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- PDB-5jm7: The structure of aerobactin synthetase IucA from a hypervirulent ... -

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Basic information

Entry
Database: PDB / ID: 5jm7
TitleThe structure of aerobactin synthetase IucA from a hypervirulent pathotype of Klebsiella pneumoniae
ComponentsAerobactin synthase IucA
KeywordsLIGASE / aerobactin NIS synthetase
Function / homology
Function and homology information


acid-amino acid ligase activity / siderophore biosynthetic process / ATP binding / metal ion binding
Similarity search - Function
Aerobactin 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
Similarity search - Domain/homology
: / Aerobactin synthase IucA
Similarity search - Component
Biological speciesKlebsiella pneumoniae subsp. pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.4 Å
AuthorsDrake, E.J. / Bailey, D.C. / Gulick, A.M.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI116998 United States
National Institutes of Health/National Center for Advancing Translational Sciences (NIH/NCATS)UL1TR001412 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI007614 United States
CitationJournal: Biochemistry / Year: 2016
Title: Structural and Functional Characterization of Aerobactin Synthetase IucA from a Hypervirulent Pathotype of Klebsiella pneumoniae.
Authors: Bailey, D.C. / Drake, E.J. / Grant, T.D. / Gulick, A.M.
History
DepositionApr 28, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 15, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 6, 2016Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Aerobactin synthase IucA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,2682
Polymers65,1721
Non-polymers961
Water91951
1
A: Aerobactin synthase IucA
hetero molecules

A: Aerobactin synthase IucA
hetero molecules

A: Aerobactin synthase IucA
hetero molecules

A: Aerobactin synthase IucA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)261,0718
Polymers260,6874
Non-polymers3844
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_655-x+1,-y,z1
crystal symmetry operation8_556x-y,-y,-z+11
crystal symmetry operation11_656-x+y+1,y,-z+11
Buried area7440 Å2
ΔGint-106 kcal/mol
Surface area79500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.790, 106.790, 264.720
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222

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Components

#1: Protein Aerobactin synthase IucA


Mass: 65171.723 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae subsp. pneumoniae (bacteria)
Gene: RJF2_26555, RJF9_26895 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0X9V8F4, UniProt: A0A1A9TA96*PLUS
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 51 / 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: 3.35 Å3/Da / Density % sol: 63.3 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: Cocktail: 500-750 mM ammonium sulfate, 100-250 mM potassium-sodium tartrate, 100 mM sodium citrate pH 5.6 Drop Ratio: 1:1 Protein: 5.5 mg/mL
Temp details: 287 or 293

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.96802 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 13, 2014
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96802 Å / Relative weight: 1
ReflectionResolution: 2.4→52.34 Å / Num. obs: 35840 / % possible obs: 100 % / Redundancy: 9.6 % / Biso Wilson estimate: 46.14 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.0927 / Net I/σ(I): 14.26
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 9.7 % / Rmerge(I) obs: 0.7257 / Mean I/σ(I) obs: 2.77 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
Cootmodel building
iMOSFLMdata reduction
PHENIXphasing
RefinementMethod to determine structure: MAD / Resolution: 2.4→52.34 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.3
RfactorNum. reflection% reflection
Rfree0.2548 1790 5 %
Rwork0.213 --
obs0.2151 35822 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 53.64 Å2
Refinement stepCycle: LAST / Resolution: 2.4→52.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4291 0 5 51 4347
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094425
X-RAY DIFFRACTIONf_angle_d1.0696041
X-RAY DIFFRACTIONf_dihedral_angle_d14.4673367
X-RAY DIFFRACTIONf_chiral_restr0.06673
X-RAY DIFFRACTIONf_plane_restr0.007787
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.46490.3541370.29032557X-RAY DIFFRACTION100
2.4649-2.53740.31481360.27452556X-RAY DIFFRACTION100
2.5374-2.61930.29071280.26382559X-RAY DIFFRACTION100
2.6193-2.71290.29721350.24492550X-RAY DIFFRACTION100
2.7129-2.82150.27831550.24842566X-RAY DIFFRACTION100
2.8215-2.94990.29521360.25322568X-RAY DIFFRACTION100
2.9499-3.10550.28231350.24952595X-RAY DIFFRACTION100
3.1055-3.30.30661400.24442593X-RAY DIFFRACTION100
3.3-3.55470.32081300.23382628X-RAY DIFFRACTION100
3.5547-3.91240.25011290.20772620X-RAY DIFFRACTION100
3.9124-4.47820.221330.17092668X-RAY DIFFRACTION100
4.4782-5.6410.19731370.17422698X-RAY DIFFRACTION100
5.641-52.35330.21211590.19542874X-RAY DIFFRACTION100
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)
11.4612-0.55730.37242.55820.09462.6307-0.0992-0.03760.26930.26430.21370.0819-0.6746-0.2193-0.15190.60190.030.09360.450.00540.464852.695542.2141107.062
20.47270.3939-0.51760.7272-0.73511.24230.03790.1920.2516-0.14770.13920.0998-0.4634-0.2484-0.17440.52970.03750.11220.49940.01750.445847.306524.2271122.8432
31.15710.21570.27650.4965-0.24410.57750.0389-0.26810.22230.17470.15170.2381-0.3909-0.5872-0.07040.22170.12980.03690.49970.13720.407527.809311.8984123.1992
40.435-0.0996-0.15730.2648-0.02340.9019-0.00010.04460.0661-0.14920.13050.0775-0.1974-0.2088-0.11150.3343-0.00720.01360.41010.06070.367446.411916.3026101.1064
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 9 through 122)
2X-RAY DIFFRACTION2chain 'A' and (resid 123 through 174)
3X-RAY DIFFRACTION3chain 'A' and (resid 175 through 357)
4X-RAY DIFFRACTION4chain 'A' and (resid 358 through 571)

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