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- PDB-2pvu: Crystal structures of the arginine-, lysine-, histidine-binding p... -

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Basic information

Entry
Database: PDB / ID: 2pvu
TitleCrystal structures of the arginine-, lysine-, histidine-binding protein ArtJ from the thermophilic bacterium Geobacillus stearothermophilus
ComponentsArtJ
KeywordsTRANSPORT PROTEIN / BASIC AMINO ACID BINDING PROTEIN / ABC TRANSPORT SYSTEM / THERMOPHILIC BACTERIUM
Function / homology
Function and homology information


ligand-gated monoatomic ion channel activity / plasma membrane
Similarity search - Function
Bacterial periplasmic substrate-binding proteins / Bacterial extracellular solute-binding proteins, family 3 / Solute-binding protein family 3/N-terminal domain of MltF / Ionotropic glutamate receptor / Eukaryotic homologues of bacterial periplasmic substrate binding proteins. / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 Å
AuthorsVahedi-Faridi, A. / Scheffel, F. / Eckey, V. / Saenger, W. / Schneider, E.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Crystal structures and mutational analysis of the arginine-, lysine-, histidine-binding protein ArtJ from Geobacillus stearothermophilus. Implications for interactions of ArtJ with its cognate ...Title: Crystal structures and mutational analysis of the arginine-, lysine-, histidine-binding protein ArtJ from Geobacillus stearothermophilus. Implications for interactions of ArtJ with its cognate ATP-binding cassette transporter, Art(MP)2
Authors: Vahedi-Faridi, A. / Eckey, V. / Scheffel, F. / Alings, C. / Landmesser, H. / Schneider, E. / Saenger, W.
History
DepositionMay 10, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / 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 / pdbx_struct_special_symmetry / 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

Downloads & links

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Assembly

Deposited unit
A: ArtJ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1215
Polymers29,6861
Non-polymers4354
Water2,774154
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.268, 73.887, 102.681
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-391-

HOH

DetailsThe biological assembly is a monomer generated from either polypeptide chain in the AU.

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Components

#1: Protein ArtJ


Mass: 29685.635 Da / Num. of mol.: 1 / Mutation: C1G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Strain: Geobacillus stearothermophilus DSMZ 13240 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 / References: UniProt: D0VWX8*PLUS
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-LYS / LYSINE


Type: L-peptide linking / Mass: 147.195 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15N2O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / 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: 2.18 Å3/Da / Density % sol: 43.58 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2 M ammoniumsulfate, 30.5 % w/v polyethylene glycol (PEG) 2000 , pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.95373 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 23, 2005 / Details: mirrirs
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 1.79→50 Å / Num. obs: 21953 / % possible obs: 93.1 % / Observed criterion σ(F): 1 / Redundancy: 6.9 % / Biso Wilson estimate: 20.7 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 23.49
Reflection shellResolution: 1.79→1.84 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.351 / Mean I/σ(I) obs: 3.5 / Num. unique all: 1713 / % possible all: 66.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.79→51.37 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.931 / SU B: 4.935 / SU ML: 0.08 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.124 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22385 1178 5.1 %RANDOM
Rwork0.17447 ---
obs0.17689 21953 93.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.127 Å2
Baniso -1Baniso -2Baniso -3
1--1.23 Å20 Å20 Å2
2--3.53 Å20 Å2
3----2.29 Å2
Refinement stepCycle: LAST / Resolution: 1.79→51.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1831 0 25 154 2010
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0221898
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5631.9842560
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8465238
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.92326.62580
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.45815359
X-RAY DIFFRACTIONr_dihedral_angle_4_deg4.114152
X-RAY DIFFRACTIONr_chiral_restr0.1160.2282
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021393
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2170.2902
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.310.21325
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.2144
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1870.232
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0810.211
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.041.51213
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.53821894
X-RAY DIFFRACTIONr_scbond_it2.8933782
X-RAY DIFFRACTIONr_scangle_it4.484.5664
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.79→1.836 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.254 47 -
Rwork0.203 1143 -
obs--66.48 %
Refinement TLS params.Method: refined / Origin x: -12.6949 Å / Origin y: 19.3176 Å / Origin z: 12.1198 Å
111213212223313233
T-0.0689 Å20.0057 Å2-0.0071 Å2--0.0873 Å20.0258 Å2---0.0476 Å2
L1.4817 °20.0463 °20.1136 °2-0.6098 °20.1971 °2--2.4958 °2
S0.0435 Å °-0.0537 Å °-0.047 Å °-0.0013 Å °0.0095 Å °0.0239 Å °0.0517 Å °-0.0687 Å °-0.053 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA17 - 10638 - 127
2X-RAY DIFFRACTION1AA108 - 193129 - 214
3X-RAY DIFFRACTION1AA194 - 203215 - 224
4X-RAY DIFFRACTION1AA204 - 251225 - 272

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