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- PDB-7bvu: Crystal structure of S. thermophilus NFeoB E66A.E67A bound to GDP... -

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Basic information

Entry
Database: PDB / ID: 7bvu
TitleCrystal structure of S. thermophilus NFeoB E66A.E67A bound to GDP.AlF4-
ComponentsFerrous iron transport protein B
KeywordsHYDROLASE / HAS-GTPase
Function / homology
Function and homology information


ferrous iron transmembrane transporter activity / GTP binding / metal ion binding / plasma membrane
Similarity search - Function
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 ...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 / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
TETRAFLUOROALUMINATE ION / GUANOSINE-5'-DIPHOSPHATE / : / Ferrous iron transport protein B
Similarity search - Component
Biological speciesStreptococcus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsBatra, S. / Prakash, B.
CitationJournal: To be published
Title: Crystal structure of S. thermophilus NFeoB E66A.E67A bound to GDP.AlF4-
Authors: Batra, S. / Prakash, B.
History
DepositionApr 11, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 14, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,41114
Polymers60,9972
Non-polymers1,41412
Water3,639202
1
A: Ferrous iron transport protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2067
Polymers30,4991
Non-polymers7076
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-12 kcal/mol
Surface area11400 Å2
MethodPISA
2
B: Ferrous iron transport protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2067
Polymers30,4991
Non-polymers7076
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-12 kcal/mol
Surface area11250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.619, 72.402, 157.957
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 1 through 46 or (resid 47...
21(chain B and (resid 1 through 62 or (resid 63...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETASNASN(chain A and (resid 1 through 46 or (resid 47...AA1 - 467 - 52
12LYSLYSLYSLYS(chain A and (resid 1 through 46 or (resid 47...AA4753
13METMETCYSCYS(chain A and (resid 1 through 46 or (resid 47...AA1 - 2557 - 261
14METMETCYSCYS(chain A and (resid 1 through 46 or (resid 47...AA1 - 2557 - 261
15METMETCYSCYS(chain A and (resid 1 through 46 or (resid 47...AA1 - 2557 - 261
16METMETCYSCYS(chain A and (resid 1 through 46 or (resid 47...AA1 - 2557 - 261
21METMETPROPRO(chain B and (resid 1 through 62 or (resid 63...BB1 - 627 - 68
22TYRTYRTYRTYR(chain B and (resid 1 through 62 or (resid 63...BB6369
23METMETVALVAL(chain B and (resid 1 through 62 or (resid 63...BB1 - 2547 - 260
24METMETVALVAL(chain B and (resid 1 through 62 or (resid 63...BB1 - 2547 - 260
25METMETVALVAL(chain B and (resid 1 through 62 or (resid 63...BB1 - 2547 - 260
26METMETVALVAL(chain B and (resid 1 through 62 or (resid 63...BB1 - 2547 - 260

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Ferrous iron transport protein B


Mass: 30498.574 Da / Num. of mol.: 2 / Fragment: GTP binding domain / Mutation: E66A,E67A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus thermophilus (strain ATCC BAA-250 / LMG 18311) (bacteria)
Strain: ATCC BAA-250 / LMG 18311 / Gene: feoB, stu0608 / Plasmid: pGEX-4T-1 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5a / References: UniProt: Q5M586

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Non-polymers , 7 types, 214 molecules

#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: 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
#4: Chemical ChemComp-ALF / TETRAFLUOROALUMINATE ION


Mass: 102.975 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: AlF4
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 202 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 46.03 % / Mosaicity: 1.164 °
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 7.5 mg/ml protein with equal volume of 100 mM Tris-8.0, 400 mM Ammonium chloride, 26 % PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 14, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.5→35 Å / Num. obs: 18799 / % possible obs: 93.4 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.029 / Rrim(I) all: 0.079 / Χ2: 1.17 / Net I/σ(I): 18.3 / Num. measured all: 141289
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.5-2.545.70.2739000.9490.1210.3010.90293
2.54-2.596.60.2559570.9610.1050.2780.94594.4
2.59-2.647.60.2459110.9680.0930.2630.83695.2
2.64-2.697.70.2179100.9730.0830.2330.82391.7
2.69-2.757.60.1879180.9770.0720.2010.8894
2.75-2.827.60.1569190.9830.060.1680.85891.4
2.82-2.897.60.1438950.9850.0550.1540.86890.4
2.89-2.967.60.1238820.9880.0480.1330.91491.3
2.96-3.057.60.1099100.9890.0420.1180.90989.1
3.05-3.157.60.098800.9930.0350.0970.87790.4
3.15-3.267.50.0818830.9950.0320.0870.90187.3
3.26-3.397.60.0688710.9950.0270.0730.90289
3.39-3.557.60.0618870.9970.0230.0651.02188.2
3.55-3.737.40.0579060.9950.0230.0621.06189.5
3.73-3.977.10.0529530.9950.0210.0561.07395.2
3.97-4.277.30.0499960.9950.020.0531.35297.6
4.27-4.77.60.05310050.9940.0220.0571.9499.7
4.7-5.388.30.0610430.9960.0230.0641.979100
5.38-6.778.60.06910480.9960.0260.0732.17100
6.77-3580.07211250.9920.0290.0781.35299.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.483
Highest resolutionLowest resolution
Rotation20 Å4 Å

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Processing

Software
NameVersionClassificationNB
HKL-2000data reduction
HKL-2000data scaling
MOLREP11.5.04phasing
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3SS8

3ss8


Resolution: 2.5→29.83 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 0.31 / Phase error: 22.57
RfactorNum. reflection% reflection
Rfree0.2293 898 4.81 %
Rwork0.1906 --
obs0.1925 18673 93.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 82.7 Å2 / Biso mean: 37.4811 Å2 / Biso min: 20.35 Å2
Refinement stepCycle: final / Resolution: 2.5→29.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3746 0 80 202 4028
Biso mean--33.86 37.04 -
Num. residues----494
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1468X-RAY DIFFRACTION5.025TORSIONAL
12B1468X-RAY DIFFRACTION5.025TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.5-2.65660.28141510.2309289894
2.6566-2.86150.29791340.227288392
2.8615-3.14920.29131200.2245284991
3.1492-3.60430.23381600.1952277388
3.6043-4.53840.21361620.1622303995
4.5384-29.830.18931710.1783333100

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