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- PDB-5dh2: Structure of the siderophore periplasmic binding protein from the... -

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Basic information

Entry
Database: PDB / ID: 5dh2
TitleStructure of the siderophore periplasmic binding protein from the fuscachelin gene cluster of Thermobifida fusca in I222
Componentssiderophore periplasmic binding protein
KeywordsPROTEIN BINDING / Siderophore / Periplasmic Binding Protein / fuscachelin
Function / homologyABC transporter periplasmic binding domain / Periplasmic binding protein / Iron siderophore/cobalamin periplasmic-binding domain profile. / Similar to iron(III) dicitrate transport permease RBL00804
Function and homology information
Biological speciesThermobifida fusca (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.59 Å
AuthorsLi, K. / Bruner, S.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1411991 United States
CitationJournal: Proteins / Year: 2016
Title: Structure and functional analysis of the siderophore periplasmic binding protein from the fuscachelin gene cluster of Thermobifida fusca.
Authors: Li, K. / Bruner, S.D.
History
DepositionAug 29, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 18, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2016Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: siderophore periplasmic binding protein
B: siderophore periplasmic binding protein


Theoretical massNumber of molelcules
Total (without water)67,4702
Polymers67,4702
Non-polymers00
Water63135
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1190 Å2
ΔGint-6 kcal/mol
Surface area24330 Å2
Unit cell
Length a, b, c (Å)106.632, 107.102, 136.287
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein siderophore periplasmic binding protein


Mass: 33735.133 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermobifida fusca (strain YX) (bacteria)
Strain: YX / Gene: Tfu_1864 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q47NS2
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 35 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.89 Å3/Da / Density % sol: 57.37 % / Description: rod-shaped
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.16 M ammonium acetate 32% w/v polyethylene glycol 4,000 0.1 M sodium acetate pH 4.6
PH range: 4.6-7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 24, 2014
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.59→37.783 Å / Num. obs: 24621 / % possible obs: 99.9 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.047 / Net I/σ(I): 23.5
Reflection shellResolution: 2.59→2.71 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.516 / Mean I/σ(I) obs: 3.8 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSOSX10.9.5_Darwin13.4.0data reduction
Aimless0.5.8data scaling
PHASER2.5.6phasing
ARP3.3.1model building
RefinementMethod to determine structure: SAD / Resolution: 2.59→37.783 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 32.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2632 1185 4.82 %RANDOM
Rwork0.2295 ---
obs0.2312 24566 99.67 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.59→37.783 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4247 0 0 35 4282
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044332
X-RAY DIFFRACTIONf_angle_d0.7445897
X-RAY DIFFRACTIONf_dihedral_angle_d14.8661546
X-RAY DIFFRACTIONf_chiral_restr0.028662
X-RAY DIFFRACTIONf_plane_restr0.003792
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.59-2.70790.32011330.3022884X-RAY DIFFRACTION100
2.7079-2.85060.34191270.29892898X-RAY DIFFRACTION99
2.8506-3.02910.3361320.29172903X-RAY DIFFRACTION100
3.0291-3.26290.37991520.2852889X-RAY DIFFRACTION100
3.2629-3.5910.27291650.24582893X-RAY DIFFRACTION100
3.591-4.11010.2581410.22142936X-RAY DIFFRACTION100
4.1101-5.17620.23181560.20082949X-RAY DIFFRACTION100
5.1762-37.78690.23491790.20673029X-RAY DIFFRACTION99

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