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- PDB-1vh9: Crystal structure of a putative thioesterase -

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Basic information

Entry
Database: PDB / ID: 1vh9
TitleCrystal structure of a putative thioesterase
ComponentsHypothetical protein ybdB
KeywordsStructural genomics / unknown function
Function / homology
Function and homology information


thiolester hydrolase activity / acyl-CoA hydrolase activity / 1,4-dihydroxy-2-naphthoyl-CoA thioesterase activity / enterobactin biosynthetic process / Hydrolases; Acting on ester bonds; Thioester hydrolases / hydrolase activity, acting on ester bonds / identical protein binding / cytosol
Similarity search - Function
Proofreading thioesterase EntH / Phenylacetic acid degradation-related domain / Thioesterase domain / Thioesterase superfamily / Hotdog Thioesterase / Thiol Ester Dehydrase; Chain A / HotDog domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Proofreading thioesterase EntH
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsStructural GenomiX
CitationJournal: Proteins / Year: 2005
Title: Structural analysis of a set of proteins resulting from a bacterial genomics project
Authors: Badger, J. / Sauder, J.M. / Adams, J.M. / Antonysamy, S. / Bain, K. / Bergseid, M.G. / Buchanan, S.G. / Buchanan, M.D. / Batiyenko, Y. / Christopher, J.A. / Emtage, S. / Eroshkina, A. / ...Authors: Badger, J. / Sauder, J.M. / Adams, J.M. / Antonysamy, S. / Bain, K. / Bergseid, M.G. / Buchanan, S.G. / Buchanan, M.D. / Batiyenko, Y. / Christopher, J.A. / Emtage, S. / Eroshkina, A. / Feil, I. / Furlong, E.B. / Gajiwala, K.S. / Gao, X. / He, D. / Hendle, J. / Huber, A. / Hoda, K. / Kearins, P. / Kissinger, C. / Laubert, B. / Lewis, H.A. / Lin, J. / Loomis, K. / Lorimer, D. / Louie, G. / Maletic, M. / Marsh, C.D. / Miller, I. / Molinari, J. / Muller-Dieckmann, H.J. / Newman, J.M. / Noland, B.W. / Pagarigan, B. / Park, F. / Peat, T.S. / Post, K.W. / Radojicic, S. / Ramos, A. / Romero, R. / Rutter, M.E. / Sanderson, W.E. / Schwinn, K.D. / Tresser, J. / Winhoven, J. / Wright, T.A. / Wu, L. / Xu, J. / Harris, T.J.
History
DepositionDec 1, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 30, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hypothetical protein ybdB
B: Hypothetical protein ybdB


Theoretical massNumber of molelcules
Total (without water)32,6972
Polymers32,6972
Non-polymers00
Water2,270126
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: Hypothetical protein ybdB

B: Hypothetical protein ybdB


Theoretical massNumber of molelcules
Total (without water)32,6972
Polymers32,6972
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area2620 Å2
ΔGint-20 kcal/mol
Surface area12240 Å2
MethodPISA
3
A: Hypothetical protein ybdB

A: Hypothetical protein ybdB


Theoretical massNumber of molelcules
Total (without water)32,6972
Polymers32,6972
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area2210 Å2
ΔGint-15 kcal/mol
Surface area12560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.822, 125.050, 83.050
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 Hypothetical protein ybdB / p15


Mass: 16348.525 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: YBDB, B0597, C0684 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A8Y8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 126 / 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: 2.14 Å3/Da / Density % sol: 42.44 %
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mMHEPES1droppH7.5
2150 mM1dropNaCl
310 mMmethionine1drop
410 %glycerol1drop
55 mMdithiothreitol1drop
610 mg/mlprotein1drop

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 32-ID / Wavelength: 0.9795 Å
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.15→34.59 Å / Num. all: 15701 / Num. obs: 15701 / % possible obs: 99.8 % / Redundancy: 6.43 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 24.9
Reflection shellResolution: 2.15→2.23 Å / Rmerge(I) obs: 0.442 / Mean I/σ(I) obs: 3.4 / % possible all: 99.6
Reflection
*PLUS
Redundancy: 6.4 % / Rmerge(I) obs: 0.07
Reflection shell
*PLUS
% possible obs: 99.6 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
REFMAC4refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→34.59 Å / σ(F): 0
RfactorNum. reflection
Rfree0.272 784
Rwork0.23 -
obs-15700
Solvent computationSolvent model: Babinet bulk solvent correction / Bsol: 367.881 Å2 / ksol: 0.935 e/Å3
Displacement parametersBiso mean: 38.504 Å2
Baniso -1Baniso -2Baniso -3
1-2.137 Å20 Å20 Å2
2--0.021 Å20 Å2
3----2.158 Å2
Refine Biso Class: all / Treatment: isotropic
Refinement stepCycle: LAST / Resolution: 2.15→34.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2086 0 0 126 2212
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.007
X-RAY DIFFRACTIONp_angle_d1.419
X-RAY DIFFRACTIONp_planar_tor1.402
X-RAY DIFFRACTIONp_chiral_restr0.101
X-RAY DIFFRACTIONp_plane_restr0.005
X-RAY DIFFRACTIONp_mcbond_it1.521
X-RAY DIFFRACTIONp_mcangle_it2.592
X-RAY DIFFRACTIONp_scbond_it2.164
X-RAY DIFFRACTIONp_scangle_it2.904
Software
*PLUS
Version: 4 / Classification: refinement
Refinement
*PLUS
Rfactor Rwork: 0.23
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.4

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