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- PDB-2wic: Crystal Structures of the N-terminal Intracellular Domain of FeoB... -

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Entry
Database: PDB / ID: 2wic
TitleCrystal Structures of the N-terminal Intracellular Domain of FeoB from Klebsiella Pneumoniae in GMPPNP binding state
ComponentsFERROUS IRON TRANSPORT PROTEIN B
KeywordsMETAL TRANSPORT / SIGNAL TRANSDUCTION / FERROUS IRON TRANSPORT / MEMBRANE PROTEIN / G PROTEIN
Function / homology
Function and homology information


ferrous iron transmembrane transporter activity / GTP binding / metal ion 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 / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / Ferrous iron transport protein B
Similarity search - Component
Biological speciesKLEBSIELLA PNEUMONIAE (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.05 Å
AuthorsHung, K.-W. / Chang, Y.-W. / Chen, J.-H. / Chen, Y.-C. / Sun, Y.-J. / Hsiao, C.-D. / Huang, T.-H.
Citation
Journal: 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.
#1: Journal: Gene / Year: 2004
Title: Sequencing and Analysis of the Large Virulence Plasmid Plvpk of Klebsiella Pneumoniae Cg43.
Authors: Chen, Y. / Chang, H. / Lai, Y. / Pan, C. / Tsai, S. / Peng, H.
History
DepositionMay 9, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 19, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FERROUS IRON TRANSPORT PROTEIN B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7044
Polymers29,1331
Non-polymers5713
Water1,08160
1
A: FERROUS IRON TRANSPORT PROTEIN B
hetero molecules

A: FERROUS IRON TRANSPORT PROTEIN B
hetero molecules

A: FERROUS IRON TRANSPORT PROTEIN B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,11212
Polymers87,3993
Non-polymers1,7129
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_545-y,z-1/2,-x+1/21
crystal symmetry operation7_555-z+1/2,-x,y+1/21
Buried area7250 Å2
ΔGint-57.5 kcal/mol
Surface area31150 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)106.897, 106.897, 106.897
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11A-1267-

MG

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Components

#1: Protein FERROUS IRON TRANSPORT PROTEIN B / FEOB


Mass: 29133.160 Da / Num. of mol.: 1 / Fragment: N-TERMINAL INTRACELLULAR DOMAIN, RESIDUES 1-267
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) KLEBSIELLA PNEUMONIAE (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834 / References: UniProt: A6TF32
#2: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / 5'-Guanylyl imidodiphosphate


Mass: 522.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 60 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.39 Å3/Da / Density % sol: 63.8 % / Description: NONE
Crystal growDetails: 100 MM TRIS-HCL PH 8.5, 25% PEG4000, 100 MM NA ACETATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 0.97869 , 0.97888, 0.96365
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.978691
20.978881
30.963651
ReflectionResolution: 2.05→25.93 Å / Num. obs: 48292 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 4.8 % / Biso Wilson estimate: 19.3 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 22.7
Reflection shellResolution: 2.05→2.12 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 3.1 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.2refinement
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 2.05→25.93 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 102628.86 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.218 1204 2.9 %RANDOM
Rwork0.215 ---
obs0.215 41181 83.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 43.8481 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 45.9 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.1 Å0.09 Å
Refinement stepCycle: LAST / Resolution: 2.05→25.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1883 0 34 60 1977
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.021
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_deg2.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d3.15
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.41.5
X-RAY DIFFRACTIONc_mcangle_it2.272
X-RAY DIFFRACTIONc_scbond_it1.992
X-RAY DIFFRACTIONc_scangle_it3.032.5
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 2.05→2.18 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.228 147 3 %
Rwork0.217 4673 -
obs--58.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER_REP.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4GNP.PARGNP.TOP

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