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- PDB-7c0x: Crystal structure of a dinucleotide-binding protein (T240A) of AB... -

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Basic information

Entry
Database: PDB / ID: 7c0x
TitleCrystal structure of a dinucleotide-binding protein (T240A) of ABC transporter endogenously bound to uridylyl-3'-5'-phospho-guanosine
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 / periplasmic space
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
ACETATE ION / CARBON DIOXIDE / Chem-FGO / DI(HYDROXYETHYL)ETHER / HYPOPHOSPHITE / Sugar ABC transporter, periplasmic sugar-binding protein
Similarity search - Component
Biological speciesThermus thermophilus HB8 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.77 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 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)91,23119
Polymers88,9502
Non-polymers2,28217
Water13,619756
1
A: Sugar ABC transporter, periplasmic sugar-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,71711
Polymers44,4751
Non-polymers1,24210
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area190 Å2
ΔGint-0 kcal/mol
Surface area16410 Å2
MethodPISA
2
B: Sugar ABC transporter, periplasmic sugar-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,5158
Polymers44,4751
Non-polymers1,0407
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area170 Å2
ΔGint0 kcal/mol
Surface area16430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.640, 58.080, 122.020
Angle α, β, γ (deg.)90.000, 95.340, 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: LYS / Beg label comp-ID: LYS / End auth comp-ID: SER / End label comp-ID: SER / Refine code: _ / Auth seq-ID: 1 - 395 / Label seq-ID: 3 - 397

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: 44474.762 Da / Num. of mol.: 2 / Mutation: T240A
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 , 8 types, 773 molecules

#2: Chemical ChemComp-PO2 / HYPOPHOSPHITE


Mass: 62.973 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O2P
#3: Chemical ChemComp-CO2 / CARBON DIOXIDE


Mass: 44.010 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CO2
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#8: 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
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 756 / 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: 2.66 Å3/Da / Density % sol: 53.79 % / 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: Jul 16, 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: 1.77→60.75 Å / Num. obs: 83929 / % possible obs: 93.1 % / Redundancy: 4.2 % / CC1/2: 0.974 / Rmerge(I) obs: 0.17 / Rpim(I) all: 0.089 / Rrim(I) all: 0.192 / Net I/σ(I): 6.6 / Num. measured all: 355385 / Scaling rejects: 799
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
1.77-1.814.10.4861600738810.7640.2620.5542.681.7
9.38-60.754.20.12827636590.9720.0650.1448.698.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.29 Å60.75 Å
Translation5.29 Å60.75 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: 1.77→60.75 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.925 / SU B: 3.695 / SU ML: 0.064 / SU R Cruickshank DPI: 0.0269 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.027 / ESU R Free: 0.026
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2264 4086 4.9 %RANDOM
Rwork0.1856 ---
obs0.1876 79825 92.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 72.08 Å2 / Biso mean: 20.411 Å2 / Biso min: 6.1 Å2
Baniso -1Baniso -2Baniso -3
1--7.8 Å2-0 Å22.21 Å2
2---1.52 Å20 Å2
3---9.31 Å2
Refinement stepCycle: final / Resolution: 1.77→60.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6080 0 152 756 6988
Biso mean--22.08 28.5 -
Num. residues----790
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0136445
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176090
X-RAY DIFFRACTIONr_angle_refined_deg2.0251.6698748
X-RAY DIFFRACTIONr_angle_other_deg1.4861.58514124
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3425810
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.80622.704307
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.199151036
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0251533
X-RAY DIFFRACTIONr_chiral_restr0.1080.2809
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.027181
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021358
Refine LS restraints NCS

Ens-ID: 1 / Number: 12856 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.06 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.773→1.819 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 284 -
Rwork0.27 5183 -
all-5467 -
obs--82.32 %
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)
10.7882-0.4063-0.23410.66880.13720.4134-0.0654-0.0830.01980.05970.0725-0.02480.00620.0032-0.00710.0280.00750.0010.0123-0.00330.001614.86354.23725.5798
20.77190.29340.24150.53850.1420.5466-0.04350.0671-0.0243-0.02560.0495-0.0071-0.00310.015-0.00590.0237-0.00290.0070.0078-0.0020.002742.6475-13.3155.0652
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 395
2X-RAY DIFFRACTION2B1 - 395

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