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- PDB-7c0k: Crystal structure of a dinucleotide-binding protein of ABC transp... -

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Basic information

Entry
Database: PDB / ID: 7c0k
TitleCrystal structure of a dinucleotide-binding protein of ABC transporter endogenously bound to uridylyl-3'-5'-phospho-guanosine (Form II)
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
2-HYDROXY BUTANE-1,4-DIOL / CARBON DIOXIDE / CARBONATE ION / Chem-FGO / 1,3-PROPANDIOL / HYPOPHOSPHITE / PHOSPHITE ION / PHOSPHATE ION / Sugar ABC transporter, periplasmic sugar-binding protein
Similarity search - Component
Biological speciesThermus thermophilus HB8 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 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
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.3Oct 23, 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
B: Sugar ABC transporter, periplasmic sugar-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,38250
Polymers89,0102
Non-polymers4,37348
Water11,476637
1
A: Sugar ABC transporter, periplasmic sugar-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,90526
Polymers44,5051
Non-polymers2,40025
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4330 Å2
ΔGint5 kcal/mol
Surface area16600 Å2
MethodPISA
2
B: Sugar ABC transporter, periplasmic sugar-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,47724
Polymers44,5051
Non-polymers1,97323
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3750 Å2
ΔGint-8 kcal/mol
Surface area16740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.170, 57.520, 121.140
Angle α, β, γ (deg.)90.000, 94.990, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: SER / End label comp-ID: SER / Refine code: _ / Auth seq-ID: 0 - 394 / Label seq-ID: 2 - 396

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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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 (bacteria) / Gene: TTHA0379 / Plasmid: pET22b / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: Q5SLB4

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Non-polymers , 14 types, 685 molecules

#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-CO2 / CARBON DIOXIDE


Mass: 44.010 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: CO2
#5: Chemical ChemComp-PO2 / HYPOPHOSPHITE


Mass: 62.973 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: O2P
#6: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#7: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#8: Chemical ChemComp-PDO / 1,3-PROPANDIOL


Mass: 76.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O2
#9: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O3
#10: Chemical ChemComp-BGQ / 2-HYDROXY BUTANE-1,4-DIOL


Mass: 105.112 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H9O3
#11: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#12: 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
#13: Chemical ChemComp-CO3 / CARBONATE ION


Mass: 60.009 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CO3
#14: Chemical ChemComp-PO3 / PHOSPHITE ION


Mass: 78.972 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO3
#15: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 637 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.6 Å3/Da / Density % sol: 52.7 % / Description: Monoclinic
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2M ammonium phosphate, 0.1M sodium cacodylate pH6.5, 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: Apr 13, 2017 / Details: VariMax HF
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→46.57 Å / Num. obs: 84314 / % possible obs: 99.9 % / Redundancy: 4.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.041 / Rrim(I) all: 0.086 / Net I/σ(I): 12.3 / Num. measured all: 361385 / Scaling rejects: 24
Reflection shell

Diffraction-ID: 1 / Redundancy: 4.2 %

Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.8-1.830.53944430.7920.3010.61999.6
9.52-46.570.0346140.9990.0180.03999.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.29 Å46.57 Å
Translation5.29 Å46.57 Å

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Processing

Software
NameVersionClassification
HKL-30003000data collection
MOSFLM7.2.2data reduction
Aimless0.7.4data scaling
PHASER2.8.3phasing
Coot0.8.9.2model building
REFMAC5.8.0258refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7C0F

7c0f


Resolution: 1.8→46.57 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.955 / SU B: 2.725 / SU ML: 0.046 / SU R Cruickshank DPI: 0.0209 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.021 / ESU R Free: 0.02
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1762 4082 4.8 %RANDOM
Rwork0.146 ---
obs0.1475 80214 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 79.55 Å2 / Biso mean: 21.452 Å2 / Biso min: 7.95 Å2
Baniso -1Baniso -2Baniso -3
1--2.96 Å2-0 Å21.89 Å2
2--4.56 Å20 Å2
3----1.6 Å2
Refinement stepCycle: final / Resolution: 1.8→46.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6108 0 276 637 7021
Biso mean--33.5 31.32 -
Num. residues----793
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0136559
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176213
X-RAY DIFFRACTIONr_angle_refined_deg2.121.6748855
X-RAY DIFFRACTIONr_angle_other_deg1.5791.58814410
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2645809
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.44522.787305
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.784151047
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.1461532
X-RAY DIFFRACTIONr_chiral_restr0.1170.2813
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.027186
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021354
Refine LS restraints NCS

Ens-ID: 1 / Number: 12840 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.07 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.8→1.847 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.257 300 -
Rwork0.189 5862 -
all-6162 -
obs--99.56 %
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.64-0.321-0.30180.59910.17340.5147-0.048-0.0507-0.00030.06080.0493-0.039-0.00720.0074-0.00130.01190.0032-0.00430.0148-0.00020.003914.74134.34455.5366
20.57340.27330.26190.49250.2170.6692-0.03630.02650.0105-0.02810.0314-0.00860.007-0.00860.0050.00930.00150.00240.00930.00320.003342.6688-12.898254.7178
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 395
2X-RAY DIFFRACTION2B-1 - 395

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