 Å °-0.1193 Å °0.1751 Å °-0.113 Å °-0.0863 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 431
2X-RAY DIFFRACTION1A434 - 682

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