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- PDB-3b1y: Crystal structure of an S. thermophilus NFeoB T35A mutant bound to GDP -

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Basic information

Entry
Database: PDB / ID: 3b1y
TitleCrystal structure of an S. thermophilus NFeoB T35A 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 / 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
AMINOPHOSPHONIC ACID-GUANYLATE ESTER / 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

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Assembly

Deposited unit
A: Ferrous iron uptake transporter protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6152
Polymers30,1731
Non-polymers4421
Water50428
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.8, 42.8, 281.2
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Ferrous iron uptake transporter protein B


Mass: 30173.123 Da / Num. of mol.: 1 / Fragment: NFeoB, UNP residues 1-270 / Mutation: T35A
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-GNH / AMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 442.216 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N6O10P2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 28 / 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: 2.13 Å3/Da / Density % sol: 42.36 % / Mosaicity: 0.469 °
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1M MIB buffer, 25%(w/v) PEG 1500, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 3, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 9980 / Num. obs: 9980 / % possible obs: 99.3 % / Redundancy: 10.1 % / Rmerge(I) obs: 0.079 / Χ2: 1.023 / Net I/σ(I): 25.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
2.5-2.543.40.3582.34310.84389.2
2.54-2.594.40.3854570.90197.6
2.59-2.646.30.3654910.89999.4
2.64-2.698.20.3694780.91699.6
2.69-2.759.40.3124810.935100
2.75-2.8210.10.2564911.046100
2.82-2.8910.30.2244901.025100
2.89-2.9610.90.1924561.094100
2.96-3.0510.70.1875201.12100
3.05-3.1511.20.144691.083100
3.15-3.2611.30.1194951.172100
3.26-3.3911.40.1075021.078100
3.39-3.5511.70.0825011.07100
3.55-3.7311.80.0724811.07100
3.73-3.97120.0695221.055100
3.97-4.2712.30.0575070.986100
4.27-4.712.20.0535140.98999.8
4.7-5.38120.0535270.98299.8
5.38-6.7811.80.0585390.981100
6.78-509.90.0446280.91299.8

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
Blu-Icedata collection
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LX8

3lx8


Resolution: 2.5→42.29 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.901 / Occupancy max: 1 / Occupancy min: 1 / SU B: 21.694 / SU ML: 0.244 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.324 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2605 973 9.9 %RANDOM
Rwork0.2203 ---
obs0.2244 9797 98.32 %-
all-9797 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 73.97 Å2 / Biso mean: 35.8876 Å2 / Biso min: 15.83 Å2
Baniso -1Baniso -2Baniso -3
1-0.55 Å20 Å20 Å2
2--0.55 Å20 Å2
3----1.1 Å2
Refinement stepCycle: LAST / Resolution: 2.5→42.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1963 0 28 28 2019
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222020
X-RAY DIFFRACTIONr_bond_other_d0.0010.021307
X-RAY DIFFRACTIONr_angle_refined_deg1.4831.9842752
X-RAY DIFFRACTIONr_angle_other_deg1.1343.0013209
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.1745253
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.70625.23386
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.40215347
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7961511
X-RAY DIFFRACTIONr_chiral_restr0.0650.2335
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022212
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02367
X-RAY DIFFRACTIONr_mcbond_it0.5221.51270
X-RAY DIFFRACTIONr_mcbond_other0.0841.5512
X-RAY DIFFRACTIONr_mcangle_it0.99622059
X-RAY DIFFRACTIONr_scbond_it1.513750
X-RAY DIFFRACTIONr_scangle_it2.5484.5693
LS refinement shellResolution: 2.497→2.562 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.354 60 -
Rwork0.315 574 -
all-634 -
obs-634 90.06 %
Refinement TLS params.Method: refined / Origin x: 5.074 Å / Origin y: 14.633 Å / Origin z: -16.451 Å
111213212223313233
T0.0633 Å2-0.0194 Å2-0.0063 Å2-0.1366 Å2-0.0689 Å2--0.0725 Å2
L1.9569 °2-0.1156 °2-1.3519 °2-0.8189 °20.0825 °2--2.1868 °2
S0.1435 Å °-0.215 Å °0.0694 Å °-0.0227 Å °-0.0939 Å °0.0348 Å °-0.2164 Å °0.0671 Å °-0.0497 Å °

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