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- PDB-4q5i: Crystal structure of a T151A mutant of the E. coli FeoB G-domain -

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Basic information

Entry
Database: PDB / ID: 4q5i
TitleCrystal structure of a T151A mutant of the E. coli FeoB G-domain
ComponentsFerrous iron transport protein B
KeywordsMETAL TRANSPORT / G PROTEIN / IRON TRANSPORT / GTPASE / TRANSMEMBRANE / GTP binding
Function / homology
Function and homology information


iron ion import across plasma membrane / ferrous iron transmembrane transporter activity / DNA damage response / GTP binding / identical protein 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 / 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
Fe(2+) transporter FeoB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsJormakka, M. / Guilfoyle, A.P. / Deshpande, C.N. / Maher, M.
CitationJournal: Biosci.Rep. / Year: 2014
Title: Exploring the correlation between the sequence composition of the nucleotide binding G5 loop of the FeoB GTPase domain (NFeoB) and intrinsic rate of GDP release.
Authors: Guilfoyle, A.P. / Deshpande, C.N. / Schenk, G. / Maher, M.J. / Jormakka, M.
History
DepositionApr 17, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 8, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
C: Ferrous iron transport protein B
D: Ferrous iron transport protein B
E: Ferrous iron transport protein B
F: Ferrous iron transport protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)178,2007
Polymers178,1036
Non-polymers961
Water1,02757
1
A: Ferrous iron transport protein B


Theoretical massNumber of molelcules
Total (without water)29,6841
Polymers29,6841
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Ferrous iron transport protein B


Theoretical massNumber of molelcules
Total (without water)29,6841
Polymers29,6841
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Ferrous iron transport protein B


Theoretical massNumber of molelcules
Total (without water)29,6841
Polymers29,6841
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Ferrous iron transport protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7802
Polymers29,6841
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Ferrous iron transport protein B


Theoretical massNumber of molelcules
Total (without water)29,6841
Polymers29,6841
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Ferrous iron transport protein B


Theoretical massNumber of molelcules
Total (without water)29,6841
Polymers29,6841
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.978, 82.779, 95.505
Angle α, β, γ (deg.)115.67, 108.50, 90.06
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Ferrous iron transport protein B


Mass: 29683.916 Da / Num. of mol.: 6 / Fragment: FeoB G-domain, UNP RESIDUES 1-270 / Mutation: T151A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: feoB, b3409, JW3372 / Plasmid: pGEX-4T-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P33650
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 57 / 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: 2.28 Å3/Da / Density % sol: 46.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 29% PEG 400, 0.1M HEPES pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 5, 2010
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. all: 45132 / Num. obs: 45132 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.066 / Net I/σ(I): 11.2
Reflection shell
Resolution (Å)Rmerge(I) obsDiffraction-ID% possible all
2.8-2.90.367196.9
2.9-3.020.283196.9
3.02-3.150.21196.9
3.15-3.320.157197.3
3.32-3.530.118197
3.53-3.80.088197.5
3.8-4.180.071197.5
4.18-4.790.053197.3
4.79-6.030.043197.3
6.03-500.032197.9

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMAC5.8.0049refinement
PDB_EXTRACT3.14data extraction
MARmosaic300 mm CCDdata collection
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→45.06 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.861 / SU B: 24.596 / SU ML: 0.461 / Cross valid method: THROUGHOUT / ESU R Free: 0.501 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29829 1907 5.1 %RANDOM
Rwork0.23854 ---
obs0.2415 35702 96.9 %-
all-45132 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 68.98 Å2
Baniso -1Baniso -2Baniso -3
1--5.19 Å20.29 Å20.79 Å2
2---4.51 Å21.72 Å2
3---4.04 Å2
Refinement stepCycle: LAST / Resolution: 2.8→45.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12068 0 5 57 12130
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.01912236
X-RAY DIFFRACTIONr_bond_other_d0.0010.0211970
X-RAY DIFFRACTIONr_angle_refined_deg0.6821.9816644
X-RAY DIFFRACTIONr_angle_other_deg0.634327432
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.77151575
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.69724.953527
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.41152106
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.1891581
X-RAY DIFFRACTIONr_chiral_restr0.0380.22012
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0213949
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022608
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6947.0086327
X-RAY DIFFRACTIONr_mcbond_other0.6947.0086326
X-RAY DIFFRACTIONr_mcangle_it1.30310.5097893
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.3957.0775909
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.872 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.404 146 -
Rwork0.347 2610 -
obs--96.53 %

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