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- PDB-7xlz: Structure of siderophore-interacting protein from Vibrio anguillarum -

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Basic information

Entry
Database: PDB / ID: 7xlz
TitleStructure of siderophore-interacting protein from Vibrio anguillarum
ComponentsSiderophore-interacting protein
KeywordsOXIDOREDUCTASE / siderophore-interacting protein / iron release / Vibrio anguillarum
Function / homology
Function and homology information


oxidoreductase activity
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. / Riboflavin synthase-like beta-barrel
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Siderophore-interacting protein
Similarity search - Component
Biological speciesVibrio anguillarum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.19 Å
AuthorsMa, Q. / Liu, C. / Han, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2024
Title: Structural analysis of the siderophore-interacting protein from Vibrio anguillarum and its implications in classification of Vibrio homologs.
Authors: Liu, C. / Han, Y. / Ma, Q.
History
DepositionApr 23, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 31, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Dec 11, 2024Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Siderophore-interacting protein
B: Siderophore-interacting protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,6754
Polymers60,1032
Non-polymers1,5712
Water10,935607
1
A: Siderophore-interacting protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,8372
Polymers30,0521
Non-polymers7861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1370 Å2
ΔGint-8 kcal/mol
Surface area12060 Å2
MethodPISA
2
B: Siderophore-interacting protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,8372
Polymers30,0521
Non-polymers7861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1360 Å2
ΔGint-8 kcal/mol
Surface area12030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.622, 58.466, 70.650
Angle α, β, γ (deg.)90.000, 114.180, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resseq 10:25 or (resid 26 and (name...
21(chain B and ((resid 10 and (name N or name...

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
11SERSERSERSER(chain A and (resseq 10:25 or (resid 26 and (name...AA10 - 2513 - 28
12LEULEULEULEU(chain A and (resseq 10:25 or (resid 26 and (name...AA2629
13SERSERFADFAD(chain A and (resseq 10:25 or (resid 26 and (name...AA - C10 - 30113
14SERSERFADFAD(chain A and (resseq 10:25 or (resid 26 and (name...AA - C10 - 30113
15SERSERFADFAD(chain A and (resseq 10:25 or (resid 26 and (name...AA - C10 - 30113
16SERSERFADFAD(chain A and (resseq 10:25 or (resid 26 and (name...AA - C10 - 30113
17SERSERFADFAD(chain A and (resseq 10:25 or (resid 26 and (name...AA - C10 - 30113
18SERSERFADFAD(chain A and (resseq 10:25 or (resid 26 and (name...AA - C10 - 30113
19SERSERFADFAD(chain A and (resseq 10:25 or (resid 26 and (name...AA - C10 - 30113
110SERSERFADFAD(chain A and (resseq 10:25 or (resid 26 and (name...AA - C10 - 30113
111SERSERFADFAD(chain A and (resseq 10:25 or (resid 26 and (name...AA - C10 - 30113
112SERSERFADFAD(chain A and (resseq 10:25 or (resid 26 and (name...AA - C10 - 30113
113SERSERFADFAD(chain A and (resseq 10:25 or (resid 26 and (name...AA - C10 - 30113
114SERSERFADFAD(chain A and (resseq 10:25 or (resid 26 and (name...AA - C10 - 30113
115SERSERFADFAD(chain A and (resseq 10:25 or (resid 26 and (name...AA - C10 - 30113
116SERSERFADFAD(chain A and (resseq 10:25 or (resid 26 and (name...AA - C10 - 30113
21SERSERSERSER(chain B and ((resid 10 and (name N or name...BB1013
22ARGARGFADFAD(chain B and ((resid 10 and (name N or name...BB - D9 - 30112
23ARGARGFADFAD(chain B and ((resid 10 and (name N or name...BB - D9 - 30112
24ARGARGFADFAD(chain B and ((resid 10 and (name N or name...BB - D9 - 30112
25ARGARGFADFAD(chain B and ((resid 10 and (name N or name...BB - D9 - 30112
26ARGARGFADFAD(chain B and ((resid 10 and (name N or name...BB - D9 - 30112
27ARGARGFADFAD(chain B and ((resid 10 and (name N or name...BB - D9 - 30112
28ARGARGFADFAD(chain B and ((resid 10 and (name N or name...BB - D9 - 30112
29ARGARGFADFAD(chain B and ((resid 10 and (name N or name...BB - D9 - 30112
210ARGARGFADFAD(chain B and ((resid 10 and (name N or name...BB - D9 - 30112

