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- PDB-6cn7: The structure of aerobactin synthetase IucC from a hypervirulent ... -

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Basic information

Entry
Database: PDB / ID: 6cn7
TitleThe structure of aerobactin synthetase IucC from a hypervirulent pathotype of Klebsiella pneumoniae
ComponentsAerobactin synthase IucC
KeywordsLIGASE / aerobactin / synthetase
Function / homologyAerobactin siderophore biosynthesis, IucA/IucC, N-terminal / Aerobactin siderophore biosynthesis, IucA/IucC-like / IucA / IucC family / Ferric iron reductase FhuF domain / Ferric iron reductase FhuF-like transporter / acid-amino acid ligase activity / siderophore biosynthetic process / IucC
Function and homology information
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsBailey, D.C. / Rice, M.R. / Gulick, A.M.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1AI116998 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI007614 United States
National Institutes of Health/National Center for Advancing Translational Sciences (NIH/NCATS)UL1TR001412 United States
CitationJournal: J. Biol. Chem. / Year: 2018
Title: Structural and functional delineation of aerobactin biosynthesis in hypervirulentKlebsiella pneumoniae.
Authors: Bailey, D.C. / Alexander, E. / Rice, M.R. / Drake, E.J. / Mydy, L.S. / Aldrich, C.C. / Gulick, A.M.
History
DepositionMar 7, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 11, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2May 30, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aerobactin synthase IucC
B: Aerobactin synthase IucC
C: Aerobactin synthase IucC
D: Aerobactin synthase IucC
E: Aerobactin synthase IucC
F: Aerobactin synthase IucC
G: Aerobactin synthase IucC
H: Aerobactin synthase IucC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)528,20310
Polymers527,8128
Non-polymers3902
Water4,468248
1
A: Aerobactin synthase IucC
C: Aerobactin synthase IucC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,1483
Polymers131,9532
Non-polymers1951
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2620 Å2
ΔGint-9 kcal/mol
Surface area44300 Å2
MethodPISA
2
B: Aerobactin synthase IucC
D: Aerobactin synthase IucC


Theoretical massNumber of molelcules
Total (without water)131,9532
Polymers131,9532
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2130 Å2
ΔGint-16 kcal/mol
Surface area43380 Å2
MethodPISA
3
E: Aerobactin synthase IucC
F: Aerobactin synthase IucC


Theoretical massNumber of molelcules
Total (without water)131,9532
Polymers131,9532
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2130 Å2
ΔGint-15 kcal/mol
Surface area44560 Å2
MethodPISA
4
G: Aerobactin synthase IucC
H: Aerobactin synthase IucC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,1483
Polymers131,9532
Non-polymers1951
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2810 Å2
ΔGint-11 kcal/mol
Surface area43390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.020, 197.690, 130.380
Angle α, β, γ (deg.)90.000, 109.600, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Aerobactin synthase IucC / IucC


Mass: 65976.562 Da / Num. of mol.: 8 / Mutation: S182G, E183S, D185T, Q187G, Q188T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: iucC, BCB67_13855, LV109 / Cell line (production host): BL21(DE3) / Production host: Escherichia coli (E. coli) / References: UniProt: Q6U605
#2: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 248 / 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: 2.85 Å3/Da / Density % sol: 56.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: Cocktail: 10-11% PEG 20,000, 100 mM MES pH 6.0. Drop Ratio, 1:1. Protein, 5.5 mg/mL

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 8, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.45→58.1 Å / Num. obs: 215668 / % possible obs: 99.6 % / Redundancy: 6.7 % / Net I/σ(I): 10
Reflection shellResolution: 2.45→2.54 Å

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.24data extraction
iMOSFLMdata reduction
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3X0Q

