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- PDB-5dh0: Structure of the siderophore periplasmic binding protein from the... -

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Basic information

Entry
Database: PDB / ID: 5dh0
TitleStructure of the siderophore periplasmic binding protein from the fuscachelin gene cluster of Thermobifida fusca in P41
Componentssiderophore periplasmic binding protein
KeywordsPROTEIN BINDING / Siderophore / Periplasmic Binding Protein / fuscachelin
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
Similar to iron(III) dicitrate transport permease RBL00804
Similarity search - Component
Biological speciesThermobifida fusca (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.444 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
B: siderophore periplasmic binding protein
A: siderophore periplasmic binding protein


Theoretical massNumber of molelcules
Total (without water)67,4702
Polymers67,4702
Non-polymers00
Water1,60389
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area630 Å2
ΔGint-1 kcal/mol
Surface area25140 Å2
Unit cell
Length a, b, c (Å)72.983, 72.983, 135.267
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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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


Mass: 18.015 Da / Num. of mol.: 89 / 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: 2.66 Å3/Da / Density % sol: 53.84 % / Description: rod-shaped
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.16 M ammonium acetate 32% w/v PEG 4,000 0.1 M MES pH 6.5
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: 0.97857 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: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.44→38.36 Å / Num. obs: 26118 / % possible obs: 99.6 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.101 / Net I/σ(I): 12.2
Reflection shellResolution: 2.44→2.54 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.689 / Mean I/σ(I) obs: 3.3 / % possible all: 97.6

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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: 2.444→38.359 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2185 1353 5.19 %Random selection
Rwork0.1707 ---
obs0.1732 26077 99.52 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.444→38.359 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4268 0 0 89 4357
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084363
X-RAY DIFFRACTIONf_angle_d1.055945
X-RAY DIFFRACTIONf_dihedral_angle_d16.0241547
X-RAY DIFFRACTIONf_chiral_restr0.041671
X-RAY DIFFRACTIONf_plane_restr0.005798
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4438-2.53110.32631230.22922404X-RAY DIFFRACTION97
2.5311-2.63240.26851310.20892478X-RAY DIFFRACTION100
2.6324-2.75220.29231210.21142492X-RAY DIFFRACTION100
2.7522-2.89720.27391530.21162469X-RAY DIFFRACTION100
2.8972-3.07870.23881190.21152502X-RAY DIFFRACTION100
3.0787-3.31630.27581290.20352488X-RAY DIFFRACTION100
3.3163-3.64980.23141420.17482464X-RAY DIFFRACTION100
3.6498-4.17730.19511480.1472465X-RAY DIFFRACTION100
4.1773-5.26080.17741530.13522477X-RAY DIFFRACTION100
5.2608-38.36370.17411340.14822485X-RAY DIFFRACTION99

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