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- PDB-7c16: Crystal structure of a dinucleotide-binding protein (Y224A/Y246A)... -

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Basic information

Entry
Database: PDB / ID: 7c16
TitleCrystal structure of a dinucleotide-binding protein (Y224A/Y246A) 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 / 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
CARBON DIOXIDE / CARBONATE ION / Chem-FGO / DI(HYDROXYETHYL)ETHER / Sugar ABC transporter, periplasmic sugar-binding protein
Similarity search - Component
Biological speciesThermus thermophilus HB8 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 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 ...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)91,15824
Polymers88,6412
Non-polymers2,51722
Water9,638535
1
A: Sugar ABC transporter, periplasmic sugar-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,56611
Polymers44,3211
Non-polymers1,24510
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area70 Å2
ΔGint-4 kcal/mol
Surface area16610 Å2
MethodPISA
2
B: Sugar ABC transporter, periplasmic sugar-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,59213
Polymers44,3211
Non-polymers1,27112
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area70 Å2
ΔGint-4 kcal/mol
Surface area16550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.520, 121.690, 65.400
Angle α, β, γ (deg.)90.000, 90.070, 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 - 394 / Label seq-ID: 3 - 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: 44320.598 Da / Num. of mol.: 2 / Mutation: Y224A, Y246A
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, 557 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-CO2 / CARBON DIOXIDE


Mass: 44.010 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: CO2
#4: Chemical ChemComp-CO3 / CARBONATE ION


Mass: 60.009 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CO3
#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.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / 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.: 535 / 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: 53.35 % / 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 22, 2019 / 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, L10.681
11-h,-k,l20.319
ReflectionResolution: 1.9→60.84 Å / Num. obs: 71958 / % possible obs: 100 % / Redundancy: 4.1 % / CC1/2: 0.969 / Rmerge(I) obs: 0.157 / Rpim(I) all: 0.089 / Rrim(I) all: 0.18 / Net I/σ(I): 6.8 / Num. measured all: 294910 / Scaling rejects: 349
Reflection shell

Diffraction-ID: 1 / Redundancy: 4 %

Resolution (Å)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.9-1.940.571857646540.6920.3290.6612.3100
9.11-60.840.08427836900.9640.050.09812.299.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation4.33 Å58.52 Å
Translation4.33 Å58.52 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: 1.9→58.52 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.902 / SU B: 3.569 / SU ML: 0.059 / SU R Cruickshank DPI: 0.027 / 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
Rfree0.2044 3510 4.9 %RANDOM
Rwork0.1629 ---
obs0.1649 68415 99.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 59.91 Å2 / Biso mean: 18.485 Å2 / Biso min: 6.25 Å2
Baniso -1Baniso -2Baniso -3
1--1.54 Å2-0 Å2-0.4 Å2
2--6.32 Å20 Å2
3----4.79 Å2
Refinement stepCycle: final / Resolution: 1.9→58.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6064 0 166 535 6765
Biso mean--26.34 25.44 -
Num. residues----791
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0136367
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175996
X-RAY DIFFRACTIONr_angle_refined_deg2.2291.6688628
X-RAY DIFFRACTIONr_angle_other_deg1.5271.58513907
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9025793
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.10623.174293
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.012151014
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7691528
X-RAY DIFFRACTIONr_chiral_restr0.1210.2803
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.027067
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021309
Refine LS restraints NCS

Ens-ID: 1 / Number: 12512 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.09 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.9→1.947 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.239 224 -
Rwork0.18 4859 -
obs--95.17 %
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)
10.44960.1502-0.2650.4276-0.22890.44670.0417-0.03370.0320.0114-0.00690.0047-0.0380.012-0.03480.01220.0002-0.01020.0089-0.00730.031623.58525.40540.6609
20.4443-0.17540.18630.4831-0.1990.47490.02410.0088-0.0189-0.00110.00450.00190.03530.0033-0.02860.01240.0019-0.01530.0008-0.00330.0234-5.5535-5.9728-28.3707
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 395
2X-RAY DIFFRACTION2B1 - 395

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