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- PDB-3c87: Crystal structure of the enterobactin esterase FES from Shigella ... -

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Basic information

Entry
Database: PDB / ID: 3c87
TitleCrystal structure of the enterobactin esterase FES from Shigella flexneri in the presence of enterobactin
ComponentsEnterochelin esterase
KeywordsHYDROLASE / siderophore / IroD / alpha-beta-alpha sandwich / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


enterochelin esterase activity / iron ion transport / iron ion binding / cytoplasm
Similarity search - Function
Enterochelin esterase, N-terminal / Enterochelin esterase, N-terminal / Esterase-like / Putative esterase / Alpha/Beta hydrolase fold, catalytic domain / Immunoglobulin E-set / Alpha/Beta hydrolase fold / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like ...Enterochelin esterase, N-terminal / Enterochelin esterase, N-terminal / Esterase-like / Putative esterase / Alpha/Beta hydrolase fold, catalytic domain / Immunoglobulin E-set / Alpha/Beta hydrolase fold / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Enterochelin esterase / Enterochelin esterase
Similarity search - Component
Biological speciesShigella flexneri 2a str. 2457T (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.17 Å
AuthorsKim, Y. / Maltseva, N. / Abergel, R. / Raymond, K. / Holzle, D. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Siderophore Mediated Iron Acquisition: Structure and Specificity of Enterobactin Esterase from Shigella flexneri.
Authors: Kim, Y. / Maltseva, N. / Abergel, R. / Raymond, K. / Holzle, D. / Joachimiak, A.
History
DepositionFeb 11, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 26, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Enterochelin esterase
B: Enterochelin esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,7264
Polymers92,6082
Non-polymers1182
Water5,441302
1
A: Enterochelin esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3272
Polymers46,3041
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Enterochelin esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3992
Polymers46,3041
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.305, 113.245, 151.123
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Enterochelin esterase


Mass: 46304.078 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shigella flexneri 2a str. 2457T (bacteria)
Species: Shigella flexneri / Strain: 2457T / Serotype 2a / Gene: fes, S0503, SF0497 / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q83SB9, UniProt: A0A0H2VTI6*PLUS
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 302 / 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: 2.19 Å3/Da / Density % sol: 43.72 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 20 % PEG 8000, 0.1 M Phosphate-citrate pH 4.2, 0.2 M NaCl, 5 mM Enterobactin, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 31, 2007 / Details: Mirrors
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.17→46.03 Å / Num. all: 43586 / Num. obs: 43586 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.1 % / Biso Wilson estimate: 35.98 Å2 / Rsym value: 0.124 / Net I/σ(I): 8.5
Reflection shellResolution: 2.17→2.25 Å / Redundancy: 7 % / Mean I/σ(I) obs: 3.25 / Num. unique all: 4165 / Rsym value: 0.697 / % possible all: 96.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SBC-Collectdata collection
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
SHELXL-97phasing
RESOLVEphasing
MLPHAREphasing
RefinementMethod to determine structure: SAD / Resolution: 2.17→46.03 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.936 / SU B: 11.702 / SU ML: 0.152 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.286 / ESU R Free: 0.209
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
RfactorNum. reflection% reflectionSelection details
Rfree0.234 2189 5 %RANDOM
Rwork0.19 ---
all0.192 41249 --
obs0.192 41249 98.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.37 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20 Å20 Å2
2--0.19 Å20 Å2
3----0.15 Å2
Refinement stepCycle: LAST / Resolution: 2.17→46.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6252 0 6 302 6560
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0226607
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6241.9279034
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5615795
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.74123.622323
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.006151050
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7091550
X-RAY DIFFRACTIONr_chiral_restr0.1130.2931
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025190
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2140.22850
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.310.24364
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1590.2314
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined00.21
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1920.248
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1620.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0041.53945
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.88326377
X-RAY DIFFRACTIONr_scbond_it2.79332909
X-RAY DIFFRACTIONr_scangle_it4.2774.52657
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.17→2.226 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 148 -
Rwork0.225 2729 -
obs-2854 89.6 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.6195-0.46760.28911.9945-0.32770.86970.1048-0.0145-0.01930.0534-0.1213-0.0267-0.07440.07680.0165-0.0998-0.058-0.0014-0.08130.0057-0.12789.019853.022817.6294
20.75720.71860.22741.9091-0.11990.8418-0.02430.03210.0482-0.130.08540.06040.1102-0.0808-0.0611-0.1245-0.01310.0059-0.0678-0.0074-0.088114.100853.879753.6496
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA4 - 3967 - 399
2X-RAY DIFFRACTION2BB4 - 3967 - 399

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