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- PDB-1vh5: Crystal structure of a putative thioesterase -

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Basic information

Entry
Database: PDB / ID: 1vh5
TitleCrystal structure of a putative thioesterase
ComponentsHypothetical protein ydiI
KeywordsStructural genomics / unknown function / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


1,4-dihydroxy-2-naphthoyl-CoA hydrolase / acyl-CoA hydrolase activity / 1,4-dihydroxy-2-naphthoyl-CoA thioesterase activity / menaquinone biosynthetic process / hydrolase activity / cytosol
Similarity search - Function
1,4-dihydroxy-2-naphthoyl-CoA hydrolase, MenI / 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
1,4-dihydroxy-2-naphthoyl-CoA hydrolase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.34 Å
AuthorsBurley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC)
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: Version format compliance
Revision 1.3Sep 13, 2017Group: Refinement description / Category: refine / software
Item: _refine.pdbx_ls_cross_valid_method / _refine.pdbx_method_to_determine_struct / _software.name
Revision 1.4Feb 3, 2021Group: Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.5Dec 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 ydiI
B: Hypothetical protein ydiI


Theoretical massNumber of molelcules
Total (without water)32,6512
Polymers32,6512
Non-polymers00
Water6,846380
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2370 Å2
ΔGint-16 kcal/mol
Surface area12750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.624, 69.937, 49.662
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-279-

HOH

21B-274-

HOH

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Components

#1: Protein Hypothetical protein ydiI


Mass: 16325.684 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: YDII, B1686 / Production host: Escherichia coli (E. coli) / References: UniProt: P77781
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 380 / 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: 41.9 %
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: 0.9794, 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97941
21.54181
ReflectionResolution: 1.28→52.71 Å / Num. obs: 67624 / % possible obs: 94.6 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 11.6
Reflection shellResolution: 1.28→1.35 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 4.2 / % possible all: 94.6
Reflection
*PLUS
Highest resolution: 1.47 Å / Num. obs: 47125 / % possible obs: 98.6 % / Redundancy: 9.2 % / Rmerge(I) obs: 0.068
Reflection shell
*PLUS
% possible obs: 91.6 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 5.4

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
TRUNCATEdata reduction
REFMAC4refinement
CCP4(SCALAdata scaling
TRUNCATEdata scaling
RefinementMethod to determine structure: MAD / Resolution: 1.34→12.27 Å / Cross valid method: FREE R-VALUE / σ(F): 0
RfactorNum. reflection
Rfree0.228 2991
Rwork0.188 -
obs-59025
Solvent computationSolvent model: Babinet bulk solvent correction / Bsol: 59.753 Å2 / ksol: 0.631 e/Å3
Displacement parametersBiso mean: 19.94 Å2
Baniso -1Baniso -2Baniso -3
1--0.906 Å20 Å20 Å2
2--0.458 Å20 Å2
3---0.448 Å2
Refine Biso Class: all / Treatment: anisotropic
Refinement stepCycle: LAST / Resolution: 1.34→12.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2166 0 0 380 2546
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.013
X-RAY DIFFRACTIONp_angle_d1.5
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.733
X-RAY DIFFRACTIONp_mcangle_it2.481
X-RAY DIFFRACTIONp_scbond_it2.779
X-RAY DIFFRACTIONp_scangle_it4.107
X-RAY DIFFRACTIONp_plane_restr0.007
X-RAY DIFFRACTIONp_chiral_restr0.113
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor5.956
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Version: 4 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.47 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.5

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