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

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Basic information

Entry
Database: PDB / ID: 2wib
TitleCrystal Structures of the N-terminal Intracellular Domain of FeoB from Klebsiella Pneumoniae in GDP 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
GUANOSINE-5'-DIPHOSPHATE / Ferrous iron transport protein B
Similarity search - Component
Biological speciesKLEBSIELLA PNEUMONIAE (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.56 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.
Remark 700 SHEET 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
B: FERROUS IRON TRANSPORT PROTEIN B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,1534
Polymers58,2662
Non-polymers8862
Water2,108117
1
A: FERROUS IRON TRANSPORT PROTEIN B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5762
Polymers29,1331
Non-polymers4431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: FERROUS IRON TRANSPORT PROTEIN B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5762
Polymers29,1331
Non-polymers4431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)86.552, 184.688, 38.168
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein FERROUS IRON TRANSPORT PROTEIN B / FEOB


Mass: 29133.160 Da / Num. of mol.: 2 / 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): BL21(DE3) / References: UniProt: A6TF32
#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.: 117 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE GENE AND PROTEIN SEQUENCE OF KLEBSIELLA PNEUMONIAE FEOB WERE PROVIDED BY DR. SHIH-FENG TASI. ...THE GENE AND PROTEIN SEQUENCE OF KLEBSIELLA PNEUMONIAE FEOB WERE PROVIDED BY DR. SHIH-FENG TASI. THE AMINO ACID SEQUENCE IS AFFIRMED AS ACCURATE. REFERENCE: SEQUENCING AND ANALYSIS OF THE LARGE VIRULENCE PLASMID PLVPK OF KLEBSIELLA PNEUMONIAE CG43,Y.-T.CHEN ET AL., GENE, VOLUME 337, 4 AUGUST 2004, PAGES 189-198.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.54 Å3/Da / Density % sol: 51.7 % / Description: NONE
Crystal growDetails: 100 MM TRIS-HCL PH 8.5, 30% PEG8000, 150 MM (NH4)2SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.56→19.53 Å / Num. obs: 19651 / % possible obs: 94.5 % / Observed criterion σ(I): 2 / Redundancy: 6.3 % / Biso Wilson estimate: 35.4 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 23.7
Reflection shellResolution: 2.56→2.65 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 3.9 / % possible all: 98.2

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Processing

Software
NameVersionClassification
CNS1.2refinement
CrystalCleardata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: STRUCTURE OF FEOB IN GMPPNP STATE

Resolution: 2.56→19.53 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 60552.9 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
Details: BULK SOLVENT MODEL USED SIDECHAINS OF RESIDUES K3, V36, I66, S67, S68, Q69, E74, Q75, E126, R131, R152, R154, E173, H176, L187, Q190, Q191, S193, R202, I213, Y214, R216, D221, D224, K225, ...Details: BULK SOLVENT MODEL USED SIDECHAINS OF RESIDUES K3, V36, I66, S67, S68, Q69, E74, Q75, E126, R131, R152, R154, E173, H176, L187, Q190, Q191, S193, R202, I213, Y214, R216, D221, D224, K225, D227, I228, L230, L233, S234, E236, I237, D238, N261 OF CHAIN A, AND R29, N32, V36, T37, V38, E39, E42, T65, I66, L72, E74, Q75, I76, R100, R131, R152, R154, D171, E173, H176, R183, Q190, Q191, R202, I213, Y214, S215, R216, Y218, D221, D224, K225, L226, I228, L230, L233, S234, D235, E236, I237, D238, Y249, N261, T262 OF CHAIN B ARE DISORDERED. FULL RESIDUES OF T262 TO P267 IN CHAIN A AND S67 TO S71, L263 TO P267 IN CHAIN B ARE DISORDERED.
RfactorNum. reflection% reflectionSelection details
Rfree0.236 849 4.9 %RANDOM
Rwork0.222 ---
obs0.222 17295 82.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 43.7078 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso mean: 51.7 Å2
Baniso -1Baniso -2Baniso -3
1--10.68 Å20 Å20 Å2
2---6.88 Å20 Å2
3---17.56 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.24 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 2.56→19.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3666 0 56 117 3839
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.034
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_deg3.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d4.37
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.221.5
X-RAY DIFFRACTIONc_mcangle_it2.12
X-RAY DIFFRACTIONc_scbond_it1.682
X-RAY DIFFRACTIONc_scangle_it2.432.5
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 2.56→2.7 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.268 101 4.5 %
Rwork0.238 2135 -
obs--65.4 %
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 DIFFRACTION4GDP.PARGDP.TOP

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