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- PDB-3tql: Structure of the amino acid ABC transporter, periplasmic amino ac... -

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Basic information

Entry
Database: PDB / ID: 3tql
TitleStructure of the amino acid ABC transporter, periplasmic amino acid-binding protein from Coxiella burnetii.
ComponentsArginine-binding protein
KeywordsTRANSPORT PROTEIN / Transport and binding proteins
Function / homology
Function and homology information


ligand-gated monoatomic ion channel activity / amino acid binding / outer membrane-bounded periplasmic space / 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
ARGININE / IMIDAZOLE / Arginine-binding protein
Similarity search - Component
Biological speciesCoxiella burnetii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.594 Å
AuthorsRudolph, M. / Cheung, J. / Franklin, M.C. / Cassidy, M. / Gary, E. / Burshteyn, F. / Love, J.
CitationJournal: Proteins / Year: 2015
Title: Structural genomics for drug design against the pathogen Coxiella burnetii.
Authors: Franklin, M.C. / Cheung, J. / Rudolph, M.J. / Burshteyn, F. / Cassidy, M. / Gary, E. / Hillerich, B. / Yao, Z.K. / Carlier, P.R. / Totrov, M. / Love, J.D.
History
DepositionSep 9, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 2011Provider: repository / Type: Initial release
Revision 1.1Jun 24, 2015Group: Database references
Revision 1.2Jan 20, 2016Group: Database references
Revision 1.3Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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: Arginine-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1813
Polymers24,9371
Non-polymers2442
Water6,071337
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.421, 66.450, 87.389
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Arginine-binding protein


Mass: 24936.877 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Coxiella burnetii (bacteria) / Strain: RSA493 / Gene: CBU_0482 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q83E49
#2: Chemical ChemComp-ARG / ARGININE


Type: L-peptide linking / Mass: 175.209 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15N4O2
#3: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 337 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.71 Å3/Da / Density % sol: 54.57 %
Crystal growTemperature: 293 K / Method: sitting drop / pH: 7.5
Details: 20% PEG 6000, 100 mM Hepes, pH 7.5, sitting drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.979 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jul 28, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.594→50 Å / Num. all: 36403 / Num. obs: 35438 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Rmerge(I) obs: 0.075 / Χ2: 2.646 / Net I/σ(I): 13.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.6-1.6340.37117741.407199.9
1.63-1.6640.38218251.249199.8
1.66-1.6940.35217691.2481100
1.69-1.7240.33117931.211199.8
1.72-1.7640.34817781.334199.9
1.76-1.83.90.34618201.537199.9
1.8-1.853.40.36817902.111199
1.85-1.92.60.32816293.069191.1
1.9-1.9530.1115433.784186
1.95-2.023.40.14617782.395197.1
2.02-2.0940.10217882.568199.6
2.09-2.1740.09217982.43199.8
2.17-2.272.90.08714983.43182.2
2.27-2.393.40.08517762.763197.3
2.39-2.543.90.07318172.672199.1
2.54-2.743.80.06818092.973199
2.74-3.013.70.05718153.277198
3.01-3.453.70.04517383.847194.4
3.45-4.349.20.05518963.471100
4.34-508.80.04320043.6971100

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.6.4_486refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.594→43.694 Å / Occupancy max: 1 / Occupancy min: 0.09 / FOM work R set: 0.8533 / SU ML: 0.18 / σ(F): 0 / Phase error: 20.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2148 1769 5.01 %RANDOM
Rwork0.1613 ---
all0.164 37048 --
obs0.164 35279 95.88 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.346 Å2 / ksol: 0.347 e/Å3
Displacement parametersBiso max: 69.04 Å2 / Biso mean: 19.0187 Å2 / Biso min: 5.1 Å2
Baniso -1Baniso -2Baniso -3
1-1.6211 Å2-0 Å20 Å2
2---1.8807 Å20 Å2
3---0.2596 Å2
Refinement stepCycle: LAST / Resolution: 1.594→43.694 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1730 0 17 337 2084
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081866
X-RAY DIFFRACTIONf_angle_d1.0772535
X-RAY DIFFRACTIONf_chiral_restr0.077286
X-RAY DIFFRACTIONf_plane_restr0.005329
X-RAY DIFFRACTIONf_dihedral_angle_d12.842690
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5942-1.65120.26341810.17513281346296
1.6512-1.71730.23421810.153634263607100
1.7173-1.79540.26741820.16883427360999
1.7954-1.89010.25991780.17223296347496
1.8901-2.00850.25241610.18893109327090
2.0085-2.16360.20651790.14923435361499
2.1636-2.38130.21451470.1413104325188
2.3813-2.72590.21811760.1633410358697
2.7259-3.43410.20841740.1623336351094
3.4341-43.71090.18232100.160236863896100

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