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- PDB-6geh: Structure and reactivity of a siderophore-interacting protein fro... -

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Basic information

Entry
Database: PDB / ID: 6geh
TitleStructure and reactivity of a siderophore-interacting protein from the marine bacterium Shewanella reveals unanticipated functional versatility.
ComponentsFAD-binding 9, siderophore-interacting domain protein
KeywordsMETAL TRANSPORT / Flavin binding / NAD(P)H binding / rossman fold
Function / homology
Function and homology information


ferric-chelate reductase (NADPH) activity / cellular response to iron ion starvation / iron import into cell / siderophore transport / FAD binding / metal ion binding
Similarity search - Function
Siderophore-interacting protein / Siderophore-interacting protein, C-terminal domain / FAD-binding 9, siderophore-interacting / Siderophore-interacting protein / Siderophore-interacting FAD-binding domain / Translation factors / Elongation Factor Tu (Ef-tu); domain 3 / FAD-binding domain, ferredoxin reductase-type / Ferredoxin-NADP reductase (FNR), nucleotide-binding domain / Ferredoxin reductase-type FAD binding domain profile. ...Siderophore-interacting protein / Siderophore-interacting protein, C-terminal domain / FAD-binding 9, siderophore-interacting / Siderophore-interacting protein / Siderophore-interacting FAD-binding domain / Translation factors / Elongation Factor Tu (Ef-tu); domain 3 / FAD-binding domain, ferredoxin reductase-type / Ferredoxin-NADP reductase (FNR), nucleotide-binding domain / Ferredoxin reductase-type FAD binding domain profile. / Riboflavin synthase-like beta-barrel / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / FORMIC ACID / FAD-binding 9, siderophore-interacting domain protein
Similarity search - Component
Biological speciesShewanella frigidimarina (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.15 Å
AuthorsTrindade, I.B. / Silva, J.P.M. / Matias, P. / Moe, E.
Funding support Portugal, 1items
OrganizationGrant numberCountry
Other governmentxx Portugal
Citation
Journal: J. Biol. Chem. / Year: 2019
Title: Structure and reactivity of a siderophore-interacting protein from the marine bacteriumShewanellareveals unanticipated functional versatility.
Authors: Trindade, I.B. / Silva, J.M. / Fonseca, B.M. / Catarino, T. / Fujita, M. / Matias, P.M. / Moe, E. / Louro, R.O.
#1: Journal: Acta Crystallogr F Struct Biol Commun / Year: 2016
Title: A putative siderophore-interacting protein from the marine bacterium Shewanella frigidimarina NCIMB 400: cloning, expression, purification, crystallization and X-ray diffraction analysis.
Authors: Trindade, I.B. / Fonseca, B.M. / Matias, P.M. / Louro, R.O. / Moe, E.
History
DepositionApr 26, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 21, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 16, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_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_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FAD-binding 9, siderophore-interacting domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,36136
Polymers28,5081
Non-polymers1,85335
Water7,764431
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6120 Å2
ΔGint-269 kcal/mol
Surface area12460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.098, 77.753, 44.917
Angle α, β, γ (deg.)90.00, 109.64, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

#1: Protein FAD-binding 9, siderophore-interacting domain protein


Mass: 28507.586 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella frigidimarina (strain NCIMB 400) (bacteria)
Strain: NCIMB 400 / Gene: Sfri_2392 / Plasmid: pETBlue-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Tuner pLacI / References: UniProt: Q080S8

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Non-polymers , 7 types, 466 molecules

#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O2
#5: Chemical...
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 431 / 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: 2.14 Å3/Da / Density % sol: 42.53 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: PEG 3350, Magnesium formate dihydrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 6, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.15→28.62 Å / Num. obs: 86403 / % possible obs: 99 % / Observed criterion σ(I): 2.4 / Redundancy: 1 % / Biso Wilson estimate: 12 Å2 / Net I/σ(I): 18.4
Reflection shellResolution: 1.15→1.19 Å

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
xia2data reduction
xia2data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YHB

4yhb


Resolution: 1.15→28.62 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 1.04 / Phase error: 17.99
RfactorNum. reflection% reflection
Rfree0.1735 4242 4.91 %
Rwork0.1449 --
obs0.1463 86396 99.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.15→28.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2064 0 52 431 2547
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092425
X-RAY DIFFRACTIONf_angle_d1.3843344
X-RAY DIFFRACTIONf_dihedral_angle_d15.926929
X-RAY DIFFRACTIONf_chiral_restr0.073371
X-RAY DIFFRACTIONf_plane_restr0.006437
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.15-1.16310.26761420.23672308X-RAY DIFFRACTION85
1.1631-1.17680.2621240.21912575X-RAY DIFFRACTION93
1.1768-1.19110.23881310.21572686X-RAY DIFFRACTION97
1.1911-1.20620.22731390.20212708X-RAY DIFFRACTION99
1.2062-1.22210.23521310.19492775X-RAY DIFFRACTION99
1.2221-1.23880.22431420.18662762X-RAY DIFFRACTION100
1.2388-1.25650.20391340.18612738X-RAY DIFFRACTION100
1.2565-1.27530.19381610.17722746X-RAY DIFFRACTION100
1.2753-1.29520.19831250.17332770X-RAY DIFFRACTION100
1.2952-1.31640.25811370.17172767X-RAY DIFFRACTION100
1.3164-1.33910.20591420.16572728X-RAY DIFFRACTION100
1.3391-1.36350.19411560.15782776X-RAY DIFFRACTION100
1.3635-1.38970.18271660.15432707X-RAY DIFFRACTION100
1.3897-1.41810.17371350.14922784X-RAY DIFFRACTION100
1.4181-1.44890.19671320.14782760X-RAY DIFFRACTION100
1.4489-1.48260.18021470.14762738X-RAY DIFFRACTION100
1.4826-1.51970.1671280.13932805X-RAY DIFFRACTION100
1.5197-1.56080.16781180.13032749X-RAY DIFFRACTION100
1.5608-1.60670.16661320.12992816X-RAY DIFFRACTION100
1.6067-1.65850.16121480.13192773X-RAY DIFFRACTION100
1.6585-1.71780.14021130.13352757X-RAY DIFFRACTION100
1.7178-1.78660.17621550.13682738X-RAY DIFFRACTION100
1.7866-1.86790.16921550.13592759X-RAY DIFFRACTION100
1.8679-1.96630.15631770.13832719X-RAY DIFFRACTION100
1.9663-2.08950.15151610.13612774X-RAY DIFFRACTION100
2.0895-2.25080.16911290.13872794X-RAY DIFFRACTION100
2.2508-2.47710.17751360.13482777X-RAY DIFFRACTION100
2.4771-2.83530.17981370.1482786X-RAY DIFFRACTION100
2.8353-3.57110.16971340.13712782X-RAY DIFFRACTION100
3.5711-28.620.15851750.13692797X-RAY DIFFRACTION100

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