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- PDB-5ggx: Crystal Structure of Fe3+ - Desferal bound siderophore binding pr... -

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Basic information

Entry
Database: PDB / ID: 5ggx
TitleCrystal Structure of Fe3+ - Desferal bound siderophore binding protein FhuD from Vibrio cholerae
ComponentsIron(III) ABC transporter, periplasmic iron-compound-binding protein
KeywordsTRANSPORT PROTEIN / Vibrio cholerae / periplasmic protein / desferal / iron-Siderophore / ABC transporter / FhuD
Function / homology
Function and homology information


iron coordination entity transport / outer membrane-bounded periplasmic space
Similarity search - Function
: / ABC transporter periplasmic binding domain / Periplasmic binding protein / Iron siderophore/cobalamin periplasmic-binding domain profile. / Nitrogenase molybdenum iron protein domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DEFEROXAMINE MESYLATE FE(III) COMPLEX / Iron(III) ABC transporter, periplasmic iron-compound-binding protein
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsAgarwal, S. / Dey, S. / Ghosh, B. / Dasgupta, J.
Funding support India, 1items
OrganizationGrant numberCountry
DAE(BRNS) India
Citation
Journal: To be published
Title: Crystal Structure of Fe3+ - Desferal bound siderophore binding protein FhuD from Vibrio cholerae
Authors: Agarwal, S. / Biswas, M. / Dasgupta, J.
#1: Journal: Acta Crystallogr F Struct Biol Commun / Year: 2015
Title: Purification, crystallization and preliminary X-ray analysis of the periplasmic haem-binding protein HutB from Vibrio cholerae.
Authors: Agarwal, S. / Biswas, M. / Dasgupta, J.
History
DepositionJun 16, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 22, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_validate_chiral
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: Iron(III) ABC transporter, periplasmic iron-compound-binding protein
B: Iron(III) ABC transporter, periplasmic iron-compound-binding protein
C: Iron(III) ABC transporter, periplasmic iron-compound-binding protein
D: Iron(III) ABC transporter, periplasmic iron-compound-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,7218
Polymers124,8344
Non-polymers2,8864
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)191.145, 191.145, 129.164
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein
Iron(III) ABC transporter, periplasmic iron-compound-binding protein


Mass: 31208.615 Da / Num. of mol.: 4 / Fragment: UNP RESIDUES 55-319
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Strain: ATCC 39541 / Classical Ogawa 395 / O395 / Gene: VC0395_A2582 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: A0A0H3AJ03
#2: Chemical
ChemComp-DEF / DEFEROXAMINE MESYLATE FE(III) COMPLEX


Mass: 721.622 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H49FeN6O11S

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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: 5.46 Å3/Da / Density % sol: 77.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.8M ammonium sulfate, 0.1M HEPES (pH 7.0), 0.1M Tris (pH 7.0)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: RRCAT INDUS-2 / Beamline: PX-BL21 / Wavelength: 0.98 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Apr 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.4→47.79 Å / Num. obs: 37750 / % possible obs: 100 % / Redundancy: 11.2 % / Net I/σ(I): 10
Reflection shellResolution: 3.4→3.55 Å

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata processing
SCALAdata scaling
PHASERmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EFD

1efd


Resolution: 3.4→43.055 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2359 2014 5.35 %
Rwork0.2001 --
obs0.2021 37640 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.4→43.055 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8299 0 140 0 8439
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0038658
X-RAY DIFFRACTIONf_angle_d0.86611856
X-RAY DIFFRACTIONf_dihedral_angle_d16.0253198
X-RAY DIFFRACTIONf_chiral_restr0.0351336
X-RAY DIFFRACTIONf_plane_restr0.0051507
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4002-3.48520.29951410.29012535X-RAY DIFFRACTION100
3.4852-3.57940.3141420.27412487X-RAY DIFFRACTION100
3.5794-3.68470.28031410.26332543X-RAY DIFFRACTION100
3.6847-3.80350.30841430.25212510X-RAY DIFFRACTION100
3.8035-3.93940.31591420.25462524X-RAY DIFFRACTION100
3.9394-4.0970.29241400.22612514X-RAY DIFFRACTION100
4.097-4.28330.26631480.21572562X-RAY DIFFRACTION100
4.2833-4.50890.26361410.19382522X-RAY DIFFRACTION100
4.5089-4.79110.21531440.17942560X-RAY DIFFRACTION100
4.7911-5.16040.23971460.18822533X-RAY DIFFRACTION100
5.1604-5.67870.22971410.19312545X-RAY DIFFRACTION100
5.6787-6.4980.25411420.19912567X-RAY DIFFRACTION100
6.498-8.17760.18681510.16852590X-RAY DIFFRACTION100
8.1776-43.05810.14291520.13712634X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 110.8917 Å / Origin y: -30.6951 Å / Origin z: 6.6762 Å
111213212223313233
T0.399 Å2-0.0501 Å20.1107 Å2-0.3563 Å2-0.033 Å2--0.3905 Å2
L0.1173 °2-0.1394 °20.1448 °2-0.3739 °20.2049 °2--0.2116 °2
S-0.0127 Å °0.0117 Å °-0.1037 Å °0.0341 Å °-0.085 Å °0.0422 Å °0.0798 Å °-0.0541 Å °-0.0726 Å °
Refinement TLS groupSelection details: all

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