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- PDB-5jm8: The structure of ATP-bound aerobactin synthetase IucA from a hype... -

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Basic information

Entry
Database: PDB / ID: 5jm8
TitleThe structure of ATP-bound 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
ADENOSINE-5'-TRIPHOSPHATE / : / Aerobactin synthase IucA
Similarity search - Component
Biological speciesKlebsiella pneumoniae subsp. pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsBailey, D.C. / Drake, E.J. / 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 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: 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 1.4Nov 1, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.5Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)525,62624
Polymers521,3748
Non-polymers4,25216
Water16,826934
1
A: Aerobactin synthase IucA
C: Aerobactin synthase IucA
E: Aerobactin synthase IucA
G: Aerobactin synthase IucA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)262,81312
Polymers260,6874
Non-polymers2,1268
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Aerobactin synthase IucA
D: Aerobactin synthase IucA
F: Aerobactin synthase IucA
H: Aerobactin synthase IucA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)262,81312
Polymers260,6874
Non-polymers2,1268
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23350 Å2
ΔGint-154 kcal/mol
Surface area155480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)170.850, 96.630, 173.230
Angle α, β, γ (deg.)90.000, 90.020, 90.000
Int Tables number4
Space group name H-MP1211
DetailshvKP IucA was shown to exist as a tetramer in solution by small angle X-ray scattering, size exclusion chromatography, and native gel electrophoresis.

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Components

#1: Protein
Aerobactin synthase IucA


Mass: 65171.723 Da / Num. of mol.: 8
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-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 934 / 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: 2.84 Å3/Da / Density % sol: 56.64 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / pH: 6
Details: Cocktail: 15-32% PEG400, 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: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 29, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
Reflection twinOperator: h,-k,-l / Fraction: 0.5
ReflectionResolution: 2.2→49.57 Å / Num. obs: 283617 / % possible obs: 99.2 % / Redundancy: 4 % / Biso Wilson estimate: 20.3 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.1194 / Net I/σ(I): 7.62
Reflection shellResolution: 2.2→2.279 Å / Redundancy: 4 % / Rmerge(I) obs: 0.4555 / Mean I/σ(I) obs: 3.15 / % possible all: 98.5

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Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
PDB_EXTRACT3.2data extraction
Cootmodel building
iMOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→49.568 Å / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.25
RfactorNum. reflection% reflection
Rfree0.249 14294 5.04 %
Rwork0.2139 --
obs0.2165 283568 99.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 120.43 Å2 / Biso mean: 29.1959 Å2 / Biso min: 2.85 Å2
Refinement stepCycle: final / Resolution: 2.2→49.568 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms34712 0 256 934 35902
Biso mean--20.14 17.88 -
Num. residues----4421
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00535864
X-RAY DIFFRACTIONf_angle_d1.01948941
X-RAY DIFFRACTIONf_chiral_restr0.0375413
X-RAY DIFFRACTIONf_plane_restr0.0046358
X-RAY DIFFRACTIONf_dihedral_angle_d16.13320140
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2-2.2380.29696900.2639133021399294
2.238-2.27860.30537400.2523132641400493
2.2786-2.32250.29266270.2539133701399794
2.3225-2.36990.27076240.2446134491407394
2.3699-2.42140.27917860.2455132661405293
2.4214-2.47770.27886080.2387134881409694
2.4777-2.53970.29996990.2335134111411094
2.5397-2.60830.27588100.2416132411405193
2.6083-2.68510.27646870.2323134381412594
2.6851-2.77170.2766680.2369134141408294
2.7717-2.87080.25386750.2259134691414494
2.8708-2.98570.26237090.231134951420494
2.9857-3.12150.27297670.231134201418794
3.1215-3.2860.2657200.2246134891420994
3.286-3.49180.24516990.2162135571425695
3.4918-3.76130.23287410.1968134821422394
3.7613-4.13950.21317680.1775135451431394
4.1395-4.73780.19427660.1645135741434094
4.7378-5.96640.21526920.1838137431443595
5.9664-41.99090.22526980.2067139501464895
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)
10.74880.03950.12530.24520.17820.85710.07670.1788-0.2982-0.0733-0.03890.0050.1540.0689-0.03140.18570.0593-0.06520.1761-0.05690.237356.25183.58470.533
20.58140.2401-0.19150.28610.11180.50840.00850.1764-0.2629-0.06340.0389-0.1140.18580.1987-0.03380.21320.0756-0.0380.3521-0.09050.228455.89334.722-15.498
30.70850.23250.09480.59420.0180.87280.01380.14390.2059-0.1215-0.02980.0468-0.1606-0.08170.01850.16850.05210.02240.13010.03140.170729.498122.14171.423
40.72550.2330.14130.65230.01580.74040.01610.22880.2742-0.1442-0.05020.0889-0.1496-0.06810.03630.17160.06590.01280.23980.07520.224529.12873.223-15.866
50.5055-0.02980.05060.47520.02130.5934-0.0105-0.2072-0.02480.07780.0015-0.0364-0.02060.13290.01030.1348-0.0392-0.03980.22190.00710.133766.475103.979112.862
61.01550.1531-0.1090.3930.13760.52840.1122-0.6718-0.01180.3602-0.0282-0.07650.10350.5175-0.0325-0.0316-0.20320.00670.9839-0.0160.180265.86656.88825.752
70.44070.1322-0.0940.4369-0.00680.56830.0828-0.1551-0.02620.0508-0.09830.0238-0.0174-0.26520.01130.1367-0.06110.01760.06490.03230.135419.51999.24112.937
80.71530.1020.21650.3338-0.12160.52790.1345-0.5321-0.01730.1798-0.10150.09480.0746-0.4895-0.03750.1985-0.10240.00970.61240.01320.160219.27751.70325.939
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 9:572 )A9 - 572
2X-RAY DIFFRACTION2( CHAIN B AND RESID 9:572 )B9 - 572
3X-RAY DIFFRACTION3( CHAIN C AND RESID 9:571 )C9 - 571
4X-RAY DIFFRACTION4( CHAIN D AND RESID 9:571 )D9 - 571
5X-RAY DIFFRACTION5( CHAIN E AND RESID 9:572 )E9 - 572
6X-RAY DIFFRACTION6( CHAIN F AND RESID 9:572 )F9 - 572
7X-RAY DIFFRACTION7( CHAIN G AND RESID 9:572 )G9 - 572
8X-RAY DIFFRACTION8( CHAIN H AND RESID 9:570 )H9 - 570

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