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- PDB-3mga: 2.4 Angstrom Crystal Structure of Ferric Enterobactin Esterase (f... -

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Basic information

Entry
Database: PDB / ID: 3mga
Title2.4 Angstrom Crystal Structure of Ferric Enterobactin Esterase (fes) from Salmonella typhimurium
ComponentsEnterochelin esterase
KeywordsHYDROLASE / Center for Structural Genomics of Infectious Diseases / CSGID / Ferric Enterobactin Esterase
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
DI(HYDROXYETHYL)ETHER / Enterochelin esterase
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsMinasov, G. / Wawrzak, Z. / Skarina, T. / Onopriyenko, O. / Papazisi, L. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: TO BE PUBLISHED
Title: 2.4 Angstrom Crystal Structure of Ferric Enterobactin Esterase (fes) from Salmonella typhimurium.
Authors: Minasov, G. / Wawrzak, Z. / Skarina, T. / Onopriyenko, O. / Papazisi, L. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionApr 5, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 21, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,06011
Polymers92,5242
Non-polymers5369
Water3,297183
1
A: Enterochelin esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,5315
Polymers46,2621
Non-polymers2694
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Enterochelin esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,5296
Polymers46,2621
Non-polymers2675
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.489, 125.552, 66.606
Angle α, β, γ (deg.)90.00, 91.43, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Enterochelin esterase / FERRIC ENTEROBACTIN ESTERASE


Mass: 46261.934 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Genus: fes / Strain: LT2 / Gene: fes, STM0586 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8ZR39

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Non-polymers , 6 types, 192 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 183 / 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: 2.37 Å3/Da / Density % sol: 48.13 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: Protein solution: 0.3M NaCl, 10mM HEPES (pH 7.5); Screen solution: 0.2M Sodium chloride, 0.1m Sodium citrate pH 5.6, 1% DMSO, 20% PEG3350, 0.3M NDSB, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 5, 2010 / Details: Beryllium lenses
RadiationMonochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. all: 33389 / Num. obs: 33389 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Redundancy: 5.3 % / Biso Wilson estimate: 45.7 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 23.5
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 2.61 / Num. unique all: 1643 / % possible all: 99

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
CRANKphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.4→29.55 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.912 / SU B: 12.649 / SU ML: 0.137 / Isotropic thermal model: Refined Individually / Cross valid method: THROUGHOUT / ESU R: 0.544 / ESU R Free: 0.277 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24498 1677 5.1 %RANDOM
Rwork0.1886 ---
all0.19147 31524 --
obs0.19147 31524 98.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 49.679 Å2
Baniso -1Baniso -2Baniso -3
1--3.09 Å20 Å20.99 Å2
2--0.52 Å20 Å2
3---2.62 Å2
Refinement stepCycle: LAST / Resolution: 2.4→29.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6337 0 30 183 6550
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0216705
X-RAY DIFFRACTIONr_bond_other_d0.0010.024602
X-RAY DIFFRACTIONr_angle_refined_deg1.2821.9259180
X-RAY DIFFRACTIONr_angle_other_deg0.791311056
X-RAY DIFFRACTIONr_dihedral_angle_1_deg1.9065816
X-RAY DIFFRACTIONr_dihedral_angle_2_deg23.3522.667330
X-RAY DIFFRACTIONr_dihedral_angle_3_deg8.779151001
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.71569
X-RAY DIFFRACTIONr_chiral_restr0.0740.2945
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0217607
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021476
X-RAY DIFFRACTIONr_mcbond_it0.7321.54035
X-RAY DIFFRACTIONr_mcbond_other0.171.51613
X-RAY DIFFRACTIONr_mcangle_it1.31726517
X-RAY DIFFRACTIONr_scbond_it2.16532670
X-RAY DIFFRACTIONr_scangle_it3.3554.52663
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 114 -
Rwork0.231 2299 -
obs-2299 97.85 %
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)
12.1015-0.0247-0.38063.2307-0.33044.8843-0.1040.49720.0588-0.54270.15670.5409-0.1218-0.3686-0.05270.1815-0.0752-0.10230.19860.00860.12198.315924.2630.7538
24.9141-2.2687-1.511516.38575.21728.0939-0.19950.3553-0.066-0.51720.5925-0.71050.29320.7957-0.3930.1684-0.1245-0.02390.3131-0.01650.060220.418519.3132-1.2127
35.1843.32952.11472.84640.54692.1947-0.1584-0.0680.21980.0413-0.0480.1570.0041-0.04790.20650.19840.02760.03120.0572-0.06120.115620.52630.59820.7458
41.96070.7092-0.49532.85160.43182.2889-0.0538-0.108-0.14910.1683-0.0336-0.19190.15910.330.08740.02310.0143-0.00550.05690.02560.026836.891724.830325.3313
50.13091.80180.567833.570710.473.2688-0.0642-0.0054-0.4271-0.99341.2032-3.4818-0.26050.3715-1.1391.12760.26970.02890.66830.26862.069437.41893.845319.4158
61.99860.04940.29154.08270.714.81570.0321-0.0286-0.38110.0929-0.218-0.03320.47790.13770.18580.1171-0.01190.05530.02730.0030.106424.754313.127525.4285
75.65430.60871.44324.10280.78454.154-0.03971.49580.2516-0.71090.1265-0.5160.07980.4706-0.08690.14250.02890.11350.50190.15690.159269.060160.50914.2434
89.0057-3.5493.312314.8313-0.82966.9231-0.02790.80930.3308-1.03140.0230.6971-0.5045-0.37140.00490.3021-0.03080.00820.5980.12190.100257.0165.82021.7698
95.80121.946-1.58762.5188-0.56931.50490.0780.0941-0.34670.0462-0.0792-0.27030.14920.11340.00120.08130.0307-0.01860.10520.07490.131156.733751.347922.2607
102.58610.52210.03333.0067-0.18991.99010.112-0.25480.17410.19070.01340.20520.0693-0.2764-0.12540.0179-0.01940.01220.07570.00720.030340.2356.432528.2286
115.1226-2.00240.45069.1822-3.65133.68030.13490.08290.82460.26170.00170.2809-0.5588-0.2383-0.13670.15560.03350.0250.0833-0.06070.288842.145275.758428.3628
122.39970.8104-1.00823.2763-1.79762.45380.2262-0.42120.47360.669-0.3238-0.2139-0.55830.34430.09760.2193-0.0544-0.05960.1705-0.02230.206653.203967.733129.5393
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 102
2X-RAY DIFFRACTION2A103 - 137
3X-RAY DIFFRACTION3A138 - 173
4X-RAY DIFFRACTION4A174 - 317
5X-RAY DIFFRACTION5A318 - 339
6X-RAY DIFFRACTION6A340 - 403
7X-RAY DIFFRACTION7B9 - 101
8X-RAY DIFFRACTION8B102 - 136
9X-RAY DIFFRACTION9B137 - 173
10X-RAY DIFFRACTION10B174 - 317
11X-RAY DIFFRACTION11B318 - 345
12X-RAY DIFFRACTION12B346 - 403

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