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- PDB-4non: Crystal structure of GDP-bound A143S mutant of the S. thermophilu... -

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Basic information

Entry
Database: PDB / ID: 4non
TitleCrystal structure of GDP-bound A143S mutant of the S. thermophilus FeoB G-domain
ComponentsFerrous iron uptake transporter protein B
KeywordsMETAL TRANSPORT / G protein / iron transport / GTPase / transmembrane / GTP binding
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 speciesStreptococcus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsGuilfoyle, A.P. / Deshpande, C.N. / Jormakka, M.
CitationJournal: Febs J. / Year: 2014
Title: Structural and functional analysis of a FeoB A143S G5 loop mutant explains the accelerated GDP release rate.
Authors: Guilfoyle, A.P. / Deshpande, C.N. / Vincent, K. / Pedroso, M.M. / Schenk, G. / Maher, M.J. / Jormakka, M.
History
DepositionNov 20, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 2, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 23, 2014Group: Database references
Revision 1.2May 14, 2014Group: Database references
Revision 1.3Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.location / _software.name / _software.type / _software.version
Revision 1.4Aug 14, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.location / _software.name / _software.type / _software.version
Revision 1.5Feb 28, 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 uptake transporter protein B
B: Ferrous iron uptake transporter protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,8044
Polymers57,9182
Non-polymers8862
Water1,78399
1
A: Ferrous iron uptake transporter protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4022
Polymers28,9591
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)29,4022
Polymers28,9591
Non-polymers4431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.684, 120.768, 49.291
Angle α, β, γ (deg.)90.000, 93.990, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Ferrous iron uptake transporter protein B


Mass: 28958.828 Da / Num. of mol.: 2 / Fragment: N-terminal domain, UNP Residues 1-260 / Mutation: A143S
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.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / 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: 2.24 Å3/Da / Density % sol: 45.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.7
Details: 0.2 M Sodium Chloride, 0.1 M Bis-Tris pH 5.7, 27 % (w/v) PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 26, 2013
RadiationMonochromator: SI VORTEX ES / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.5→60.384 Å / Num. all: 17501 / Num. obs: 17501 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 25.823 Å2 / Rsym value: 0.12 / Net I/σ(I): 8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.5-2.643.40.5051.4876225570.50599.3
2.64-2.83.40.4031.4810524000.40398.9
2.8-2.993.40.272.7769322750.2799.2
2.99-3.233.30.1814.1704821070.18199.5
3.23-3.543.30.1335646319570.13399.3
3.54-3.953.20.0995.6575417710.09999.5
3.95-4.563.20.06410.7493215570.06499.1
4.56-5.592.80.0514.2357212540.0595.7
5.59-7.913.50.05212.5367310410.052100
7.91-49.1713.50.0421420235820.04299.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.20data scaling
PHASERphasing
REFMAC5.7.0029refinement
PDB_EXTRACT3.11data extraction
ADSCQuantumdata collection
PHENIXrefinerefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→49.22 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.879 / Occupancy max: 1 / Occupancy min: 0.43 / SU B: 11.96 / SU ML: 0.265 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.33 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2573 890 5.1 %RANDOM
Rwork0.2086 ---
all0.2112 17477 --
obs0.2112 17477 98.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 69.98 Å2 / Biso mean: 35.5556 Å2 / Biso min: 11.11 Å2
Baniso -1Baniso -2Baniso -3
1--0.56 Å2-0 Å20.44 Å2
2--0.96 Å2-0 Å2
3----0.43 Å2
Refinement stepCycle: LAST / Resolution: 2.5→49.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4011 0 56 99 4166
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONf_bond_refined_d0.0040.0194144
X-RAY DIFFRACTIONf_bond_other_d0.0010.023988
X-RAY DIFFRACTIONf_angle_refined_deg0.8761.995644
X-RAY DIFFRACTIONf_angle_other_deg0.66139171
X-RAY DIFFRACTIONf_dihedral_angle_1_deg4.6855521
X-RAY DIFFRACTIONf_dihedral_angle_2_deg36.96425.333180
X-RAY DIFFRACTIONf_dihedral_angle_3_deg12.49815726
X-RAY DIFFRACTIONf_dihedral_angle_4_deg14.2411523
X-RAY DIFFRACTIONf_chiral_restr0.0470.2678
X-RAY DIFFRACTIONf_gen_planes_refined0.0030.024659
X-RAY DIFFRACTIONf_gen_planes_other0.0010.02876
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 60 -
Rwork0.237 1258 -
all-1318 -
obs--99.1 %

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