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Components

#1: Protein Siderophore-interacting protein / vaSIP


Mass: 30051.711 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio anguillarum (strain ATCC 68554 / 775) (bacteria)
Strain: ATCC 68554 / 775 / Gene: VAA_01637 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: F7YRY1
#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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 607 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.03 Å3/Da / Density % sol: 39.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: The crystal of VaSIP was grown in the drop containing 1.4 ul protein solution (60 mg/ml in 10 mM Hepes, 150 mM NaCl, pH 7.5, 1 mM DTT) and 1.4 ul reservoir solution (0.1 M KBr, 30% (W/V) mPEG 2000).

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97852 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97852 Å / Relative weight: 1
ReflectionResolution: 1.19→58.951 Å / Num. obs: 147256 / % possible obs: 95.8 % / Redundancy: 6.7 % / CC1/2: 0.999 / Rpim(I) all: 0.021 / Rrim(I) all: 0.055 / Rsym value: 0.051 / Net I/σ(I): 20.2
Reflection shellResolution: 1.19→1.194 Å / Redundancy: 6.1 % / Mean I/σ(I) obs: 3.3 / Num. unique obs: 1171 / CC1/2: 0.885 / Rpim(I) all: 0.21 / Rrim(I) all: 0.528 / Rsym value: 0.482 / % possible all: 74.6

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.27data extraction
XDSJan 10, 2022, built on 20220220data reduction
Aimlessversion 0.5.29data scaling
PHASER2.6.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2gpj

2gpj


Resolution: 1.19→58.951 Å / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 15.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1615 7417 5.04 %
Rwork0.1378 139797 -
obs0.139 147214 95.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 46.2 Å2 / Biso mean: 14.8159 Å2 / Biso min: 5.65 Å2
Refinement stepCycle: final / Resolution: 1.19→58.951 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3877 0 106 607 4590
Biso mean--7.76 25.05 -
Num. residues----487
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084132
X-RAY DIFFRACTIONf_angle_d1.0325627
X-RAY DIFFRACTIONf_chiral_restr0.081611
X-RAY DIFFRACTIONf_plane_restr0.007794
X-RAY DIFFRACTIONf_dihedral_angle_d18.3941577
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2331X-RAY DIFFRACTION6.925TORSIONAL
12B2331X-RAY DIFFRACTION6.925TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.19-1.20320.20181760.1757387880
1.2032-1.21740.19372300.1695438190
1.2174-1.23220.19392490.1838453095
1.2322-1.24780.19852230.1537464195
1.2478-1.26430.2382310.2048462795
1.2643-1.28160.18552210.1604461296
1.2816-1.29990.21332340.1692461794
1.2999-1.31930.17532550.1428462996
1.3193-1.33990.16382810.1318460195
1.3399-1.36190.18642570.1414454894
1.3619-1.38540.20152310.1538466396
1.3854-1.41060.15052550.1211466597
1.4106-1.43770.14772610.1296466897
1.4377-1.4670.15612340.1341472696
1.467-1.4990.17742460.1306467796
1.499-1.53380.18612490.1342468297
1.5338-1.57220.13312260.1091453993
1.5722-1.61470.15432380.1099468996
1.6147-1.66220.13622410.1101473698
1.6622-1.71590.1392690.1136474298
1.7159-1.77720.1482670.116475498
1.7772-1.84840.14422340.1266481698
1.8484-1.93250.1672540.1352468397
1.9325-2.03440.15222390.1277469296
2.0344-2.16180.16012330.1329482198
2.1618-2.32880.14252600.1357481599
2.3288-2.56310.15332600.1346486099
2.5631-2.9340.16882900.1465473197
2.934-3.69640.15613000.14434858100
3.6964-58.9510.16622730.1459491698

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