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- PDB-4r98: Chimera of the N-terminal domain of E. coli FeoB -

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Basic information

Entry
Database: PDB / ID: 4r98
TitleChimera of the N-terminal domain of E. coli FeoB
ComponentsFerrous iron transport protein B
KeywordsMETAL TRANSPORT / FeoB
Function / homology
Function and homology information


iron ion import across plasma membrane / ferrous iron transmembrane transporter activity / DNA damage response / GTP binding / identical protein 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 / 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 / Fe(2+) transporter FeoB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.22 Å
AuthorsMaher, M.J. / Jormakka, M.
CitationJournal: Biophys.J. / Year: 2014
Title: A GTPase Chimera Illustrates an Uncoupled Nucleotide Affinity and Release Rate, Providing Insight into the Activation Mechanism.
Authors: Guilfoyle, A.P. / Deshpande, C.N. / Font Sadurni, J. / Ash, M.R. / Tourle, S. / Schenk, G. / Maher, M.J. / Jormakka, M.
History
DepositionSep 3, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 11, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 transport protein B
B: Ferrous iron transport protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,2203
Polymers59,7782
Non-polymers4421
Water48627
1
A: Ferrous iron transport protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3312
Polymers29,8891
Non-polymers4421
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Ferrous iron transport protein B


Theoretical massNumber of molelcules
Total (without water)29,8891
Polymers29,8891
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.452, 48.452, 233.393
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein Ferrous iron transport protein B


Mass: 29889.139 Da / Num. of mol.: 2 / Fragment: N-terminal domain (UNP residues 1-270)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: feoB, b3409, JW3372 / Production host: Escherichia coli (E. coli) / References: UniProt: P33650
#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.: 27 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS STRUCTURE IS REPRESENTING A MODIFIED SUB CLONE OF FEOB, WHERE A SHORT SEGMENT HAS BEEN ...THIS STRUCTURE IS REPRESENTING A MODIFIED SUB CLONE OF FEOB, WHERE A SHORT SEGMENT HAS BEEN REPLACED FOR FUNCTIONAL STUDIES

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.29 Å3/Da / Density % sol: 46.32 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 6.5
Details: 22 % PEG 3350, 0.1 M Bis Tris Propane pH 6.5 and 0.2 M Sodium formate, VAPOR DIFFUSION, HANGING DROP

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Data collection

Diffraction
IDCrystal-ID
11
21
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
ROTATING ANODEAPS 23-ID-BRIGAKU RU20011.54
Australian Synchrotron MX22
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Sep 1, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.502
11-H, K, -L20.498
ReflectionResolution: 2.2→50 Å / Num. all: 26345 / Num. obs: 26345 / % possible obs: 97.1 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 6.8 % / Rmerge(I) obs: 0.044
Reflection shellResolution: 2.2→2.28 Å / Rmerge(I) obs: 0.224 / % possible all: 73.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.22→44.75 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.911 / SU B: 7.185 / SU ML: 0.183 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.081 / ESU R Free: 0.054 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28101 1320 5 %RANDOM
Rwork0.24928 ---
obs0.25089 24927 99.03 %-
all-26247 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 38.766 Å2
Baniso -1Baniso -2Baniso -3
1-6.27 Å20 Å20 Å2
2--6.27 Å20 Å2
3----12.54 Å2
Refinement stepCycle: LAST / Resolution: 2.22→44.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3960 0 28 27 4015
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0194052
X-RAY DIFFRACTIONr_bond_other_d0.0010.023947
X-RAY DIFFRACTIONr_angle_refined_deg0.8841.9865522
X-RAY DIFFRACTIONr_angle_other_deg0.66639035
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6375514
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.80725.141177
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.14315691
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6571525
X-RAY DIFFRACTIONr_chiral_restr0.0450.2671
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024596
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02873
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.2953.9542065
X-RAY DIFFRACTIONr_mcbond_other0.2953.9542064
X-RAY DIFFRACTIONr_mcangle_it0.5615.9272573
X-RAY DIFFRACTIONr_mcangle_other0.5615.9272574
X-RAY DIFFRACTIONr_scbond_it0.0993.9541987
X-RAY DIFFRACTIONr_scbond_other0.0993.9541988
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.2415.9262949
X-RAY DIFFRACTIONr_long_range_B_refined1.26430.854481
X-RAY DIFFRACTIONr_long_range_B_other1.26430.8554481
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.217→2.274 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.426 95 -
Rwork0.335 1703 -
obs--92.92 %

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