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- PDB-3hxp: Crystal structure of the FhuD fold-family BSU3320, a periplasmic ... -

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Basic information

Entry
Database: PDB / ID: 3hxp
TitleCrystal structure of the FhuD fold-family BSU3320, a periplasmic binding protein component of a Fep/Fec-like ferrichrome ABC transporter from Bacillus subtilis. Northeast Structural Genomics Consortium Target SR577
ComponentsIron(3+)-hydroxamate-binding protein fhuD
KeywordsTRANSPORT PROTEIN / alpha-beta protein / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG / Cell membrane / Ion transport / Iron / Iron transport / Lipoprotein / Membrane / Palmitate / Transport
Function / homology
Function and homology information


iron ion transport / outer membrane-bounded periplasmic space / membrane raft / plasma membrane
Similarity search - Function
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
Iron(3+)-hydroxamate-binding protein FhuD
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.2 Å
AuthorsForouhar, F. / Neely, H. / Seetharaman, J. / Fang, F. / Xiao, R. / Cunningham, K. / Ma, L. / Chen, C.X. / Everett, J.K. / Nair, R. ...Forouhar, F. / Neely, H. / Seetharaman, J. / Fang, F. / Xiao, R. / Cunningham, K. / Ma, L. / Chen, C.X. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Northeast Structural Genomics Consortium Target SR577
Authors: Forouhar, F. / Neely, H. / Seetharaman, J. / Fang, F. / Xiao, R. / Cunningham, K. / Ma, L. / Chen, C.X. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F.
History
DepositionJun 21, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 7, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.contact_author / _software.contact_author_email ..._software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Iron(3+)-hydroxamate-binding protein fhuD


Theoretical massNumber of molelcules
Total (without water)33,3731
Polymers33,3731
Non-polymers00
Water25214
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)71.453, 126.955, 38.610
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Iron(3+)-hydroxamate-binding protein fhuD / Iron(III)-hydroxamate-binding protein fhuD / Ferrichrome-binding protein / Ferric hydroxamate uptake protein D


Mass: 33373.027 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 / Gene: BSU33320, fhuD / Plasmid: pET21 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)+ Magic / References: UniProt: P37580
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 2.62 Å3/Da / Density % sol: 53.12 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 9
Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5) . Reservoir solution: 50 mM TAPS (pH 9), 20% PEG 8K, and 25mM KCl. , VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 10, 2008 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 3.2→30 Å / Num. all: 11667 / Num. obs: 10255 / % possible obs: 87.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 76.3 Å2 / Rmerge(I) obs: 0.076 / Rsym value: 0.061 / Net I/σ(I): 16.2
Reflection shellResolution: 3.2→3.31 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.229 / Mean I/σ(I) obs: 2.6 / Num. unique all: 1171 / Rsym value: 0.215 / % possible all: 81.6

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Processing

Software
NameVersionClassificationNB
CNS1.2 & XtalViewrefinement
PDB_EXTRACT3data extraction
ADSCQuantumdata collection
DENZOdata reduction
SCALEPACKdata scaling
SnBthen SOLVE/RESOLVEphasing
REFMACrefinement
RefinementMethod to determine structure: SAD / Resolution: 3.2→19.31 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 375966.906 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.272 776 10 %RANDOM
Rwork0.222 ---
all0.227 11149 --
obs0.225 7749 69.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 2.232 Å2 / ksol: 0.25 e/Å3
Displacement parametersBiso mean: 83.5 Å2
Baniso -1Baniso -2Baniso -3
1--26.68 Å20 Å20 Å2
2--49.92 Å20 Å2
3----23.24 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.59 Å0.49 Å
Luzzati d res low-5 Å
Luzzati sigma a1.02 Å0.69 Å
Refinement stepCycle: LAST / Resolution: 3.2→19.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2123 0 0 14 2137
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d23.3
X-RAY DIFFRACTIONc_improper_angle_d0.82
LS refinement shellResolution: 3.2→3.31 Å / Rfactor Rfree error: 0.054 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.373 47 8.7 %
Rwork0.292 491 -
obs-538 48.5 %

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