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- PDB-6gi2: Crystal structure of the ferric enterobactin esterase (pfeE) muta... -

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Basic information

Entry
Database: PDB / ID: 6gi2
TitleCrystal structure of the ferric enterobactin esterase (pfeE) mutant(S157A) from Pseudomonas aeruginosa in complex with Tris-catechol vector
ComponentsFerric enterobactin esterase
KeywordsHYDROLASE / PfeE / PA2689
Function / homology
Function and homology information


iron(III)-enterobactin esterase / carboxylic ester hydrolase activity / hydrolase activity, acting on ester bonds / periplasmic space
Similarity search - Function
: / Esterase-like / Putative esterase / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
Chem-8SW / : / NITRATE ION / Iron(III) enterobactin esterase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 Å
AuthorsMoynie, L. / Naismith, J.H.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
United Kingdom
CitationJournal: ACS Chem. Biol. / Year: 2018
Title: A Key Role for the Periplasmic PfeE Esterase in Iron Acquisition via the Siderophore Enterobactin in Pseudomonas aeruginosa.
Authors: Perraud, Q. / Moynie, L. / Gasser, V. / Munier, M. / Godet, J. / Hoegy, F. / Mely, Y. / Mislin, G.L.A. / Naismith, J.H. / Schalk, I.J.
History
DepositionMay 9, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 20, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 22, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 3, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.3Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ferric enterobactin esterase
B: Ferric enterobactin esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,13312
Polymers61,2632
Non-polymers1,86910
Water4,684260
1
A: Ferric enterobactin esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5045
Polymers30,6321
Non-polymers8734
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ferric enterobactin esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6287
Polymers30,6321
Non-polymers9976
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.794, 76.602, 129.867
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: VAL / End label comp-ID: VAL / Refine code: _ / Auth seq-ID: 11 - 275 / Label seq-ID: 14 - 278

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Ferric enterobactin esterase


Mass: 30631.729 Da / Num. of mol.: 2 / Mutation: S157A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Gene: PA2689 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9I0F2

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Non-polymers , 5 types, 270 molecules

#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-8SW / ~{N}-[2-[[(2~{S})-2-[[2,3-bis(oxidanyl)phenyl]carbonylamino]-3-[[(2~{S})-2-[[2,3-bis(oxidanyl)phenyl]carbonylamino]-3-oxidanylidene-3-(prop-2-ynylamino)propyl]amino]-3-oxidanylidene-propyl]amino]-2-oxidanylidene-ethyl]-2,3-bis(oxidanyl)benzamide


Mass: 692.629 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C32H32N6O12
#4: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO3
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 260 / 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: 2.35 Å3/Da / Density % sol: 47.57 %
Crystal growTemperature: 294 K / Method: vapor diffusion / Details: PEG MME 2000, Sodium acetate, potassium nitrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 27, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 1.48→129.87 Å / Num. obs: 95776 / % possible obs: 100 % / Redundancy: 7.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.058 / Net I/σ(I): 16.8
Reflection shellResolution: 1.48→1.51 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.796 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 4729 / CC1/2: 0.863 / % possible all: 99.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6GI0

6gi0


Resolution: 1.49→65.98 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.962 / SU B: 1.29 / SU ML: 0.047 / Cross valid method: THROUGHOUT / ESU R: 0.065 / ESU R Free: 0.067 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19895 4849 5.1 %RANDOM
Rwork0.17312 ---
obs0.17439 90838 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 26.077 Å2
Baniso -1Baniso -2Baniso -3
1-1.76 Å20 Å20 Å2
2---0.16 Å20 Å2
3----1.6 Å2
Refinement stepCycle: 1 / Resolution: 1.49→65.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4010 0 126 260 4396
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.024325
X-RAY DIFFRACTIONr_bond_other_d0.0010.024056
X-RAY DIFFRACTIONr_angle_refined_deg1.4232.0025868
X-RAY DIFFRACTIONr_angle_other_deg0.7543.0049274
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5055532
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.33521.237194
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.0915638
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6641561
X-RAY DIFFRACTIONr_chiral_restr0.0920.2615
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0214914
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02983
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.8992.2982128
X-RAY DIFFRACTIONr_mcbond_other2.8982.2982129
X-RAY DIFFRACTIONr_mcangle_it4.0393.4222660
X-RAY DIFFRACTIONr_mcangle_other4.0383.4222661
X-RAY DIFFRACTIONr_scbond_it4.2782.7942197
X-RAY DIFFRACTIONr_scbond_other4.2772.7942197
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.4094.0033209
X-RAY DIFFRACTIONr_long_range_B_refined7.7527.474778
X-RAY DIFFRACTIONr_long_range_B_other7.7527.4734779
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 15868 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.11 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.485→1.524 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 355 -
Rwork0.279 6681 -
obs--99.91 %

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