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- PDB-3r5t: Crystal structure of holo-ViuP -

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Basic information

Entry
Database: PDB / ID: 3r5t
TitleCrystal structure of holo-ViuP
ComponentsFerric vibriobactin ABC transporter, periplasmic ferric vibriobactin-binding protein
KeywordsMETAL TRANSPORT / Iron-vibriobactin transport protein / Periplasmic transport protein / Iron-siderophore binding
Function / homology
Function and homology information


: / ABC transporter periplasmic binding domain / Periplasmic binding protein / Iron siderophore/cobalamin periplasmic-binding domain profile. / Nitrogenase molybdenum iron protein domain / Prokaryotic membrane lipoprotein lipid attachment site profile. / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETIC ACID / : / METHANOL / Chem-VBN / Fe2+-enterobactin ABC transporter substrate-binding protein
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsLi, N. / Zhang, C. / Li, B. / Liu, X. / Huang, Y. / Xu, S. / Gu, L.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Unique iron coordination in iron-chelating molecule vibriobactin helps Vibrio cholerae evade mammalian siderocalin-mediated immune response.
Authors: Li, N. / Zhang, C. / Li, B. / Liu, X. / Huang, Y. / Xu, S. / Gu, L.
History
DepositionMar 19, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 8, 2012Provider: repository / Type: Initial release
Revision 1.1May 30, 2012Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / struct_ref_seq_dif / struct_site
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ferric vibriobactin ABC transporter, periplasmic ferric vibriobactin-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0266
Polymers34,1111
Non-polymers9165
Water6,792377
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)82.496, 55.545, 69.542
Angle α, β, γ (deg.)90.00, 117.02, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-548-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Ferric vibriobactin ABC transporter, periplasmic ferric vibriobactin-binding protein / Periplasmic binding protein


Mass: 34110.531 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 29-325
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Strain: N16961 / Gene: viuP, VC_0776 / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9RCF6

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Non-polymers , 6 types, 382 molecules

#2: Chemical ChemComp-VBN / (4S,5R)-N-{3-[(2,3-dihydroxybenzoyl)amino]propyl}-2-(2,3-dihydroxyphenyl)-N-[3-({[(4S,5R)-2-(2,3-dihydroxyphenyl)-5-met hyl-4,5-dihydro-1,3-oxazol-4-yl]carbonyl}amino)propyl]-5-methyl-4,5-dihydro-1,3-oxazole-4-carboxamide / vibriobactin


Mass: 705.711 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C35H39N5O11
#3: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#4: Chemical ChemComp-MOH / METHANOL


Mass: 32.042 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH4O
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 377 / 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: 2.08 Å3/Da / Density % sol: 40.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.2M Ammonium acetate, 0.1M Sodium acetate pH 4.6, 30% w/v Polyethylene glycol 4000, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 20, 2009
RadiationMonochromator: SAGITTALLY FOCUSED SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.45→50 Å / Num. all: 48330 / Num. obs: 48330 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 25.96 Å2 / Rmerge(I) obs: 0.06 / Rsym value: 0.06 / Net I/σ(I): 17.99
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allRsym value% possible all
1.45-1.52.50.2833.1643480.28388
3.12-503.40.04720.847560.04793.9

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
PHENIX(phenix.refine: 1.6.2_432)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.45→24.601 Å / SU ML: 0.19 / σ(F): 0.08 / σ(I): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2086 1927 4.14 %Random
Rwork0.1819 ---
all0.183 46569 --
obs0.183 46569 93.63 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.011 Å2 / ksol: 0.331 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-5.2702 Å20 Å2-1.8048 Å2
2---0.9626 Å20 Å2
3----4.1766 Å2
Refinement stepCycle: LAST / Resolution: 1.45→24.601 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2321 0 62 377 2760
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072529
X-RAY DIFFRACTIONf_angle_d1.1813478
X-RAY DIFFRACTIONf_dihedral_angle_d16.865971
X-RAY DIFFRACTIONf_chiral_restr0.073398
X-RAY DIFFRACTIONf_plane_restr0.008448
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.4498-1.4860.23541030.2414241271
1.486-1.52620.25041230.2349290086
1.5262-1.57110.23261320.2083310092
1.5711-1.62180.19711400.1861319895
1.6218-1.67980.21831420.1846325295
1.6798-1.7470.20271440.1866326997
1.747-1.82650.21241390.1809327496
1.8265-1.92280.20171410.1821331097
1.9228-2.04320.18381470.1858335498
2.0432-2.20080.20461440.1771333598
2.2008-2.42210.20381470.1807335998
2.4221-2.77220.22131430.1802335598
2.7722-3.49110.22181400.1791325095
3.4911-24.60440.19331420.1681327494

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