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- PDB-3r5s: Crystal structure of apo-ViuP -

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Basic information

Entry
Database: PDB / ID: 3r5s
TitleCrystal structure of apo-ViuP
ComponentsFerric vibriobactin ABC transporter, periplasmic ferric vibriobactin-binding protein
KeywordsMETAL TRANSPORT / Iron-vibriobactin transport protein / Periplasmic transport protein
Function / homologyABC 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 / Fe2+-enterobactin ABC transporter substrate-binding protein
Function and homology information
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.791 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)34,2511
Polymers34,2511
Non-polymers00
Water6,197344
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)76.925, 61.068, 66.852
Angle α, β, γ (deg.)90.00, 120.56, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-520-

HOH

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Components

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


Mass: 34251.215 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
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 344 / 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: 1.97 Å3/Da / Density % sol: 37.68 %
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: 0.979 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 28, 2009
RadiationMonochromator: SAGITTALLY FOCUSED SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.79→50 Å / Num. all: 49200 / Num. obs: 49200 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 23.15 Å2 / Rmerge(I) obs: 0.05 / Rsym value: 0.05 / Net I/σ(I): 27.56
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allRsym value% possible all
1.79-1.853.30.2513.9844040.25188.2
3.86-503.80.02155.46249670.02199.8

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
SOLVEphasing
PHENIX(phenix.refine: 1.6.2_432)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.791→33.119 Å / SU ML: 0.21 / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2132 3731 7.98 %Random
Rwork0.1766 ---
all0.1796 46783 --
obs0.1796 46783 94.83 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.04 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 15.337 Å2
Baniso -1Baniso -2Baniso -3
1-0.9926 Å2-0 Å2-0.1963 Å2
2---1.9769 Å2-0 Å2
3---0.9843 Å2
Refinement stepCycle: LAST / Resolution: 1.791→33.119 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2369 0 0 344 2713
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072420
X-RAY DIFFRACTIONf_angle_d1.0313300
X-RAY DIFFRACTIONf_dihedral_angle_d15.149882
X-RAY DIFFRACTIONf_chiral_restr0.067383
X-RAY DIFFRACTIONf_plane_restr0.004429
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.7911-1.81380.28791350.2456154888
1.8138-1.83760.25851290.2208155994
1.8376-1.86280.26331440.2023156094
1.8628-1.88940.22421370.1998157393
1.8894-1.91760.38241180.2678126276
1.9176-1.94760.24351020.201134780
1.9476-1.97950.211600.1608158794
1.9795-2.01360.18831000.1511163797
2.0136-2.05020.2251530.1758158992
2.0502-2.08970.37241350.2519138085
2.0897-2.13230.19531390.1625164797
2.1323-2.17870.19961230.164167499
2.1787-2.22930.26431500.1792150192
2.2293-2.28510.26391260.2279147488
2.2851-2.34680.21941340.1667170099
2.3468-2.41590.20621530.1676167399
2.4159-2.49380.18651610.1607163899
2.4938-2.58290.21561170.176169699
2.5829-2.68630.21861680.1816160199
2.6863-2.80850.2021350.1737167399
2.8085-2.95650.21951490.17971692100
2.9565-3.14160.19481370.17231672100
3.1416-3.38390.18811420.16891677100
3.3839-3.7240.1951490.15361676100
3.724-4.2620.1411400.143164898
4.262-5.36590.17731410.15031689100
5.3659-33.12460.20351540.19511679100

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