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- PDB-3c8d: Crystal structure of the enterobactin esterase FES from Shigella ... -

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Basic information

Entry
Database: PDB / ID: 3c8d
TitleCrystal structure of the enterobactin esterase FES from Shigella flexneri in the presence of 2,3-Di-hydroxy-N-benzoyl-glycine
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
CITRIC ACID / 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: 1.8 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 11, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)184,4848
Polymers183,7164
Non-polymers7684
Water20,1771120
1
A: Enterochelin esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,1212
Polymers45,9291
Non-polymers1921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Enterochelin esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,1212
Polymers45,9291
Non-polymers1921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Enterochelin esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3133
Polymers45,9291
Non-polymers3842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Enterochelin esterase


Theoretical massNumber of molelcules
Total (without water)45,9291
Polymers45,9291
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: Enterochelin esterase
B: Enterochelin esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,2424
Polymers91,8582
Non-polymers3842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3250 Å2
MethodPISA
6
C: Enterochelin esterase
D: Enterochelin esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,2424
Polymers91,8582
Non-polymers3842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.297, 155.972, 48.480
Angle α, β, γ (deg.)90.00, 90.01, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Enterochelin esterase


Mass: 45928.922 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: Chemical
ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H8O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1120 / 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: 2.29 Å3/Da / Density % sol: 46.3 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 20% PEG 3000, 0.1 M Citrate pH 5.5, 3 mM DHBG, 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: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 8, 2006 / Details: Mirrors
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
Reflection twinType: merohedral / Operator: h,-k,-l / Fraction: 0.354
ReflectionResolution: 1.8→48.48 Å / Num. all: 149451 / Num. obs: 149451 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Biso Wilson estimate: 26.65 Å2 / Rsym value: 0.062 / Net I/σ(I): 10.4
Reflection shellResolution: 1.8→1.81 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 2.39 / Num. unique all: 13227 / Rsym value: 0.379 / % possible all: 86.7

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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: 1.8→48.48 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: 0.354. 2. When refining TLS, the output PDB file always has the ANISOU records for the atoms involved in TLS groups. The anisotropic B-factor ...Details: 1. TWINNING: TWIN LAW: h,-k,-l, TWIN FRACTION: 0.354. 2. 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
Rfree0.194 14889 9.97 %RANDOM
Rwork0.15 ---
all-149377 --
obs-149377 90.03 %-
Solvent computationBsol: 42.52 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 39.09 Å2
Baniso -1Baniso -2Baniso -3
1--2.03 Å2-0 Å20.58 Å2
2---7.16 Å2-0 Å2
3---9.19 Å2
Refinement stepCycle: LAST / Resolution: 1.8→48.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12555 0 52 1120 13727
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.004
X-RAY DIFFRACTIONf_angle_d0.637
X-RAY DIFFRACTIONf_dihedral_angle_d12.042
X-RAY DIFFRACTIONf_chiral_restr0.049
X-RAY DIFFRACTIONf_plane_restr0.003
LS refinement shellResolution: 1.8→1.83 Å / Total num. of bins used: 10
RfactorNum. reflection
Rfree0.34 644
Rwork0.31 5615
obs-6259
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)
10.09370.0222-0.01450.0265-0.0190.0625-0.0436-0.0069-0.0522-0.0155-0.0008-0.01450.0103-0.01460.03920.0811-0.00280.02250.092-0.01950.10681.3076-0.28531.3719
20.0565-0.0152-0.01170.03890.01660.0458-0.01350.02330.01720.0337-0.01-0.01350.0096-0.02960.01760.08690.0015-0.01450.1171-0.00070.08120.746535.1929-3.3536
30.05290.01950.01630.06710.00140.0715-0.0215-0.0197-0.027-0.0386-0.0208-0.036-0.0251-0.03570.03930.14450.0110.00790.1572-0.00410.148256.28974.157125.4354
40.0538-0.03540.0160.0657-0.01980.0803-0.03240.01380.07520.01360.005-0.06460.03-0.02060.02490.09250.0098-0.03050.1112-0.01370.14256.779839.292620.2906
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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