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- PDB-3hyr: Structural Insight into G Protein Coupling and Regulation of Fe2+... -

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Basic information

Entry
Database: PDB / ID: 3hyr
TitleStructural Insight into G Protein Coupling and Regulation of Fe2+ Membrane Transport
ComponentsFerrous iron transport protein B
KeywordsMETAL TRANSPORT / iron transport / G protein / Cell inner membrane / Cell membrane / GTP-binding / Ion transport / Iron / Membrane / Nucleotide-binding / Transmembrane / Transport
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
Fe(2+) transporter FeoB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.2 Å
AuthorsMaher, M.J. / Jormakka, M.
CitationJournal: Embo J. / Year: 2009
Title: Structural basis of GDP release and gating in G protein coupled Fe2+ transport.
Authors: Guilfoyle, A. / Maher, M.J. / Rapp, M. / Clarke, R. / Harrop, S. / Jormakka, M.
History
DepositionJun 23, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 25, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 13, 2013Group: Database references

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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
C: Ferrous iron transport protein B


Theoretical massNumber of molelcules
Total (without water)89,7053
Polymers89,7053
Non-polymers00
Water8,647480
1
A: Ferrous iron transport protein B


Theoretical massNumber of molelcules
Total (without water)29,9021
Polymers29,9021
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Ferrous iron transport protein B


Theoretical massNumber of molelcules
Total (without water)29,9021
Polymers29,9021
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Ferrous iron transport protein B


Theoretical massNumber of molelcules
Total (without water)29,9021
Polymers29,9021
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)146.120, 84.440, 66.240
Angle α, β, γ (deg.)90.00, 108.46, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C

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Components

#1: Protein Ferrous iron transport protein B


Mass: 29901.518 Da / Num. of mol.: 3 / Fragment: N-terminal domain
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 480 / 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: 2.16 Å3/Da / Density % sol: 43.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 30% PEG 400, 100mM MgCl2, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 1, 2008
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.2→72.17 Å / % possible obs: 99.9 %
Reflection shellResolution: 2.2→2.32 Å / % possible all: 99.9

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Processing

Software
NameVersionClassification
SHARPphasing
REFMAC5.5.0063refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MIR / Resolution: 2.2→50 Å / Cor.coef. Fo:Fc: 0.902 / Cor.coef. Fo:Fc free: 0.838 / SU B: 19.147 / SU ML: 0.212 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.372 / ESU R Free: 0.266 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28718 1948 5 %RANDOM
Rwork0.22501 ---
obs0.22817 36896 100 %-
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: 20.993 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20 Å20.31 Å2
2---0.31 Å20 Å2
3---0.55 Å2
Refinement stepCycle: LAST / Resolution: 2.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5790 0 0 480 6270
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0225930
X-RAY DIFFRACTIONr_angle_refined_deg1.4861.9818081
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8915779
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.5224.805256
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.059151033
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.8671542
X-RAY DIFFRACTIONr_chiral_restr0.0970.2979
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214410
X-RAY DIFFRACTIONr_mcbond_it0.7951.53807
X-RAY DIFFRACTIONr_mcangle_it1.56926126
X-RAY DIFFRACTIONr_scbond_it2.632123
X-RAY DIFFRACTIONr_scangle_it4.4744.51942
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 1935 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
Atight positional0.040.05
Btight positional0.040.05
Ctight positional0.040.05
Atight thermal0.110.5
Btight thermal0.110.5
Ctight thermal0.110.5
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.361 145 -
Rwork0.322 2697 -
obs--100 %
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)
11.51090.29390.0611.2514-0.07410.1710.0120.0042-0.08270.0063-0.010.1473-0.02180.0232-0.0020.0535-0.0013-0.0130.0602-0.00610.03112.105535.6483-9.9792
21.2193-0.226-0.90854.72692.42011.765-0.22660.0177-0.2840.02210.02860.03750.138400.19810.0810.00940.04710.0306-0.01590.070832.585126.4164-20.0229
31.21280.00290.15611.0025-0.17120.4601-0.0195-0.03430.02690.00810.0187-0.0906-0.01-0.03750.00080.05190.00970.00260.0528-0.00950.011546.997353.4748-9.9002
42.2251-0.1062-1.16480.03330.23821.92470.10580.05710.3555-0.0171-0.00450.0005-0.219-0.0962-0.10130.0670.02070.03050.00720.0110.076344.626475.6057-20.342
50.94130.3317-0.05781.5439-0.05750.07880.00510.00230.1773-0.0191-0.01060.23560.04420.01970.00550.058800.00490.06430.00550.060714.030574.8612-10.1152
62.0155-0.50661.36441.7481-0.50642.01920.0351-0.05020.1088-0.28650.02850.45520.0759-0.2902-0.06370.0516-0.0141-0.09860.11710.01430.2721-4.03961.7566-20.6978
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 171
2X-RAY DIFFRACTION2A172 - 260
3X-RAY DIFFRACTION3B2 - 171
4X-RAY DIFFRACTION4B172 - 260
5X-RAY DIFFRACTION5C2 - 171
6X-RAY DIFFRACTION6C172 - 260

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