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- PDB-3k53: Crystal Structure of NFeoB from P. furiosus -

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Basic information

Entry
Database: PDB / ID: 3k53
TitleCrystal Structure of NFeoB from P. furiosus
ComponentsFerrous iron transport protein b
KeywordsMETAL TRANSPORT / GTPase fold / helical bundle / G-protein / prokaryote / GTP-binding / Nucleotide-binding
Function / homology
Function and homology information


ferrous iron transmembrane transporter activity / membrane => GO:0016020 / GTP binding / plasma membrane
Similarity search - Function
Helix Hairpins - #1770 / FeoB, cytosolic helical domain / FeoB cytosolic helical domain / Ferrous iron transport protein B, C-terminal / Ferrous iron transport protein B C terminus / Ferrous iron transport protein B / FeoB-type guanine nucleotide-binding (G) domain / Ferrous iron transport protein B / FeoB-type guanine nucleotide-binding (G) domain profile. / Nucleoside transporter/FeoB GTPase, Gate domain ...Helix Hairpins - #1770 / FeoB, cytosolic helical domain / FeoB cytosolic helical domain / Ferrous iron transport protein B, C-terminal / Ferrous iron transport protein B C terminus / Ferrous iron transport protein B / FeoB-type guanine nucleotide-binding (G) domain / Ferrous iron transport protein B / FeoB-type guanine nucleotide-binding (G) domain profile. / Nucleoside transporter/FeoB GTPase, Gate domain / Nucleoside recognition / GTP binding domain / Helix Hairpins / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Ferrous iron transport protein b
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å
AuthorsEng, E.T. / Dong, G. / Unger, V.M.
CitationJournal: J.Struct.Biol. / Year: 2010
Title: Structural fold, conservation and Fe(II) binding of the intracellular domain of prokaryote FeoB.
Authors: Hung, K.W. / Chang, Y.W. / Eng, E.T. / Chen, J.H. / Chen, Y.C. / Sun, Y.J. / Hsiao, C.D. / Dong, G. / Spasov, K.A. / Unger, V.M. / Huang, T.H.
History
DepositionOct 6, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 26, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ferrous iron transport protein b
B: Ferrous iron transport protein b
C: Ferrous iron transport protein b
D: Ferrous iron transport protein b


Theoretical massNumber of molelcules
Total (without water)124,7634
Polymers124,7634
Non-polymers00
Water99155
1
A: Ferrous iron transport protein b
B: Ferrous iron transport protein b


Theoretical massNumber of molelcules
Total (without water)62,3822
Polymers62,3822
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2210 Å2
ΔGint-5 kcal/mol
Surface area24090 Å2
MethodPISA
2
C: Ferrous iron transport protein b
D: Ferrous iron transport protein b


Theoretical massNumber of molelcules
Total (without water)62,3822
Polymers62,3822
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2230 Å2
ΔGint-10 kcal/mol
Surface area24150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.256, 106.108, 253.892
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
Ferrous iron transport protein b


Mass: 31190.826 Da / Num. of mol.: 4 / Fragment: N-terminal domain (UNP residues 2-270)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8U2H8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / 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: 2.98 Å3/Da / Density % sol: 58.76 %
Crystal growTemperature: 296 K / pH: 5
Details: sodium acetate, PEG 1000, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 296K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.98
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 17, 2007
RadiationMonochromator: SINGLE CRYSTAL SIDE BOUNCE MONOCHROMATOR, KOHZU HLD8-24
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 98053 / % possible obs: 98.8 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 17.9
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.595 / % possible all: 90.5

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
CNSrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data reduction
RefinementMethod to determine structure: SAD / Resolution: 2.7→50 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.286 4036 5.1 %
Rwork0.23 --
obs0.23 74508 94.1 %
Solvent computationBsol: 48.09 Å2
Displacement parametersBiso mean: 72.76 Å2
Baniso -1Baniso -2Baniso -3
1-25.71 Å20 Å20 Å2
2---0.781 Å20 Å2
3----24.929 Å2
Refinement stepCycle: LAST / Resolution: 2.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8641 0 0 55 8696
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d
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_deg
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.2411.5
X-RAY DIFFRACTIONc_mcangle_it2.1952
X-RAY DIFFRACTIONc_scbond_it1.5992
X-RAY DIFFRACTIONc_scangle_it2.5892.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PROTEIN_REP.PARAM
X-RAY DIFFRACTION2WATER.PARAM
X-RAY DIFFRACTION3WATER_REP.PARAM

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