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- PDB-3b1w: Crystal structure of an S. thermophilus NFeoB E67A mutant bound to GDP -

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Basic information

Entry
Database: PDB / ID: 3b1w
TitleCrystal structure of an S. thermophilus NFeoB E67A mutant bound to GDP
ComponentsFerrous iron uptake transporter protein B
KeywordsMETAL TRANSPORT / G protein / iron transport / GTPase / transmembrane / potassium
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
GUANOSINE-5'-DIPHOSPHATE / Ferrous iron transport protein B
Similarity search - Component
Biological speciesStreptococcus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsAsh, M.R. / Maher, M.J. / Guss, J.M. / Jormakka, M.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2011
Title: A suite of Switch I and Switch II mutant structures from the G-protein domain of FeoB
Authors: Ash, M.R. / Maher, M.J. / Guss, J.M. / Jormakka, M.
History
DepositionJul 15, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 2, 2011Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2012Group: Database references
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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 uptake transporter protein B
B: Ferrous iron uptake transporter protein B
C: Ferrous iron uptake transporter protein B
D: Ferrous iron uptake transporter protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,3538
Polymers120,5804
Non-polymers1,7734
Water1,982110
1
A: Ferrous iron uptake transporter protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5882
Polymers30,1451
Non-polymers4431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Ferrous iron uptake transporter protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5882
Polymers30,1451
Non-polymers4431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Ferrous iron uptake transporter protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5882
Polymers30,1451
Non-polymers4431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Ferrous iron uptake transporter protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5882
Polymers30,1451
Non-polymers4431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.6, 92.1, 206.8
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Ferrous iron uptake transporter protein B


Mass: 30145.115 Da / Num. of mol.: 4 / Fragment: NFeoB, UNP residues 1-270 / Mutation: E67A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus thermophilus (bacteria) / Strain: LMG 18311 / Gene: FeoB / Plasmid: pGEX-4T-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5M586
#2: Chemical
ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / 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: 2.55 Å3/Da / Density % sol: 51.78 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: 0.1M ammonium acetate, 0.1M bis-tris(pH 6.0), 11%(w/v) PEG 10000, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95369 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 2, 2010
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95369 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 43672 / Num. obs: 43672 / % possible obs: 98.5 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 16.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allDiffraction-ID% possible all
2.5-2.544.50.5482.52110198.3
2.54-2.594.60.4952147198.3
2.59-2.644.70.4672148197.9
2.64-2.694.70.4322140198.6
2.69-2.754.70.3432119197.5
2.75-2.824.70.2982167198.4
2.82-2.894.70.2632141197.6
2.89-2.964.70.2262115196.6
2.96-3.054.70.1882117198.1
3.05-3.154.70.162161197.1
3.15-3.264.70.1392130196.8
3.26-3.394.70.1182157198.7
3.39-3.554.70.1032181198.8
3.55-3.734.80.0912200199.6
3.73-3.974.90.0842208199.6
3.97-4.2750.0742224199.8
4.27-4.75.10.0682254199.5
4.7-5.385.40.0652244199.8
5.38-6.785.30.05722901100
6.78-505.30.0342419199.7

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LX8

3lx8


Resolution: 2.5→47.09 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.902 / SU B: 20.693 / SU ML: 0.22 / Cross valid method: THROUGHOUT / ESU R Free: 0.297 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25905 2182 5.1 %RANDOM
Rwork0.21699 ---
obs0.21915 42786 98.17 %-
all-42786 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.12 Å2
Baniso -1Baniso -2Baniso -3
1-1.16 Å20 Å20 Å2
2--1.22 Å20 Å2
3----2.39 Å2
Refinement stepCycle: LAST / Resolution: 2.5→47.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7908 0 112 110 8130
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0228171
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4031.98111138
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.11551034
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.83225.436344
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.025151396
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6731540
X-RAY DIFFRACTIONr_chiral_restr0.0760.21354
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0216011
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.5821.55164
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.09728370
X-RAY DIFFRACTIONr_scbond_it1.68317
X-RAY DIFFRACTIONr_scangle_it2.8634.52768
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 168 -
Rwork0.276 2937 -
obs-3105 98.17 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.64330.14280.20571.71540.99512.13150.0498-0.01340.02460.01970.0221-0.09890.13290.0691-0.0720.0823-0.00240.00790.19430.04330.13487.655-18.567-8.833
20.81290.188-0.40621.7934-0.95711.79620.0110.07860.0552-0.00470.03410.0517-0.0812-0.0708-0.04510.16550.03230.03250.1123-0.00980.065526.572-63.584-43.028
30.98210.63550.11252.23181.02071.7265-0.12260.2217-0.131-0.17850.2062-0.08150.11990.0214-0.08370.1144-0.0245-0.01510.15820.02320.07825.285-21.456-41.735
40.59090.12420.14841.973-0.94662.04420.0272-0.0028-0.03540.15080.05250.0426-0.1525-0.0853-0.07980.2166-0.00220.01580.0844-0.01370.071829.133-70.643-9.546
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 261
2X-RAY DIFFRACTION2B0 - 259
3X-RAY DIFFRACTION3C1 - 260
4X-RAY DIFFRACTION4D1 - 257

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