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

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Basic information

Entry
Database: PDB / ID: 2wjg
TitleStructure and function of the FeoB G-domain from Methanococcus jannaschii
Components
  • FERROUS IRON TRANSPORT PROTEIN B HOMOLOG
  • POLYALANINE
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)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 9, 2019Group: Data collection / Other / Source and taxonomy / Category: pdbx_database_status / pdbx_entity_src_syn / Item: _pdbx_database_status.status_code_sf

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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
C: POLYALANINE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,9425
Polymers42,0563
Non-polymers8862
Water2,432135
1
A: FERROUS IRON TRANSPORT PROTEIN B HOMOLOG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2132
Polymers20,7701
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)21,2132
Polymers20,7701
Non-polymers4431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: POLYALANINE


  • defined by author&software
  • 516 Da, 1 polymers
Theoretical massNumber of molelcules
Total (without water)5161
Polymers5161
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)84.770, 84.770, 137.900
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-2081-

HOH

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Components

#1: Protein FERROUS IRON TRANSPORT PROTEIN B HOMOLOG / FEOB


Mass: 20770.178 Da / Num. of mol.: 2 / Fragment: FEOB G-DOMAIN, RESIDUES 1-184
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) METHANOCALDOCOCCUS JANNASCHII (archaea)
Plasmid: PET / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q57986
#2: Protein/peptide POLYALANINE


Mass: 515.560 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: 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
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 135 / 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: 3.15 Å3/Da / Density % sol: 60.62 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. obs: 24483 / % possible obs: 93.3 % / Observed criterion σ(I): 4.8 / Redundancy: 14.1 % / Biso Wilson estimate: 38.7 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 29.2
Reflection shellResolution: 2.23→2.4 Å / Rmerge(I) obs: 0.78 / Mean I/σ(I) obs: 3.5 / % possible all: 89.3

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→29.287 Å / SU ML: 0.38 / σ(F): 1.99 / Phase error: 29.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2442 1225 5 %
Rwork0.2162 --
obs0.2177 24457 93.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 75.994 Å2 / ksol: 0.364 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-7.3496 Å20 Å2-0 Å2
2--7.3496 Å20 Å2
3----14.6991 Å2
Refinement stepCycle: LAST / Resolution: 2.2→29.287 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2620 0 56 135 2811
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072711
X-RAY DIFFRACTIONf_angle_d1.2153673
X-RAY DIFFRACTIONf_dihedral_angle_d20.3191007
X-RAY DIFFRACTIONf_chiral_restr0.074439
X-RAY DIFFRACTIONf_plane_restr0.004452
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2001-2.28820.61231320.61772496X-RAY DIFFRACTION92
2.2882-2.39230.2609700.28091330X-RAY DIFFRACTION49
2.3923-2.51830.29921430.23452709X-RAY DIFFRACTION100
2.5183-2.6760.26591430.21622717X-RAY DIFFRACTION100
2.676-2.88250.2261440.20142737X-RAY DIFFRACTION100
2.8825-3.17220.26921450.21332756X-RAY DIFFRACTION100
3.1722-3.63050.27541450.20452746X-RAY DIFFRACTION99
3.6305-4.57130.19221470.15832790X-RAY DIFFRACTION99
4.5713-29.28960.17121560.16032951X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -2.6248 Å / Origin y: 21.1218 Å / Origin z: -17.9231 Å
111213212223313233
T0.2925 Å20.0584 Å20.0041 Å2-0.2822 Å20.0601 Å2--0.2557 Å2
L0.7487 °20.071 °2-1.1627 °2-0.7926 °20.2207 °2--2.04 °2
S-0.1065 Å °-0.2768 Å °-0.051 Å °0.1779 Å °-0.0818 Å °0.0536 Å °0.0371 Å °0.4213 Å °0.1731 Å °
Refinement TLS groupSelection details: ALL

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