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- PDB-7c1b: Crystal structure of a dinucleotide-binding protein (F79A/Y224A/Y... -

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Basic information

Entry
Database: PDB / ID: 7c1b
TitleCrystal structure of a dinucleotide-binding protein (F79A/Y224A/Y246A and deletion of residues 50-75) of ABC transporter (unbound form)
ComponentsSugar ABC transporter, periplasmic sugar-binding protein
KeywordsTRANSPORT PROTEIN / c-di-GMP/AMP / Substrate-binding protein / Thermus thermophilus / tRNA synthesis and/or modification / Venus Fly-trap mechanism / UgpB
Function / homology: / Bacterial extracellular solute-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / transmembrane transport / periplasmic space / DI(HYDROXYETHYL)ETHER / Sugar ABC transporter, periplasmic sugar-binding protein
Function and homology information
Biological speciesThermus thermophilus HB8 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsKanaujia, S.P. / Chandravanshi, M. / Samanta, R.
Funding support India, 1items
OrganizationGrant numberCountry
Science and Engineering Research Board (SERB)SB/YS/LS-120/2013 India
CitationJournal: Febs J. / Year: 2021
Title: Structural and thermodynamic insights into the novel dinucleotide-binding protein of ABC transporter unveils its moonlighting function.
Authors: Chandravanshi, M. / Samanta, R. / Kanaujia, S.P.
History
DepositionMay 2, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 10, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 18, 2021Group: Database references / Category: citation / database_2
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sugar ABC transporter, periplasmic sugar-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,7233
Polymers41,5541
Non-polymers1682
Water2,162120
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint0 kcal/mol
Surface area16940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.930, 55.470, 124.400
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 Sugar ABC transporter, periplasmic sugar-binding protein


Mass: 41554.344 Da / Num. of mol.: 1 / Mutation: F79A, Y224A, Y246A and deletion of residues 50-75
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus HB8 (bacteria) / Gene: TTHA0379 / Plasmid: pET22b / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: Q5SLB4
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.2 Å3/Da / Density % sol: 44.17 % / Description: Orthorhombic
Crystal growTemperature: 277 K / Method: microbatch / pH: 6.5
Details: 0.2M ammonium sulphate, 0.1M sodium cacodylate pH 6.5, 30% PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Dec 8, 2019 / Details: VariMax HF
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→62.2 Å / Num. obs: 16950 / % possible obs: 100 % / Redundancy: 10.7 % / CC1/2: 0.997 / Rmerge(I) obs: 0.15 / Rpim(I) all: 0.048 / Rrim(I) all: 0.157 / Net I/σ(I): 11.5 / Num. measured all: 181309 / Scaling rejects: 496
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.3-2.3810.80.5591728016070.9280.1770.5864.1100
8.91-62.28.90.05431993580.9990.0180.05823.299.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation4.96 Å62.2 Å
Translation4.96 Å62.2 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0266refinement
HKL-30003000data collection
MOSFLM7.2.2data reduction
Aimless0.7.4data scaling
PHASER2.8.3phasing
Coot0.8.9.2model building
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7C0F

7c0f


Resolution: 2.3→62.2 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.876 / WRfactor Rfree: 0.2519 / WRfactor Rwork: 0.1827 / FOM work R set: 0.8125 / SU B: 15.515 / SU ML: 0.193 / SU R Cruickshank DPI: 0.3787 / SU Rfree: 0.27 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.379 / ESU R Free: 0.27 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2695 829 4.9 %RANDOM
Rwork0.195 ---
obs0.1986 16069 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 81.58 Å2 / Biso mean: 30.045 Å2 / Biso min: 10.7 Å2
Baniso -1Baniso -2Baniso -3
1-2.08 Å20 Å2-0 Å2
2---1.77 Å20 Å2
3----0.32 Å2
Refinement stepCycle: final / Resolution: 2.3→62.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2817 0 11 120 2948
Biso mean--37.43 27.2 -
Num. residues----367
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0132888
X-RAY DIFFRACTIONr_bond_other_d0.0020.0172801
X-RAY DIFFRACTIONr_angle_refined_deg1.8211.643915
X-RAY DIFFRACTIONr_angle_other_deg1.371.5776430
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8325366
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.42723.309139
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.8515467
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.0451513
X-RAY DIFFRACTIONr_chiral_restr0.0830.2363
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023328
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02671
LS refinement shellResolution: 2.3→2.36 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 66 -
Rwork0.209 1138 -
all-1204 -
obs--99.92 %
Refinement TLS params.Method: refined / Origin x: 26.2028 Å / Origin y: 16.3681 Å / Origin z: 14.2605 Å
111213212223313233
T0.0173 Å2-0.0108 Å20.0094 Å2-0.0183 Å20.0023 Å2--0.0292 Å2
L0.8603 °20.0876 °2-0.4967 °2-0.9518 °2-0.684 °2--1.5337 °2
S0.0616 Å °0.0231 Å °0.153 Å °0.0432 Å °-0.0026 Å °-0.0079 Å °-0.0953 Å °-0.0004 Å °-0.0591 Å °

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