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- PDB-7bwv: Crystal structure of S. thermophilus NFeoB E67A bound to GDP.AlF4- -

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Basic information

Entry
Database: PDB / ID: 7bwv
TitleCrystal structure of S. thermophilus NFeoB 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 / : / DI(HYDROXYETHYL)ETHER / Ferrous iron transport protein B
Similarity search - Component
Biological speciesStreptococcus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.35 Å
AuthorsBatra, S. / Prakash, B.
CitationJournal: To be published
Title: Crystal structure of S. thermophilus NFeoB E67A bound to GDP.AlF4-
Authors: Batra, S. / Prakash, B.
History
DepositionApr 16, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 21, 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

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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)62,67815
Polymers61,1132
Non-polymers1,56413
Water3,063170
1
A: Ferrous iron transport protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4148
Polymers30,5571
Non-polymers8577
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-12 kcal/mol
Surface area11750 Å2
MethodPISA
2
B: Ferrous iron transport protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2647
Polymers30,5571
Non-polymers7076
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-12 kcal/mol
Surface area11740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.699, 73.614, 156.754
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 76 or (resid 77...
21(chain B and (resid 1 through 44 or (resid 45...

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
11METMETSERSER(chain A and (resid 1 through 76 or (resid 77...AA1 - 767 - 82
12GLNGLNGLNGLN(chain A and (resid 1 through 76 or (resid 77...AA7783
13METMETGLNGLN(chain A and (resid 1 through 76 or (resid 77...AA1 - 2567 - 262
14METMETGLNGLN(chain A and (resid 1 through 76 or (resid 77...AA1 - 2567 - 262
15METMETGLNGLN(chain A and (resid 1 through 76 or (resid 77...AA1 - 2567 - 262
21METMETLYSLYS(chain B and (resid 1 through 44 or (resid 45...BB1 - 447 - 50
22LYSLYSLYSLYS(chain B and (resid 1 through 44 or (resid 45...BB4551
23METMETCYSCYS(chain B and (resid 1 through 44 or (resid 45...BB1 - 2557 - 261
24METMETCYSCYS(chain B and (resid 1 through 44 or (resid 45...BB1 - 2557 - 261
25METMETCYSCYS(chain B and (resid 1 through 44 or (resid 45...BB1 - 2557 - 261
26METMETCYSCYS(chain B and (resid 1 through 44 or (resid 45...BB1 - 2557 - 261
27METMETCYSCYS(chain B and (resid 1 through 44 or (resid 45...BB1 - 2557 - 261

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Ferrous iron transport protein B


Mass: 30556.613 Da / Num. of mol.: 2 / Fragment: GTP binding domain / Mutation: E67A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus thermophilus (strain ATCC BAA-250 / LMG 18311) (bacteria)
Gene: feoB, stu0608 / Plasmid: pGEX-4T-1 / Production host: Escherichia coli DH5alpha (bacteria) / References: UniProt: Q5M586

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Non-polymers , 8 types, 183 molecules

#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine 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: Chemical ChemComp-ALF / TETRAFLUOROALUMINATE ION


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


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


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


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#8: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C2H6O2
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 170 / 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: 2.3 Å3/Da / Density % sol: 46.49 % / Mosaicity: 0.18 °
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 7mg/ml protein with equal volume of 100mM Tris-8.0, 50mM Ammonium chloride, 30% 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 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.35→48.7 Å / Num. obs: 24365 / % possible obs: 99.9 % / Redundancy: 13.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.113 / Rpim(I) all: 0.032 / Rrim(I) all: 0.118 / Net I/σ(I): 20.2 / Num. measured all: 328219 / Scaling rejects: 1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.35-2.4112.70.842204517310.850.2420.8763.498.4
10.5-48.79.40.02731363330.9990.0090.02857.398.8

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation4.61 Å46.51 Å
Translation4.61 Å46.51 Å

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Processing

Software
NameVersionClassificationNB
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimless0.5.21data scaling
PHASER2.8.1phasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3SS8

3ss8


Resolution: 2.35→35.63 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2318 1214 5 %
Rwork0.1932 23072 -
obs0.1951 24286 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 105.63 Å2 / Biso mean: 40.8489 Å2 / Biso min: 16.95 Å2
Refinement stepCycle: final / Resolution: 2.35→35.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3820 0 90 170 4080
Biso mean--40.26 38.12 -
Num. residues----498
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1480X-RAY DIFFRACTION4.571TORSIONAL
12B1480X-RAY DIFFRACTION4.571TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.35-2.440.32171330.23742521265499
2.44-2.550.31851310.220724932624100
2.55-2.690.29841330.234525302663100
2.69-2.860.2891340.22225342668100
2.86-3.080.28811330.229425322665100
3.08-3.380.26941340.21425562690100
3.38-3.870.20731350.181825712706100
3.87-4.880.19091380.152826162754100
4.88-35.630.17491430.177927192862100

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