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- PDB-7c0f: Crystal structure of a dinucleotide-binding protein of ABC transp... -

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Basic information

Entry
Database: PDB / ID: 7c0f
TitleCrystal structure of a dinucleotide-binding protein of ABC transporter endogenously bound to uridylyl-3'-5'-phospho-guanosine (Form I)
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
Function and homology information


transmembrane transport
Similarity search - Function
Bacterial extracellular solute-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein
Similarity search - Domain/homology
CARBON DIOXIDE / Chem-FGO / 1,3-PROPANDIOL / DI(HYDROXYETHYL)ETHER / S-1,2-PROPANEDIOL / R-1,2-PROPANEDIOL / HYPOPHOSPHITE / Sugar ABC transporter, periplasmic sugar-binding protein
Similarity search - Component
Biological speciesThermus thermophilus HB8 (unknown)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.15 Å
AuthorsKanaujia, S.P. / Chandravanshi, M.
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 1, 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

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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
B: Sugar ABC transporter, periplasmic sugar-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,94337
Polymers89,0102
Non-polymers3,93335
Water7,476415
1
A: Sugar ABC transporter, periplasmic sugar-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,69521
Polymers44,5051
Non-polymers2,19020
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Sugar ABC transporter, periplasmic sugar-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,24816
Polymers44,5051
Non-polymers1,74315
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.160, 120.880, 66.060
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A1 - 395
2010B1 - 395

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Sugar ABC transporter, periplasmic sugar-binding protein


Mass: 44504.785 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus HB8 (unknown) / Gene: TTHA0379 / Plasmid: pET22b / Production host: Escherichia coli BL21(DE3) (unknown) / Variant (production host): Rosetta / References: UniProt: Q5SLB4

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Non-polymers , 13 types, 450 molecules

#2: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-PO2 / HYPOPHOSPHITE / Phosphinate


Mass: 62.973 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: O2P
#4: Chemical
ChemComp-CO2 / CARBON DIOXIDE / Carbon dioxide


Mass: 44.010 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: CO2
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#8: Chemical ChemComp-PDO / 1,3-PROPANDIOL / 1,3-Propanediol


Mass: 76.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O2
#9: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#10: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#11: Chemical ChemComp-FGO / [(1S,3R,3aR,6aS)-3-(2-azanyl-6-oxidanylidene-1H-purin-9-yl)-5,5-bis(oxidanyl)-1,3,3a,4,6,6a-hexahydrocyclopenta[c]furan-1-yl]methyl [(2R,3S,4R,5R)-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-2-(hydroxymethyl)-4-oxidanyl-oxolan-3-yl] hydrogen phosphate


Mass: 629.471 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H28N7O13P / Feature type: SUBJECT OF INVESTIGATION
#12: Chemical ChemComp-PGO / S-1,2-PROPANEDIOL / Propanediol


Mass: 76.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O2
#13: Chemical ChemComp-PGR / R-1,2-PROPANEDIOL


Mass: 76.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O2
#14: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 415 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.63 Å3/Da / Density % sol: 53.22 % / Description: Monoclinic
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2M ammonium phosphate, 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: Mar 23, 2017 / Details: VariMax HF
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.86
11-h,-k,l20.14
ReflectionResolution: 2.15→66.06 Å / Num. obs: 48571 / % possible obs: 98.2 % / Redundancy: 2.8 % / CC1/2: 0.987 / Rmerge(I) obs: 0.105 / Rpim(I) all: 0.104 / Rrim(I) all: 0.148 / Net I/σ(I): 6.9
Reflection shellResolution: 2.15→2.21 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.429 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 3803 / CC1/2: 0.697 / Rpim(I) all: 0.41 / Rrim(I) all: 0.594 / % possible all: 95.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.26 Å66.06 Å
Translation5.26 Å66.06 Å

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Processing

Software
NameVersionClassification
HKL-30003000data collection
MOSFLM7.2.2data reduction
Aimless7.2.2data scaling
PHASER2.8.3phasing
Coot0.8.9.2model building
REFMAC5.8.0258refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MFI
Resolution: 2.15→66.06 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.92 / SU B: 6.219 / SU ML: 0.088 / SU R Cruickshank DPI: 0.0441 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.044 / ESU R Free: 0.037
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2041 2429 5 %RANDOM
Rwork0.1582 ---
obs0.1604 46107 97.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 90.29 Å2 / Biso mean: 23.322 Å2 / Biso min: 8.62 Å2
Baniso -1Baniso -2Baniso -3
1--6.44 Å2-0 Å20.66 Å2
2--6.57 Å20 Å2
3----0.13 Å2
Refinement stepCycle: final / Resolution: 2.15→66.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6084 0 255 415 6754
Biso mean--33.07 29.52 -
Num. residues----790
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0136492
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176149
X-RAY DIFFRACTIONr_angle_refined_deg1.9271.6738764
X-RAY DIFFRACTIONr_angle_other_deg1.4681.5914261
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4755796
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.89422.848302
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.725151025
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7881531
X-RAY DIFFRACTIONr_chiral_restr0.0950.2806
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.027112
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021341
Refine LS restraints NCS

Ens-ID: 1 / Number: 12459 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.15→2.206 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.268 180 -
Rwork0.194 3245 -
all-3425 -
obs--94.35 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.5475-0.11970.44040.4675-0.29290.75680.06440.0359-0.0472-0.016-0.005-0.01430.04360.0065-0.05940.02370.00610.00270.0054-0.00090.012122.9832-5.704532.1695
20.49270.1855-0.33130.6202-0.29510.66310.0515-0.02170.03970.00480.00250.0009-0.05120.013-0.05390.0304-0.0060.00140.0022-0.0020.0077-5.88395.434361.5742
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 395
2X-RAY DIFFRACTION2B1 - 395

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