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- PDB-2q2a: Crystal structures of the arginine-, lysine-, histidine-binding p... -

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Basic information

Entry
Database: PDB / ID: 2q2a
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 26, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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
Remark 999Sequence No suitable database references were found at time of processing

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ArtJ
B: ArtJ
C: ArtJ
D: ArtJ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,82812
Polymers118,7434
Non-polymers1,0858
Water15,889882
1
A: ArtJ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9573
Polymers29,6861
Non-polymers2712
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ArtJ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9573
Polymers29,6861
Non-polymers2712
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: ArtJ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9573
Polymers29,6861
Non-polymers2712
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: ArtJ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9573
Polymers29,6861
Non-polymers2712
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.512, 67.794, 102.676
Angle α, β, γ (deg.)90.00, 95.16, 90.00
Int Tables number4
Space group name H-MP1211
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.: 4 / 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 / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-ARG / ARGININE / Arginine


Type: L-peptide linking / Mass: 175.209 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H15N4O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 882 / 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: 2.09 Å3/Da / Density % sol: 41.06 %
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: Nov 5, 2005 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 1.62→50 Å / Num. obs: 112699 / % possible obs: 90.7 % / Observed criterion σ(F): 1 / Redundancy: 2.3 % / Biso Wilson estimate: 15.4 Å2 / Rmerge(I) obs: 0.051 / Χ2: 0.993 / Net I/σ(I): 12
Reflection shellResolution: 1.62→1.68 Å / Redundancy: 2 % / Rmerge(I) obs: 0.191 / Mean I/σ(I) obs: 4.13 / Num. unique all: 8541 / Χ2: 0.822 / % possible all: 69.4

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT2data extraction
ADSCQuantumdata collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.79→50 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.92 / SU B: 2.562 / SU ML: 0.083 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.151 / ESU R Free: 0.142 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.237 4356 5.1 %RANDOM
Rwork0.192 ---
obs0.194 85724 92.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.938 Å2
Baniso -1Baniso -2Baniso -3
1-1.53 Å20 Å2-0.05 Å2
2---0.47 Å20 Å2
3----1.07 Å2
Refinement stepCycle: LAST / Resolution: 1.79→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7539 0 20 882 8441
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0227688
X-RAY DIFFRACTIONr_angle_refined_deg1.3381.97810359
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7985974
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.32126.42324
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.06151441
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6381512
X-RAY DIFFRACTIONr_chiral_restr0.0920.21141
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025692
X-RAY DIFFRACTIONr_nbd_refined0.1970.23630
X-RAY DIFFRACTIONr_nbtor_refined0.3050.25379
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1280.2686
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1990.2200
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1640.277
X-RAY DIFFRACTIONr_mcbond_it0.811.54963
X-RAY DIFFRACTIONr_mcangle_it1.25327738
X-RAY DIFFRACTIONr_scbond_it2.21333107
X-RAY DIFFRACTIONr_scangle_it3.5224.52616
LS refinement shellResolution: 1.79→1.836 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 345 -
Rwork0.214 6091 -
obs-6436 94.86 %

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