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- PDB-2wjh: Structure and function of the FeoB G-domain from Methanococcus ja... -

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Basic information

Entry
Database: PDB / ID: 2wjh
TitleStructure and function of the FeoB G-domain from Methanococcus jannaschii
ComponentsFERROUS IRON TRANSPORT PROTEIN B HOMOLOG
KeywordsMETAL TRANSPORT / MEMBRANE G-PROTEINS / FERROUS IRON TRANSPORT / CELL MEMBRANE / ION TRANSPORT / TRANSMEMBRANE / NUCLEOTIDE BINDING MOTIFS / IRON / GNBPS / MEMBRANE / TRANSPORT / GTP-BINDING / IRON TRANSPORT / NUCLEOTIDE-BINDING
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 / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CITRATE ANION / GUANOSINE-5'-DIPHOSPHATE / Fe(2+) transporter FeoB
Similarity search - Component
Biological speciesMETHANOCALDOCOCCUS JANNASCHII (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsKoester, S. / Wehner, M. / Herrmann, C. / Kuehlbrandt, W. / Yildiz, O.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Structure and Function of the Feob G-Domain from Methanococcus Jannaschii
Authors: Koester, S. / Wehner, M. / Herrmann, C. / Kuehlbrandt, W. / Yildiz, O.
History
DepositionMay 26, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 28, 2009Provider: repository / Type: Initial release
Revision 1.1May 19, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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_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_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_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_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 HOMOLOG
B: FERROUS IRON TRANSPORT PROTEIN B HOMOLOG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1967
Polymers36,4912
Non-polymers7055
Water3,117173
1
A: FERROUS IRON TRANSPORT PROTEIN B HOMOLOG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,7374
Polymers18,2451
Non-polymers4923
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: FERROUS IRON TRANSPORT PROTEIN B HOMOLOG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,4593
Polymers18,2451
Non-polymers2132
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)104.200, 50.400, 94.700
Angle α, β, γ (deg.)90.00, 120.60, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein FERROUS IRON TRANSPORT PROTEIN B HOMOLOG / FEOB


Mass: 18245.260 Da / Num. of mol.: 2 / Fragment: FEOB G-DOMAIN, RESIDUES 1-165
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) METHANOCALDOCOCCUS JANNASCHII (archaea)
Plasmid: PET / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q57986
#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 173 / 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: 2.75 Å3/Da / Density % sol: 54.9 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9395
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 8, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9395 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. obs: 24931 / % possible obs: 99.6 % / Observed criterion σ(I): 2.9 / Redundancy: 10.2 % / Biso Wilson estimate: 31.64 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 14.5
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 2.9 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WJG

2wjg


Resolution: 2.1→42.944 Å / SU ML: 0.37 / σ(F): 2.02 / Phase error: 24.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2461 1247 5 %
Rwork0.2104 --
obs0.2122 24927 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.836 Å2 / ksol: 0.347 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--5.5582 Å20 Å2-7.2549 Å2
2---0.2243 Å2-0 Å2
3---5.7824 Å2
Refinement stepCycle: LAST / Resolution: 2.1→42.944 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2558 0 44 173 2775
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082637
X-RAY DIFFRACTIONf_angle_d1.1153570
X-RAY DIFFRACTIONf_dihedral_angle_d18.788992
X-RAY DIFFRACTIONf_chiral_restr0.065430
X-RAY DIFFRACTIONf_plane_restr0.004443
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.18410.28061370.24572601X-RAY DIFFRACTION100
2.1841-2.28350.28241370.23072614X-RAY DIFFRACTION100
2.2835-2.40390.28771380.22582618X-RAY DIFFRACTION100
2.4039-2.55440.2891370.22022601X-RAY DIFFRACTION100
2.5544-2.75160.25681390.22082630X-RAY DIFFRACTION100
2.7516-3.02850.25571370.22472612X-RAY DIFFRACTION100
3.0285-3.46650.26571390.21162644X-RAY DIFFRACTION100
3.4665-4.36680.21061400.18322647X-RAY DIFFRACTION100
4.3668-42.95280.20791430.17942713X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -23.256 Å / Origin y: 9.5226 Å / Origin z: -18.5593 Å
111213212223313233
T0.1742 Å2-0.0189 Å2-0.0091 Å2-0.1623 Å20.0009 Å2--0.1416 Å2
L1.0104 °20.2291 °20.0007 °2-0.3173 °20.1016 °2--0.5545 °2
S-0.0699 Å °0.1925 Å °-0.0403 Å °-0.0717 Å °0.0731 Å °0.0328 Å °-0.024 Å °0.0271 Å °-0.0048 Å °
Refinement TLS groupSelection details: ALL

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