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- PDB-3dhx: Crystal structure of isolated C2 domain of the methionine uptake ... -

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Basic information

Entry
Database: PDB / ID: 3dhx
TitleCrystal structure of isolated C2 domain of the methionine uptake transporter
ComponentsMethionine import ATP-binding protein metN
KeywordsHYDROLASE / Methionine uptake / regulation / Amino-acid transport / ATP-binding / Inner membrane / Membrane / Nucleotide-binding / Transport
Function / homology
Function and homology information


L-methionine transmembrane transporter activity / methionine import across plasma membrane / methionine-importing ABC transporter complex / ABC-type methionine transporter / ABC-type D-methionine transporter activity / D-methionine transmembrane transport / Gram-negative-bacterium-type cell wall / ATPase-coupled transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP hydrolysis activity ...L-methionine transmembrane transporter activity / methionine import across plasma membrane / methionine-importing ABC transporter complex / ABC-type methionine transporter / ABC-type D-methionine transporter activity / D-methionine transmembrane transport / Gram-negative-bacterium-type cell wall / ATPase-coupled transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP hydrolysis activity / ATP binding / membrane
Similarity search - Function
ABC transporter, methionine import, ATP-binding protein MetN, proteobacteria / NIL domain / NIL domain / Methionine import ATP-binding protein metN family profile. / NIL / Methionine import ATP-binding protein MetN, ATP-binding domain / : / ACT domain / ACT-like domain / ABC transporter-like, conserved site ...ABC transporter, methionine import, ATP-binding protein MetN, proteobacteria / NIL domain / NIL domain / Methionine import ATP-binding protein metN family profile. / NIL / Methionine import ATP-binding protein MetN, ATP-binding domain / : / ACT domain / ACT-like domain / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / Alpha-Beta Plaits / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
IODIDE ION / Methionine import ATP-binding protein MetN
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SAD / Resolution: 2.1 Å
AuthorsJohnson, E. / Kaiser, J.T. / Lee, A.T. / Rees, D.C.
CitationJournal: Science / Year: 2008
Title: The high-affinity E. coli methionine ABC transporter: structure and allosteric regulation.
Authors: Kadaba, N.S. / Kaiser, J.T. / Johnson, E. / Lee, A. / Rees, D.C.
History
DepositionJun 18, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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: Methionine import ATP-binding protein metN
B: Methionine import ATP-binding protein metN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,86414
Polymers24,3412
Non-polymers1,52312
Water4,684260
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2210 Å2
ΔGint-3.9 kcal/mol
Surface area9990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.277, 53.277, 150.495
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Methionine import ATP-binding protein metN


Mass: 12170.624 Da / Num. of mol.: 2 / Fragment: C2 domain: Residues 246-343
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: metN, abc, b0199, JW0195 / Production host: Escherichia coli (E. coli)
References: UniProt: P30750, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to catalyse transmembrane movement of substances
#2: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: I
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 260 / 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: 2.53 Å3/Da / Density % sol: 51.44 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.1→44.11 Å / Num. obs: 14058

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
CrystalCleardata collection
MOSFLMdata reduction
SCALAdata scaling
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 2.1→44.11 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.927 / SU B: 3.803 / SU ML: 0.108 / Cross valid method: THROUGHOUT / ESU R: 0.215 / ESU R Free: 0.186 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23845 731 4.9 %RANDOM
Rwork0.19061 ---
obs0.19303 14058 97.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.126 Å2
Baniso -1Baniso -2Baniso -3
1-0.37 Å20.18 Å20 Å2
2--0.37 Å20 Å2
3----0.55 Å2
Refinement stepCycle: LAST / Resolution: 2.1→44.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1570 0 12 260 1842
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0221600
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9841.9492172
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9395196
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.9725.47684
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.49215270
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.181158
X-RAY DIFFRACTIONr_chiral_restr0.1340.2244
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021232
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2420.2817
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.310.21088
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.3650.2215
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.7650.23
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2390.262
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3830.243
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3651.5999
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.23621588
X-RAY DIFFRACTIONr_scbond_it3.9053658
X-RAY DIFFRACTIONr_scangle_it6.344.5584
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 44 -
Rwork0.142 823 -
obs--79.91 %

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