3x0q


Resolution: 2.45→58.067 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.98
RfactorNum. reflection% reflection
Rfree0.2403 10520 4.88 %
Rwork0.2128 --
obs0.2142 215510 99.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 131.93 Å2 / Biso mean: 73.4 Å2 / Biso min: 30.94 Å2
Refinement stepCycle: final / Resolution: 2.45→58.067 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms33319 0 24 248 33591
Biso mean--97.72 53.93 -
Num. residues----4344
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00334200
X-RAY DIFFRACTIONf_angle_d0.54446685
X-RAY DIFFRACTIONf_chiral_restr0.0385229
X-RAY DIFFRACTIONf_plane_restr0.0035985
X-RAY DIFFRACTIONf_dihedral_angle_d12.20120068
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.45-2.47780.35173430.32896773711698
2.4778-2.5070.36853660.32856740710699
2.507-2.53760.33613500.31016807715799
2.5376-2.56970.31753370.29336730706799
2.5697-2.60350.31113670.29146767713499
2.6035-2.63920.33043840.28836752713699
2.6392-2.67690.29843620.28456760712299
2.6769-2.71680.32143530.28076847720099
2.7168-2.75930.31493430.27076784712799
2.7593-2.80450.29213470.260367747121100
2.8045-2.85290.29663500.267368447194100
2.8529-2.90480.26923410.25816824716599
2.9048-2.96060.29043090.26116883719299
2.9606-3.02110.28563430.262668367179100
3.0211-3.08670.29163610.271367887149100
3.0867-3.15850.28863400.26546814715499
3.1585-3.23750.27213390.251968557194100
3.2375-3.3250.30353720.250468147186100
3.325-3.42290.25473390.239668997238100
3.4229-3.53330.25673930.236968077200100
3.5333-3.65960.24433280.227468827210100
3.6596-3.80610.23243540.203668307184100
3.8061-3.97930.20413390.194768967235100
3.9793-4.1890.21413590.186268577216100
4.189-4.45140.18323650.173168487213100
4.4514-4.79490.20473490.163668927241100
4.7949-5.27720.18893550.169168827237100
5.2772-6.04010.22793540.201468687222100
6.0401-7.60720.22153400.199669537293100
7.6072-58.08370.21863380.172169847322100
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)
10.5057-0.0524-0.46550.9809-0.13162.08230.0333-0.08520.0183-0.0471-0.095-0.1092-0.00510.20620.07620.4074-0.04340.05030.35620.0510.4572-1.5271183.54879.4277
21.98290.47440.12091.938-0.23880.7732-0.23120.29220.1673-0.2170.22330.1961-0.2372-0.05410.00090.5003-0.0177-0.02190.38580.03860.3732-53.6517148.227763.3436
32.0333-0.55640.73861.922-0.52112.5252-0.0882-0.3055-0.22670.32980.0038-0.10050.12730.09090.06620.4070.01850.04010.4653-0.01640.3993-2.3268168.1886128.6765
41.64150.8538-0.8852.2558-1.522.88160.0287-0.3291-0.00680.1084-0.08-0.23290.16360.15560.03520.45810.0854-0.00360.324-0.00420.4059-55.6452106.449592.4997
51.1230.5746-0.61152.8581-0.90742.889-0.29280.2752-0.1225-0.39930.10220.04190.5645-0.07080.18270.47350.05120.03710.60710.0350.487910.5082140.089963.2235
61.83690.2152-0.87950.9384-0.8232.3281-0.1193-0.2283-0.29710.0312-0.2492-0.31560.43070.4840.3340.6530.17620.08950.58080.21880.73784.0005121.3431111.5691
70.8564-0.11310.25081.8036-0.48231.44960.1244-0.2538-0.03020.1596-0.1812-0.02940.1464-0.25130.06790.4863-0.116-0.04270.6506-0.0540.4528-56.11131.7836133.4446
81.26220.20130.67531.6983-0.55372.7661-0.1851-0.05830.39010.0436-0.036-0.0279-0.5778-0.10170.22860.53140.0776-0.13880.5036-0.19010.699-63.1956174.0126104.4574
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 1 through 577)A1 - 577
2X-RAY DIFFRACTION2(chain 'B' and resid 2 through 576)B2 - 576
3X-RAY DIFFRACTION3(chain 'C' and resid 2 through 576)C2 - 576
4X-RAY DIFFRACTION4(chain 'D' and resid 1 through 576)D1 - 576
5X-RAY DIFFRACTION5(chain 'E' and resid 2 through 576)E2 - 576
6X-RAY DIFFRACTION6(chain 'F' and resid 2 through 576)F2 - 576
7X-RAY DIFFRACTION7(chain 'G' and resid 2 through 576)G2 - 576
8X-RAY DIFFRACTION8(chain 'H' and resid 0 through 576)H0 - 576

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