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- PDB-3c8h: Crystal structure of the enterobactin esterase FES from Shigella ... -

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Basic information

Entry
Database: PDB / ID: 3c8h
TitleCrystal structure of the enterobactin esterase FES from Shigella flexneri in the presence of 2,3-Di-hydroxy-N-benzoyl-serine
ComponentsEnterochelin esterase
KeywordsHYDROLASE / alpha-beta-alpha sandwich / IroD / Iron aquisition / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


enterochelin esterase activity / iron(III)-enterobactin esterase / 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 / Immunoglobulin-like fold / Immunoglobulins ...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 / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Iron(III) enterobactin esterase / Iron(III) enterobactin esterase
Similarity search - Component
Biological speciesShigella flexneri 2a str. 2457T (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.48 Å
AuthorsKim, Y. / Maltseva, N. / Abergel, R. / Holzle, D. / Raymond, K. / 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. / Holzle, D. / Raymond, K. / Joachimiak, A.
History
DepositionFeb 12, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 26, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Enterochelin esterase
B: Enterochelin esterase
C: Enterochelin esterase
D: Enterochelin esterase


Theoretical massNumber of molelcules
Total (without water)185,2164
Polymers185,2164
Non-polymers00
Water5,999333
1
A: Enterochelin esterase


Theoretical massNumber of molelcules
Total (without water)46,3041
Polymers46,3041
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Enterochelin esterase


Theoretical massNumber of molelcules
Total (without water)46,3041
Polymers46,3041
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Enterochelin esterase


Theoretical massNumber of molelcules
Total (without water)46,3041
Polymers46,3041
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Enterochelin esterase


Theoretical massNumber of molelcules
Total (without water)46,3041
Polymers46,3041
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: Enterochelin esterase
B: Enterochelin esterase


Theoretical massNumber of molelcules
Total (without water)92,6082
Polymers92,6082
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3120 Å2
MethodPISA
6
C: Enterochelin esterase
D: Enterochelin esterase


Theoretical massNumber of molelcules
Total (without water)92,6082
Polymers92,6082
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.508, 48.777, 156.399
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Enterochelin esterase


Mass: 46304.078 Da / Num. of mol.: 4
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 333 / 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: 2.3 Å3/Da / Density % sol: 46.44 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 20 % PEG 3000, 0.1 M Tri-sodium citrate pH 5.6, 3 mM DHBS, 1 mM FeCl3, 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: 0.9793 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 3, 2006 / Details: Mirrors
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.48→47.23 Å / Num. all: 57160 / Num. obs: 57160 / % possible obs: 95.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 40.47 Å2 / Rsym value: 0.106 / Net I/σ(I): 8.6
Reflection shellResolution: 2.48→2.59 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 2.12 / Num. unique all: 4512 / Rsym value: 0.462 / % possible all: 76

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Processing

Software
NameClassification
PHENIXrefinement
SBC-Collectdata collection
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2B20

2b20


Resolution: 2.48→47.23 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: 1. TWINNING: TWIN LAW=-H,-K,L, TWIN FRACTION: 0.502. 2. Structure has been refined using PHENIX.REFINE, PHENIX.XTRIAGE programs. 3. When refining TLS, the output PDB file always has the ...Details: 1. TWINNING: TWIN LAW=-H,-K,L, TWIN FRACTION: 0.502. 2. Structure has been refined using PHENIX.REFINE, PHENIX.XTRIAGE programs. 3. When refining TLS, the output PDB file always has the ANISOU records for the atoms involved in TLS groups. The anisotropic B-factor in ANISOU records is the total B-factor (B_tls + B_individual). The isotropic equivalent B-factor in ATOM records is the mean of the trace of the ANISOU matrix divided by 10000 and multiplied by 8*pi^2 and represents the isotropic equivalent of the total B-factor (B_tls + B_individual). To obtain the individual B-factors, one needs to compute the TLS component (B_tls) using the TLS records in the PDB file header and then subtract it from the total B-factors (on the ANISOU records).
RfactorNum. reflection% reflectionSelection details
Rfree0.225 2886 5.06 %RANDOM
Rwork0.183 ---
all0.183 56986 --
obs0.183 56986 94.15 %-
Solvent computationBsol: 53.56 Å2 / ksol: 0.36 e/Å3
Displacement parametersBiso mean: 56.15 Å2
Baniso -1Baniso -2Baniso -3
1--4.61 Å20 Å20.15 Å2
2--11.16 Å20 Å2
3----6.54 Å2
Refinement stepCycle: LAST / Resolution: 2.48→47.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12378 0 0 333 12711
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.006
X-RAY DIFFRACTIONf_angle_d0.683
X-RAY DIFFRACTIONf_dihedral_angle_d14.225
X-RAY DIFFRACTIONf_chiral_restr0.049
X-RAY DIFFRACTIONf_plane_restr0.003
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree: 0.32 / Total num. of bins used: 20

Resolution (Å)Num. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs
2.48-2.521100.3916731873
2.52-2.571270.282279
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDMethodL11 (°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)
1refined0.1269-0.0290.00650.02340.00020.139-0.04150.120.05530.00820.108-0.02650.057-0.0587-0.06630.1267-0.0476-0.00650.2401-0.05370.137382.524421.286859.0346
20.05020.0410.02310.0886-0.02490.0877-0.0424-0.0734-0.01550.00830.1226-0.0301-0.0344-0.0947-0.07960.17550.0948-0.01480.2456-0.05880.1696
30.0839-0.0459-0.00990.0512-0.01770.0763-0.04250.03140.0279-0.0070.0983-0.0160.0506-0.0424-0.05510.1528-0.0575-0.00180.1579-0.02570.1348
40.111-0.0698-0.01980.11170.02020.0411-0.0093-0.07250.0118-0.07620.0340.0066-0.01370.0118-0.02440.12850.0282-0.00090.104-0.01350.1002
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C
4X-RAY DIFFRACTION4chain D

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