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

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Basic information

Entry
Database: PDB / ID: 2wia
TitleCrystal Structures of the N-terminal Intracellular Domain of FeoB from Klebsiella Pneumoniae in Apo Form
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 / Ferrous iron transport protein B, C-terminal / Ferrous iron transport protein B C terminus / FeoB, cytosolic helical domain / FeoB cytosolic helical domain / 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. ...Helix Hairpins - #1770 / Ferrous iron transport protein B, C-terminal / Ferrous iron transport protein B C terminus / FeoB, cytosolic helical domain / FeoB cytosolic helical domain / 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 / 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 speciesKLEBSIELLA PNEUMONIAE (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 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
Revision 1.3May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,3154
Polymers58,2662
Non-polymers492
Water3,567198
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)87,4726
Polymers87,3993
Non-polymers733
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area3760 Å2
ΔGint-11.6 kcal/mol
Surface area31430 Å2
MethodPISA
2
B: FERROUS IRON TRANSPORT PROTEIN B
hetero molecules

B: FERROUS IRON TRANSPORT PROTEIN B
hetero molecules

B: FERROUS IRON TRANSPORT PROTEIN B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,4726
Polymers87,3993
Non-polymers733
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation2_555-y,x-y,z1
Buried area4580 Å2
ΔGint-61.6 kcal/mol
Surface area31060 Å2
MethodPISA
3
A: FERROUS IRON TRANSPORT PROTEIN B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1572
Polymers29,1331
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
B: FERROUS IRON TRANSPORT PROTEIN B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1572
Polymers29,1331
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.204, 84.204, 122.457
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11A-1262-

MG

21B-1262-

MG

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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-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 198 / 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: 2.09 Å3/Da / Density % sol: 41.2 % / Description: NONE
Crystal growDetails: 100 MM TRIS-HCL PH 8.5, 30% PEG4000, 200 MM MGCL2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.45→25.13 Å / Num. obs: 18109 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 4.6 % / Biso Wilson estimate: 19 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 18.9
Reflection shellResolution: 2.45→2.54 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 6.1 / % possible all: 100

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Processing

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

Resolution: 2.45→25.13 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 59095.74 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
Details: BULK SOLVENT MODEL USED SIDE CHAIN OF RESIDUES K3, Q51, Q69, T70, E74, E126, K127, Q128, Q129, R131, R152, E173, L187, D224, L226, D227, I228, L233, S234, D235, E236, L242 IN CHAIN A, AND ...Details: BULK SOLVENT MODEL USED SIDE CHAIN OF RESIDUES K3, Q51, Q69, T70, E74, E126, K127, Q128, Q129, R131, R152, E173, L187, D224, L226, D227, I228, L233, S234, D235, E236, L242 IN CHAIN A, AND K3, Q51, T70, E74, I124, E126, K127, Q128, R131, R152, E173, L187, Q190, Q191, S193, Q195, I196, I213, Y214, R216, K225, L226, D227, L233, D235, I237, D238, L242 IN CHAIN B ARE DISORDERED. WHOLE RESIDUE OF T65 TO S68, V149 TO T151 IN CHAIN A, AND T65 TO Q69, V149 TO T151 IN CHAIN B ARE DISORDERED.
RfactorNum. reflection% reflectionSelection details
Rfree0.23 817 4.8 %RANDOM
Rwork0.209 ---
obs0.209 16910 93.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 38.1939 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 30 Å2
Baniso -1Baniso -2Baniso -3
1--5.77 Å20 Å20 Å2
2---5.77 Å20 Å2
3---11.53 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.1 Å0.1 Å
Refinement stepCycle: LAST / Resolution: 2.45→25.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3689 0 2 198 3889
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.031
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_deg2.7
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d2.78
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.141.5
X-RAY DIFFRACTIONc_mcangle_it1.922
X-RAY DIFFRACTIONc_scbond_it1.772
X-RAY DIFFRACTIONc_scangle_it2.522.5
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 2.45→2.6 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.191 133 5.3 %
Rwork0.196 2375 -
obs--83.2 %
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

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