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- PDB-3g9q: Crystal structure of the FhuD fold-family BSU3320, a periplasmic ... -

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Basic information

Entry
Database: PDB / ID: 3g9q
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 SR577A
ComponentsFerrichrome-binding protein
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 subsp. subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å
AuthorsForouhar, F. / Neely, H. / Seetharaman, J. / Janjua, H. / Mao, L. / Xiao, R. / Ciccosanti, C. / Foote, E.L. / Lee, D. / Nair, R. ...Forouhar, F. / Neely, H. / Seetharaman, J. / Janjua, H. / Mao, L. / Xiao, R. / Ciccosanti, C. / Foote, E.L. / Lee, D. / 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: Crystal 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 ...Title: Crystal 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 SR577A.
Authors: Forouhar, F. / Neely, H. / Seetharaman, J. / Janjua, H. / Mao, L. / Xiao, R. / Ciccosanti, C. / Foote, E.L. / Lee, D. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F.
History
DepositionFeb 13, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ferrichrome-binding protein


Theoretical massNumber of molelcules
Total (without water)31,2371
Polymers31,2371
Non-polymers00
Water55831
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)35.517, 69.898, 114.169
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 Ferrichrome-binding protein


Mass: 31236.990 Da / Num. of mol.: 1 / Fragment: UNP residues 45-315
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis (bacteria)
Strain: 168 / Gene: BSU33320, fhuD / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: P37580
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / 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: 2.27 Å3/Da / Density % sol: 45.78 %
Crystal growTemperature: 291 K / pH: 7.5
Details: Protein solution: 10 mM Tris-HCl pH 7.5, 100 mM Sodium chloride, 5 mM DTT. Reservoir solution: 20% PEG 3350, 200 mM NaNO3, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.97862
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Feb 4, 2009 / Details: MIRRORS
RadiationMonochromator: SI(111) CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97862 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. obs: 16199 / % possible obs: 96.6 % / Observed criterion σ(I): 0 / Redundancy: 6.3 % / Biso Wilson estimate: 34.8 Å2 / Rmerge(I) obs: 0.077 / Rsym value: 0.069 / Net I/σ(I): 25.87
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 6 % / Rmerge(I) obs: 0.214 / Mean I/σ(I) obs: 4.9 / Rsym value: 0.198 / % possible all: 88.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SnBphasing
SOLVEphasing
RESOLVEmodel building
CNS1.2refinement
HKL-2000data reduction
SCALEPACKdata scaling
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.6→19.12 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1160204.83 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: ENGH & HUBER / Details: PROGRAM XTALVIEW HAS ALSO BEEN USED IN REFINEMENT
RfactorNum. reflection% reflectionSelection details
Rfree0.291 1349 9.6 %RANDOM
Rwork0.222 ---
obs0.222 13992 83.5 %-
all-16199 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 21.14 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso mean: 59.3 Å2
Baniso -1Baniso -2Baniso -3
1-28.87 Å20 Å20 Å2
2---13.52 Å20 Å2
3----15.36 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.57 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.63 Å0.45 Å
Refinement stepCycle: LAST / Resolution: 2.6→19.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2021 0 0 31 2052
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.79
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.6→2.69 Å / Rfactor Rfree error: 0.051 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.463 83 8.8 %
Rwork0.32 858 -
obs--55 %

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