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- PDB-7lrn: Structure of the Siderophore Interacting Protein from Acinetbacte... -

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Basic information

Entry
Database: PDB / ID: 7lrn
TitleStructure of the Siderophore Interacting Protein from Acinetbacter baumannii
ComponentsNADPH-dependent ferric siderophore reductase
KeywordsOXIDOREDUCTASE / SIDEROPHORE-INTERACTING PROTEIN / FLAVIN BINDING
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
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 / FAD-binding domain, ferredoxin reductase-type / Ferredoxin-NADP reductase (FNR), nucleotide-binding domain / Ferredoxin reductase-type FAD binding domain profile.
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / NADPH-dependent ferric siderophore reductase
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsTanner, J.J. / Korasick, D.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CHE-2003986 United States
CitationJournal: Acs Omega / Year: 2021
Title: Structural and Biochemical Characterization of the Flavin-Dependent Siderophore-Interacting Protein from Acinetobacter baumannii .
Authors: Valentino, H. / Korasick, D.A. / Bohac, T.J. / Shapiro, J.A. / Wencewicz, T.A. / Tanner, J.J. / Sobrado, P.
History
DepositionFeb 16, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 21, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 25, 2021Group: Database references / Category: citation / database_2
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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

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Assembly

Deposited unit
A: NADPH-dependent ferric siderophore reductase
B: NADPH-dependent ferric siderophore reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,6914
Polymers69,1202
Non-polymers1,5712
Water00
1
A: NADPH-dependent ferric siderophore reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,3462
Polymers34,5601
Non-polymers7861
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: NADPH-dependent ferric siderophore reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,3462
Polymers34,5601
Non-polymers7861
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)86.790, 127.252, 150.304
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETGLUGLU(chain A and (resid 25 through 26 or (resid 27...AA25 - 2640 - 41
12GLNGLNGLNGLN(chain A and (resid 25 through 26 or (resid 27...AA2742
13METMETFADFAD(chain A and (resid 25 through 26 or (resid 27...AA - C25 - 30140
14METMETFADFAD(chain A and (resid 25 through 26 or (resid 27...AA - C25 - 30140
15METMETFADFAD(chain A and (resid 25 through 26 or (resid 27...AA - C25 - 30140
16METMETFADFAD(chain A and (resid 25 through 26 or (resid 27...AA - C25 - 30140
21METMETASPASP(chain B and (resid 25 through 102 or (resid 103...BB25 - 10240 - 117
22LEULEULEULEU(chain B and (resid 25 through 102 or (resid 103...BB103118
23GLNGLNFADFAD(chain B and (resid 25 through 102 or (resid 103...BB - D23 - 30138
24GLNGLNFADFAD(chain B and (resid 25 through 102 or (resid 103...BB - D23 - 30138
25GLNGLNFADFAD(chain B and (resid 25 through 102 or (resid 103...BB - D23 - 30138
26GLNGLNFADFAD(chain B and (resid 25 through 102 or (resid 103...BB - D23 - 30138

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Components

#1: Protein NADPH-dependent ferric siderophore reductase


Mass: 34560.102 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Gene: A7M79_07860, BGC29_02895 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1E3M8P2
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
Has ligand of interestY

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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 Å3/Da / Density % sol: 59.03 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7.5
Details: 1.6 M ammonium sulfate, 0.1 M NaCl, 5 % PEG 400, and 0.1 M HEPES-Na pH 7.5 at 17.5 mg/mL of BauF.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 20, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.85→150.3 Å / Num. obs: 19818 / % possible obs: 100 % / Redundancy: 7.3 % / Biso Wilson estimate: 81.44 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.177 / Rpim(I) all: 0.07 / Rrim(I) all: 0.191 / Net I/σ(I): 7.6 / Num. measured all: 145243
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.85-37.52.4672113128320.3210.9632.6520.8100
9.01-150.36.60.04946466990.9990.020.05424.999.8

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
PHENIX1.19.1refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GPJ

2gpj


Resolution: 2.85→75.15 Å / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 27.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2639 991 5.01 %
Rwork0.2183 18785 -
obs0.2205 19776 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 188.13 Å2 / Biso mean: 84.9253 Å2 / Biso min: 56.9 Å2
Refinement stepCycle: final / Resolution: 2.85→75.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3824 0 106 0 3930
Biso mean--67.84 --
Num. residues----496
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2297X-RAY DIFFRACTION7.793TORSIONAL
12B2297X-RAY DIFFRACTION7.793TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.85-30.35021440.324226222766
3-3.190.35191350.303126622797
3.19-3.430.32811350.271426552790
3.43-3.780.27921520.223226582810
3.78-4.330.2591370.226742811
4.33-5.450.22771440.186927072851
5.45-75.150.24361440.205128072951
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)
12.6320.44070.06312.98610.53473.4911-0.01550.2641-0.0235-0.16370.0050.0453-0.03780.17890.02110.47670.05-0.01310.52290.03110.4557-30.769615.3944-13.658
23.42090.27951.38471.84070.42792.93850.1984-0.41870.13840.3985-0.18330.1523-0.1-0.1967-0.0150.6056-0.11450.0360.5822-0.05030.5315-18.819925.44120.1507
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A'A0
2X-RAY DIFFRACTION2chain 'B'B0

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