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- PDB-6y16: CRYSTAL STRUCTURE OF TMARGBP DOMAIN 1 IN COMPLEX WITH THE GUANIDI... -

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Basic information

Entry
Database: PDB / ID: 6y16
TitleCRYSTAL STRUCTURE OF TMARGBP DOMAIN 1 IN COMPLEX WITH THE GUANIDINIUM ION
ComponentsAmino acid ABC transporter, periplasmic amino acid-binding protein,Amino acid ABC transporter, periplasmic amino acid-binding protein
KeywordsTRANSPORT PROTEIN / Complex
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.
Similarity search - Domain/homology
GUANIDINE / Amino acid ABC transporter, periplasmic amino acid-binding protein
Similarity search - Component
Biological speciesThermotoga maritima MSB8 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsRuggiero, A. / Balasco, N. / Smaldone, G. / Graziano, G. / Vitagliano, L.
CitationJournal: Int.J.Biol.Macromol. / Year: 2020
Title: Guanidinium binding to proteins: The intriguing effects on the D1 and D2 domains of Thermotoga maritima Arginine Binding Protein and a comprehensive analysis of the Protein Data Bank.
Authors: Cozzolino, S. / Balasco, N. / Vigorita, M. / Ruggiero, A. / Smaldone, G. / Del Vecchio, P. / Vitagliano, L. / Graziano, G.
History
DepositionFeb 11, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 15, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 22, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Amino acid ABC transporter, periplasmic amino acid-binding protein,Amino acid ABC transporter, periplasmic amino acid-binding protein
B: Amino acid ABC transporter, periplasmic amino acid-binding protein,Amino acid ABC transporter, periplasmic amino acid-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4796
Polymers28,2362
Non-polymers2424
Water4,702261
1
A: Amino acid ABC transporter, periplasmic amino acid-binding protein,Amino acid ABC transporter, periplasmic amino acid-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2393
Polymers14,1181
Non-polymers1212
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Amino acid ABC transporter, periplasmic amino acid-binding protein,Amino acid ABC transporter, periplasmic amino acid-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2393
Polymers14,1181
Non-polymers1212
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)35.447, 45.812, 52.408
Angle α, β, γ (deg.)64.070, 70.330, 90.020
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Amino acid ABC transporter, periplasmic amino acid-binding protein,Amino acid ABC transporter, periplasmic amino acid-binding protein


Mass: 14118.161 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima MSB8 (bacteria) / Gene: TM_0593 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9WZ62
#2: Chemical ChemComp-GAI / GUANIDINE


Mass: 59.070 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH5N3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 261 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 51.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: THE BEST CRYSTALS OF D1 DOMAIN WERE OBTAINED USING A PROTEIN CONCENTRATION OF 8 MG/ML IN A SOLUTION CONTAINING 0.2 M NACL, 0.1M BIS-TRIS (PH 5.5), 25% (W/V) POLYETHYLENE GLYCOL (PEG) 3,350., ...Details: THE BEST CRYSTALS OF D1 DOMAIN WERE OBTAINED USING A PROTEIN CONCENTRATION OF 8 MG/ML IN A SOLUTION CONTAINING 0.2 M NACL, 0.1M BIS-TRIS (PH 5.5), 25% (W/V) POLYETHYLENE GLYCOL (PEG) 3,350., VAPOR DIFFUSION, HANGING DROP,

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: Cu FINE FOCUS / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Jun 6, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.698→50 Å / Num. obs: 25777 / % possible obs: 85 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 20.2
Reflection shellResolution: 1.7→1.76 Å / Rmerge(I) obs: 0.251 / Num. unique obs: 1392 / % possible all: 45

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6GPC

6gpc


Resolution: 1.7→23.63 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.954 / SU B: 1.966 / SU ML: 0.065 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.112 / ESU R Free: 0.104 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.187 1371 5.3 %RANDOM
Rwork0.161 ---
obs0.162 24401 85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 87.17 Å2 / Biso mean: 18.63 Å2 / Biso min: 9.98 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20.01 Å20.01 Å2
2--0.01 Å2-0.01 Å2
3----0.01 Å2
Refinement stepCycle: final / Resolution: 1.7→23.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1960 0 16 261 2237
Biso mean--20.27 27.93 -
Num. residues----254
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0132022
X-RAY DIFFRACTIONr_bond_other_d00.0171969
X-RAY DIFFRACTIONr_angle_refined_deg1.6231.6362725
X-RAY DIFFRACTIONr_angle_other_deg1.4621.5854560
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2295260
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.14323.069101
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.55615366
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.1011512
X-RAY DIFFRACTIONr_chiral_restr0.0780.2266
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.022260
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02412
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded

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