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- PDB-3b1x: Crystal structure of an S. thermophilus NFeoB E66A mutant bound t... -

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Basic information

Entry
Database: PDB / ID: 3b1x
TitleCrystal structure of an S. thermophilus NFeoB E66A mutant bound to GMPPNP
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
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / Ferrous iron transport protein B
Similarity search - Component
Biological speciesStreptococcus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.61 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 1.2Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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.ptnr2_auth_asym_id / _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_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)61,3836
Polymers60,2902
Non-polymers1,0934
Water1,02757
1
A: Ferrous iron uptake transporter protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6923
Polymers30,1451
Non-polymers5472
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)30,6923
Polymers30,1451
Non-polymers5472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.7, 74.4, 156.1
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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.: 2 / Fragment: NFeoB, UNP residues 1-270 / Mutation: E66A
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-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / 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: 2.35 Å3/Da / Density % sol: 47.55 % / Mosaicity: 0.32 °
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1M SPG 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 210r / 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: 2.6→50 Å / Num. all: 17841 / Num. obs: 17841 / % possible obs: 99.3 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.153 / Χ2: 1.105 / Net I/σ(I): 11.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
2.6-2.644.50.5742.17870.88389.4
2.64-2.694.90.5248601.04597.2
2.69-2.745.80.5158680.952100
2.74-2.86.10.4278530.982100
2.8-2.8660.3989281.005100
2.86-2.936.20.3418481.026100
2.93-36.10.3148841.093100
3-3.086.10.2728961.121100
3.08-3.176.10.2378681.157100
3.17-3.2860.29081.107100
3.28-3.396.10.1828771.184100
3.39-3.5360.1638981.212100
3.53-3.6960.1348921.297100
3.69-3.8860.1178871.083100
3.88-4.1360.1028951.169100
4.13-4.455.90.0889191.34100
4.45-4.8960.0849071.057100
4.89-5.65.90.0979151.109100
5.6-7.055.70.1059411.142100
7.05-505.30.06210101.02199.7

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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 / Resolution: 2.61→46.5 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.865 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 21.568 / SU ML: 0.235 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.345 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2591 928 5.2 %RANDOM
Rwork0.214 ---
obs0.2163 17682 98.56 %-
all-17682 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 56.2 Å2 / Biso mean: 25.1491 Å2 / Biso min: 5.02 Å2
Baniso -1Baniso -2Baniso -3
1--0.68 Å20 Å20 Å2
2--0.24 Å20 Å2
3---0.43 Å2
Refinement stepCycle: LAST / Resolution: 2.61→46.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4007 0 66 57 4130
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0224167
X-RAY DIFFRACTIONr_angle_refined_deg1.4421.9935678
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.5825522
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.42125.455187
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.97915734
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.3131524
X-RAY DIFFRACTIONr_chiral_restr0.0640.2680
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0213082
X-RAY DIFFRACTIONr_mcbond_it0.4471.52592
X-RAY DIFFRACTIONr_mcangle_it0.8624216
X-RAY DIFFRACTIONr_scbond_it1.23431575
X-RAY DIFFRACTIONr_scangle_it2.214.51462
LS refinement shellResolution: 2.609→2.677 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 66 -
Rwork0.243 1095 -
all-1161 -
obs-1161 88.97 %
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)
11.81350.6304-0.77790.5993-0.31920.83830.02670.09620.06960.01080.02250.0283-0.0448-0.0322-0.04910.0540.0189-0.01170.0403-0.00750.0294-3.94517.687-22.331
22.0574-0.8021-0.77090.57830.66710.86090.0040.01460.1417-0.0222-0.0032-0.0051-0.0572-0.0057-0.00080.0707-0.0236-0.00640.05010.01480.0269-21.96614.728-60.943
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 259
2X-RAY DIFFRACTION2B1 - 257

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