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- PDB-3tef: Crystal Structure of the Periplasmic Catecholate-Siderophore Bind... -

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Basic information

Entry
Database: PDB / ID: 3tef
TitleCrystal Structure of the Periplasmic Catecholate-Siderophore Binding Protein VctP from Vibrio Cholerae
ComponentsIron(III) ABC transporter, periplasmic iron-compound-binding protein
KeywordsTRANSPORT PROTEIN / siderophore-binding protein
Function / homology
Function and homology information


iron ion transport / outer membrane-bounded periplasmic space
Similarity search - Function
FatB domain / : / 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
Iron(III) ABC transporter, periplasmic iron-compound-binding protein
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.698 Å
AuthorsLiu, X. / Wang, Z. / Liu, S. / Li, N. / Chen, Y. / Zhu, C. / Zhu, D. / Wei, T. / Huang, Y. / Xu, S. / Gu, L.
CitationJournal: Febs Lett. / Year: 2012
Title: Crystal structure of periplasmic catecholate-siderophore binding protein VctP from Vibrio cholerae at 1.7 A resolution
Authors: Liu, X. / Du, Q. / Wang, Z. / Liu, S. / Li, N. / Chen, Y. / Zhu, C. / Zhu, D. / Wei, T. / Huang, Y. / Xu, S. / Gu, L.
History
DepositionAug 13, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 15, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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


Theoretical massNumber of molelcules
Total (without water)32,6391
Polymers32,6391
Non-polymers00
Water3,279182
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)32.112, 73.282, 112.819
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 32638.666 Da / Num. of mol.: 1 / Fragment: residues 51-333
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Gene: VC_A0227 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9KMU2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 182 / 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: 2.03 Å3/Da / Density % sol: 39.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2M ammonium acetate, 0.1M Tris-HCl buffer, 20% PEG3350, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9762 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jul 9, 2009
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.698→50 Å / Num. all: 30253 / Num. obs: 30253 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.7 % / Rmerge(I) obs: 0.085 / Rsym value: 0.085 / Net I/σ(I): 23.1
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.597 / Mean I/σ(I) obs: 2.3 / Num. unique all: 2900 / Rsym value: 0.597 / % possible all: 98.1

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.698→33.458 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.17 / σ(F): 0 / Phase error: 22.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2132 1932 6.65 %RANDOM
Rwork0.1908 ---
all0.1923 29042 --
obs0.1923 29042 95.85 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.404 Å2 / ksol: 0.373 e/Å3
Displacement parametersBiso max: 76.61 Å2 / Biso mean: 32.4961 Å2 / Biso min: 10.03 Å2
Baniso -1Baniso -2Baniso -3
1--9.4042 Å20 Å2-0 Å2
2--11.8317 Å2-0 Å2
3----2.4276 Å2
Refinement stepCycle: LAST / Resolution: 1.698→33.458 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2186 0 0 182 2368
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062232
X-RAY DIFFRACTIONf_angle_d0.9783024
X-RAY DIFFRACTIONf_chiral_restr0.071338
X-RAY DIFFRACTIONf_plane_restr0.004390
X-RAY DIFFRACTIONf_dihedral_angle_d13.244817
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6979-1.74030.33151180.2751624174282
1.7403-1.78740.32471280.24711786191489
1.7874-1.840.26661320.21011784191691
1.84-1.89940.26461360.19941874201093
1.8994-1.96730.26011300.19531849197995
1.9673-2.0460.20161380.18651955209397
2.046-2.13910.20681400.18821967210798
2.1391-2.25190.23481390.19051960209999
2.2519-2.39290.18711390.18581998213799
2.3929-2.57760.21181420.19892013215599
2.5776-2.83690.24551440.195920132157100
2.8369-3.24710.26131460.200520612207100
3.2471-4.08980.19451470.166320752222100
4.0898-33.46450.17151530.19022151230498

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