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- PDB-3a1u: Crystal structue of the cytosolic domain of T. maritima FeoB iron... -

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Basic information

Entry
Database: PDB / ID: 3a1u
TitleCrystal structue of the cytosolic domain of T. maritima FeoB iron iransporter in GMPPNP form
ComponentsIron(II) transport protein B
KeywordsTRANSPORT PROTEIN / FeoB / iron transpoter / small GTPase / G protein / GDI
Function / homology
Function and homology information


ferrous iron transmembrane transporter activity / GTP binding / metal ion binding / plasma membrane
Similarity search - Function
Helix Hairpins - #1770 / Ferrous iron transport protein B, C-terminal / Ferrous iron transport protein B C terminus / FeoB, cytosolic helical domain / FeoB cytosolic helical domain / 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. ...Helix Hairpins - #1770 / Ferrous iron transport protein B, C-terminal / Ferrous iron transport protein B C terminus / FeoB, cytosolic helical domain / FeoB cytosolic helical domain / 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 / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 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 speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsHattori, M. / Ishitani, R. / Nureki, O.
CitationJournal: Structure / Year: 2009
Title: Structural basis of novel interactions between the small-GTPase and GDI-like domains in prokaryotic FeoB iron transporter
Authors: Hattori, M. / Jin, Y. / Nishimasu, H. / Tanaka, Y. / Mochizuki, M. / Uchiumi, T. / Ishitani, R. / Ito, K. / Nureki, O.
History
DepositionApr 22, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 22, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_asym_id / _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_asym_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_conn.ptnr2_label_seq_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

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Assembly

Deposited unit
A: Iron(II) transport protein B
B: Iron(II) transport protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,8159
Polymers58,4622
Non-polymers1,3547
Water8,197455
1
A: Iron(II) transport protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9205
Polymers29,2311
Non-polymers6894
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Iron(II) transport protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8964
Polymers29,2311
Non-polymers6653
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.613, 109.396, 57.261
Angle α, β, γ (deg.)90.00, 97.99, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Iron(II) transport protein B


Mass: 29230.844 Da / Num. of mol.: 2 / Fragment: UNP residues 17-269
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TM0051 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3) / References: UniProt: Q9WXQ8
#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-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 455 / 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: 2.31 Å3/Da / Density % sol: 46.84 %
Crystal growpH: 7.5 / Details: 60-66% MPD, 0.1M HEPES, pH7.5, 4% 1-3-butanediol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU
DetectorDate: Feb 14, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 48359

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Processing

SoftwareName: PHENIX / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3A1S

3a1s


Resolution: 1.8→39.368 Å / SU ML: 0.24 / σ(F): 2.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2187 2462 5.09 %
Rwork0.1833 --
obs0.1852 48359 49.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 63.933 Å2 / ksol: 0.36 e/Å3
Refinement stepCycle: LAST / Resolution: 1.8→39.368 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3895 0 83 455 4433
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054037
X-RAY DIFFRACTIONf_angle_d0.9755463
X-RAY DIFFRACTIONf_dihedral_angle_d17.6071488
X-RAY DIFFRACTIONf_chiral_restr0.062630
X-RAY DIFFRACTIONf_plane_restr0.003670
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7982-1.83280.24181140.19992388X-RAY DIFFRACTION46
1.8328-1.87020.24991340.20012456X-RAY DIFFRACTION48
1.8702-1.91080.22781380.18862513X-RAY DIFFRACTION48
1.9108-1.95530.2661310.18582482X-RAY DIFFRACTION49
1.9553-2.00420.23991120.19342540X-RAY DIFFRACTION49
2.0042-2.05840.24721390.19012571X-RAY DIFFRACTION50
2.0584-2.11890.2541310.18472555X-RAY DIFFRACTION50
2.1189-2.18730.22191610.1822585X-RAY DIFFRACTION50
2.1873-2.26550.21841230.17352537X-RAY DIFFRACTION50
2.2655-2.35620.22241330.18232567X-RAY DIFFRACTION50
2.3562-2.46340.23141420.18312584X-RAY DIFFRACTION50
2.4634-2.59330.22981410.17862584X-RAY DIFFRACTION50
2.5933-2.75570.21211450.18872578X-RAY DIFFRACTION50
2.7557-2.96840.23211400.17922577X-RAY DIFFRACTION51
2.9684-3.2670.2241330.18742607X-RAY DIFFRACTION50
3.267-3.73940.20961630.17552585X-RAY DIFFRACTION51
3.7394-4.710.17051480.15722608X-RAY DIFFRACTION51
4.71-39.37720.23261340.2032580X-RAY DIFFRACTION50

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