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- PDB-2wjj: Structure and function of the FeoB G-domain from Methanococcus ja... -

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Basic information

Entry
Database: PDB / ID: 2wjj
TitleStructure and function of the FeoB G-domain from Methanococcus jannaschii
ComponentsFERROUS IRON TRANSPORT PROTEIN B HOMOLOG
KeywordsMETAL TRANSPORT / MEMBRANE G-PROTEINS / FERROUS IRON TRANSPORT / CELL MEMBRANE / ION TRANSPORT / TRANSMEMBRANE / NUCLEOTIDE BINDING MOTIFS / IRON / GNBPS / MEMBRANE / TRANSPORT / GTP-BINDING / IRON TRANSPORT / NUCLEOTIDE-BINDING
Function / homology
Function and homology information


ferrous iron transmembrane transporter activity / GTP binding / metal ion binding / plasma membrane
Similarity search - Function
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 ...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 / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / Fe(2+) transporter FeoB
Similarity search - Component
Biological speciesMETHANOCALDOCOCCUS JANNASCHII (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.405 Å
AuthorsKoester, S. / Wehner, M. / Herrmann, C. / Kuehlbrandt, W. / Yildiz, O.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Structure and Function of the Feob G-Domain from Methanococcus Jannaschii
Authors: Koester, S. / Wehner, M. / Herrmann, C. / Kuehlbrandt, W. / Yildiz, O.
History
DepositionMay 26, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 28, 2009Provider: repository / Type: Initial release
Revision 1.1May 19, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FERROUS IRON TRANSPORT PROTEIN B HOMOLOG
B: FERROUS IRON TRANSPORT PROTEIN B HOMOLOG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,2784
Polymers37,3922
Non-polymers8862
Water1,29772
1
A: FERROUS IRON TRANSPORT PROTEIN B HOMOLOG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,1392
Polymers18,6961
Non-polymers4431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: FERROUS IRON TRANSPORT PROTEIN B HOMOLOG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,1392
Polymers18,6961
Non-polymers4431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)84.670, 84.670, 137.870
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-2032-

HOH

21A-2036-

HOH

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Components

#1: Protein FERROUS IRON TRANSPORT PROTEIN B HOMOLOG


Mass: 18696.016 Da / Num. of mol.: 2 / Fragment: FEOB G-DOMAIN, RESIDUES 1-167
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) METHANOCALDOCOCCUS JANNASCHII (archaea)
Plasmid: PET / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q57986
#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 72 / 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: 3.26 Å3/Da / Density % sol: 62.03 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9786
DetectorType: ADSC CCD / Detector: CCD / Date: May 25, 2007
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.4→20 Å / Num. obs: 37096 / % possible obs: 99 % / Observed criterion σ(I): 1.98 / Redundancy: 9.7 % / Biso Wilson estimate: 55.66 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 18
Reflection shellResolution: 2.4→2.5 Å / Redundancy: 5.1 % / Rmerge(I) obs: 1.13 / Mean I/σ(I) obs: 1.92 / % possible all: 91.9

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 2.405→45.202 Å / SU ML: 0.37 / σ(F): 1.48 / Phase error: 23.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2279 1832 4.9 %
Rwork0.1826 --
obs0.1848 37015 99.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 74.478 Å2 / ksol: 0.355 e/Å3
Displacement parametersBiso mean: 69.17 Å2
Baniso -1Baniso -2Baniso -3
1-7.1086 Å20 Å20 Å2
2--7.1086 Å20 Å2
3----14.2171 Å2
Refinement stepCycle: LAST / Resolution: 2.405→45.202 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2566 0 56 72 2694
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072667
X-RAY DIFFRACTIONf_angle_d1.1363617
X-RAY DIFFRACTIONf_dihedral_angle_d20.15998
X-RAY DIFFRACTIONf_chiral_restr0.064433
X-RAY DIFFRACTIONf_plane_restr0.004444
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4047-2.46980.32991340.29392586X-RAY DIFFRACTION96
2.4698-2.54240.30481410.25412721X-RAY DIFFRACTION100
2.5424-2.62450.29161420.23472712X-RAY DIFFRACTION100
2.6245-2.71830.28791470.23092740X-RAY DIFFRACTION100
2.7183-2.82710.24121430.21492718X-RAY DIFFRACTION100
2.8271-2.95570.26891380.21022721X-RAY DIFFRACTION100
2.9557-3.11150.24621440.19682715X-RAY DIFFRACTION100
3.1115-3.30640.27351380.19062730X-RAY DIFFRACTION100
3.3064-3.56160.25171490.18772715X-RAY DIFFRACTION100
3.5616-3.91990.22841410.15842709X-RAY DIFFRACTION100
3.9199-4.48660.1641420.14192738X-RAY DIFFRACTION100
4.4866-5.6510.18361400.14012717X-RAY DIFFRACTION100
5.651-45.21040.20961330.18122661X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: 40.4815 Å / Origin y: 21.5794 Å / Origin z: 52.3056 Å
111213212223313233
T0.3918 Å2-0.0779 Å2-0.0023 Å2-0.3588 Å20.0822 Å2--0.2995 Å2
L1.2897 °20.198 °21.2539 °2-0.9395 °20.4522 °2--2.077 °2
S-0.0944 Å °0.2688 Å °0.1269 Å °-0.1593 Å °-0.0935 Å °0.0695 Å °-0.1308 Å °0.4049 Å °0.1811 Å °
Refinement TLS groupSelection details: ALL

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