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- PDB-1s5u: Crystal Structure of Hypothetical Protein EC709 from Escherichia coli -

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Basic information

Entry
Database: PDB / ID: 1s5u
TitleCrystal Structure of Hypothetical Protein EC709 from Escherichia coli
ComponentsProtein ybgC
KeywordsHYDROLASE / Structural genomics / Hypothetical protein / Thioesterase fold / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


thiolester hydrolase activity / fatty acyl-CoA hydrolase activity / Hydrolases; Acting on ester bonds; Thioester hydrolases / lipid metabolic process / plasma membrane
Similarity search - Function
Tol-Pal system-associated acyl-CoA thioesterase / 4-hydroxybenzoyl-CoA thioesterase, active site / 4-hydroxybenzoyl-CoA thioesterase family active site. / Acyl-CoA thioester hydrolase YbgC/YbaW family / Thioesterase domain / Thioesterase superfamily / Hotdog Thioesterase / Thiol Ester Dehydrase; Chain A / HotDog domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Acyl-CoA thioester hydrolase YbgC
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å
AuthorsKim, Y. / Joachimiak, A. / Skarina, T. / Savchenko, A. / Edwards, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal Structure of Hypothetical Protein EC709 from Escherichia coli
Authors: Kim, Y. / Joachimiak, A. / Skarina, T. / Savchenko, A. / Edwards, A.
History
DepositionJan 21, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 11, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 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: Protein ybgC
B: Protein ybgC
C: Protein ybgC
D: Protein ybgC
E: Protein ybgC
F: Protein ybgC
G: Protein ybgC
H: Protein ybgC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,83425
Polymers127,3718
Non-polymers1,46317
Water13,475748
1
A: Protein ybgC
B: Protein ybgC
C: Protein ybgC
D: Protein ybgC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,38612
Polymers63,6854
Non-polymers7018
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9450 Å2
ΔGint-114 kcal/mol
Surface area22790 Å2
MethodPISA
2
E: Protein ybgC
F: Protein ybgC
G: Protein ybgC
H: Protein ybgC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,44813
Polymers63,6854
Non-polymers7639
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8680 Å2
ΔGint-74 kcal/mol
Surface area23610 Å2
MethodPISA
3
A: Protein ybgC
B: Protein ybgC
C: Protein ybgC
D: Protein ybgC
hetero molecules

E: Protein ybgC
F: Protein ybgC
G: Protein ybgC
H: Protein ybgC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,83425
Polymers127,3718
Non-polymers1,46317
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_645x+1,y-1,z1
Buried area19850 Å2
ΔGint-185 kcal/mol
Surface area44680 Å2
MethodPISA
4


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18630 Å2
ΔGint-185 kcal/mol
Surface area45900 Å2
MethodPISA
5
A: Protein ybgC
B: Protein ybgC
C: Protein ybgC
D: Protein ybgC
hetero molecules

E: Protein ybgC
F: Protein ybgC
G: Protein ybgC
H: Protein ybgC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,83425
Polymers127,3718
Non-polymers1,46317
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_545x,y-1,z1
Buried area21470 Å2
ΔGint-204 kcal/mol
Surface area43060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.108, 70.187, 71.525
Angle α, β, γ (deg.)103.47, 95.15, 97.58
Int Tables number1
Space group name H-MP1
Detailstetramer:There are two tetramers in the asymmetric unit.

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Components

#1: Protein
Protein ybgC / Hypothetical Protein EC709


Mass: 15921.326 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: YBGC, B0736, C0815, Z0904, ECS0771, SF0561, S0574 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: P0A8Z3
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 748 / 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: 2.15 Å3/Da / Density % sol: 42.85 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.3
Details: ammonium sulfate, sodium cacodylate, sodium chloride, ethylene glycol, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.28, 0.9795, 0.9793, 0.956
DetectorType: SBC-2 / Detector: CCD / Date: Dec 18, 2003 / Details: mirror
RadiationMonochromator: double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.281
20.97951
30.97931
40.9561
ReflectionResolution: 1.7→23.64 Å / Num. all: 105882 / Num. obs: 102856 / % possible obs: 88.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.28 % / Biso Wilson estimate: 18.4 Å2 / Rmerge(I) obs: 0.041 / Net I/σ(I): 14.2
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.227 / Mean I/σ(I) obs: 3.34 / % possible all: 46.9

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Processing

Software
NameVersionClassification
CNS1.1refinement
SBC-Collectdata collection
HKL-2000data scaling
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.7→23.64 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 778265.91 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.23 10122 10 %RANDOM
Rwork0.2 ---
all0.203 115913 --
obs0.2 100881 86.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 50.5806 Å2 / ksol: 0.384944 e/Å3
Displacement parametersBiso mean: 24.4 Å2
Baniso -1Baniso -2Baniso -3
1--2.09 Å2-3.66 Å2-2.73 Å2
2---1.09 Å21.62 Å2
3---3.17 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 1.7→23.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8488 0 80 748 9316
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.74
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.651.5
X-RAY DIFFRACTIONc_mcangle_it2.262
X-RAY DIFFRACTIONc_scbond_it3.012
X-RAY DIFFRACTIONc_scangle_it3.82.5
LS refinement shellResolution: 1.7→1.81 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.312 899 9.8 %
Rwork0.264 8231 -
obs-8231 46.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4LIGAND.PARAMLIGAND.TOP

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