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- PDB-4fle: Crystal structure of the esterase YqiA (YE3661) from Yersinia ent... -

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Basic information

Entry
Database: PDB / ID: 4fle
TitleCrystal structure of the esterase YqiA (YE3661) from Yersinia enterocolitica, Northeast Structural Genomics Consortium Target YeR85
Componentsesterase
KeywordsHYDROLASE / Structural Genomics / PSI-Biology / Northeast Structural Genomics Consortium / NESG / alpha-beta protein / Rossmann Fold / Displays esterase activity toward palmitoyl-CoA and pNP-butyrate
Function / homologyUncharacterised protein family UPF0227/Esterase YqiA / Uncharacterised protein family (UPF0227) / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Esterase YqiA
Function and homology information
Biological speciesYersinia enterocolitica subsp. enterocolitica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsForouhar, F. / Lew, S. / Seetharaman, J. / Shastry, R. / Kohan, E. / Maglaqui, M. / Mao, L. / Xiao, R. / Acton, T.B. / Everett, J.K. ...Forouhar, F. / Lew, S. / Seetharaman, J. / Shastry, R. / Kohan, E. / Maglaqui, M. / Mao, L. / Xiao, R. / Acton, T.B. / Everett, J.K. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal structure of the esterase YqiA (YE3661) from Yersinia enterocolitica, Northeast Structural Genomics Consortium Target YeR85 (CASP Target)
Authors: Forouhar, F. / Lew, S. / Seetharaman, J. / Shastry, R. / Kohan, E. / Maglaqui, M. / Mao, L. / Xiao, R. / Acton, T.B. / Everett, J.K. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast ...Authors: Forouhar, F. / Lew, S. / Seetharaman, J. / Shastry, R. / Kohan, E. / Maglaqui, M. / Mao, L. / Xiao, R. / Acton, T.B. / Everett, J.K. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium
History
DepositionJun 14, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 8, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.2Oct 16, 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 / pdbx_modification_feature / 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

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Assembly

Deposited unit
A: esterase


Theoretical massNumber of molelcules
Total (without water)23,0751
Polymers23,0751
Non-polymers00
Water3,297183
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.056, 79.543, 46.060
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Detailsmonomer according to static light scattering.

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Components

#1: Protein esterase


Mass: 23075.115 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia enterocolitica subsp. enterocolitica (bacteria)
Strain: 8081 / Gene: YE3661 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: A1JQU0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 183 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.19 Å3/Da / Density % sol: 43.72 %
Crystal growTemperature: 277 K / Method: microbatch underoil / pH: 8
Details: Protein solution: 10 mM Tris (pH 7.5), 100 mM sodium chloride, and 5 mM DTT. Crystillization solution: 100 mM Tris (pH 8), 24% PEG 20K, and 100 mM Mg(NO3)2:6H2O. , microbatch underoil, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97911 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 8, 2012 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97911 Å / Relative weight: 1
ReflectionResolution: 2.1→46.06 Å / Num. obs: 22631 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Biso Wilson estimate: 9.8 Å2 / Rmerge(I) obs: 0.067 / Rsym value: 0.058 / Net I/σ(I): 31.5
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.207 / Mean I/σ(I) obs: 7.35 / Rsym value: 0.214 / % possible all: 92.2

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Processing

Software
NameVersionClassification
CNS1.3refinement
ADSCQuantumdata collection
DENZOdata reduction
SCALEPACKdata scaling
SHELXSphasing
RefinementMethod to determine structure: SAD / Resolution: 2.1→46.06 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 161453.65 / 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
Rfree0.249 2078 9.4 %RANDOM
Rwork0.194 ---
obs0.194 22145 97.1 %-
all-22631 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 54.5435 Å2 / ksol: 0.38 e/Å3
Displacement parametersBiso mean: 18.8 Å2
Baniso -1Baniso -2Baniso -3
1--0.85 Å20 Å20 Å2
2---0.49 Å20 Å2
3---1.34 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.15 Å0.07 Å
Refinement stepCycle: LAST / Resolution: 2.1→46.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1543 0 0 183 1726
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
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_d23.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.72
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.246 342 9.9 %
Rwork0.186 3109 -
obs--91.6 %

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