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- PDB-4nmw: Crystal Structure of Carboxylesterase BioH from Salmonella enterica -

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Basic information

Entry
Database: PDB / ID: 4nmw
TitleCrystal Structure of Carboxylesterase BioH from Salmonella enterica
ComponentsPimelyl-[acyl-carrier protein] methyl ester esterase
KeywordsHYDROLASE / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases / CSGID / alpha-beta structure / alpha-beta-alpha sandwich
Function / homology
Function and homology information


pimelyl-[acyl-carrier protein] methyl ester esterase / biotin biosynthetic process / carboxylic ester hydrolase activity / cytoplasm
Similarity search - Function
Pimeloyl-[acyl-carrier protein] methyl ester esterase / : / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Pimeloyl-[acyl-carrier protein] methyl ester esterase
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.496 Å
AuthorsKim, Y. / Zhou, M. / Grimshaw, S. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: Crystal Structure of Carboxylesterase BioH from Salmonella enterica
Authors: Kim, Y. / Zhou, M. / Grimshaw, S. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionNov 15, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2013Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pimelyl-[acyl-carrier protein] methyl ester esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0863
Polymers28,9441
Non-polymers1422
Water5,386299
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)99.059, 54.211, 66.769
Angle α, β, γ (deg.)90.00, 126.13, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-504-

HOH

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Components

#1: Protein Pimelyl-[acyl-carrier protein] methyl ester esterase / Biotin synthesis protein BioH / Carboxylesterase BioH


Mass: 28943.973 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Strain: LT2 / Gene: bioH, STM3509 / Plasmid: pMCSG53 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) bold
References: UniProt: Q8ZLI9, pimelyl-[acyl-carrier protein] methyl ester esterase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 299 / 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: 2.5 Å3/Da / Density % sol: 50.83 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M magnessium chloride, 0.1 M MES pH 6.5, 10 %(w/v) PEG4000, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97924 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 27, 2013 / Details: mirrors
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97924 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. all: 45820 / Num. obs: 45820 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 12.55 Å2 / Rsym value: 0.062 / Net I/σ(I): 11.3
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 2.54 / Num. unique all: 2258 / Rsym value: 0.345 / % possible all: 97.3

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
SHELXSphasing
MLPHAREphasing
DMmodel building
PHENIX(phenix.refine: 1.8.4_1496)refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RefinementMethod to determine structure: SAD / Resolution: 1.496→26.963 Å / SU ML: 0.13 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 17.21 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.179 2144 5.09 %random
Rwork0.141 ---
obs0.143 42118 91.17 %-
all-42118 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 12.55 Å2
Refinement stepCycle: LAST / Resolution: 1.496→26.963 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1974 0 8 299 2281
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092289
X-RAY DIFFRACTIONf_angle_d1.2653150
X-RAY DIFFRACTIONf_dihedral_angle_d14.584848
X-RAY DIFFRACTIONf_chiral_restr0.082344
X-RAY DIFFRACTIONf_plane_restr0.005422
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
1.4963-1.53110.2118840.14981481156551
1.5311-1.56940.2038950.13111909200465
1.5694-1.61190.19421110.12452217232876
1.6119-1.65930.1511300.12922486261686
1.6593-1.71280.17211550.12792733288894
1.7128-1.7740.15941580.13112844300299
1.774-1.84510.19691480.132929223070100
1.8451-1.9290.19571250.131529523077100
1.929-2.03070.19911700.130829023072100
2.0307-2.15780.1981510.132629293080100
2.1578-2.32440.15841750.13528943069100
2.3244-2.55810.17261530.14329423095100
2.5581-2.92790.20571670.155729163083100
2.9279-3.68740.16551550.147529293084100
3.6874-26.96770.16921670.14762918308597

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