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- PDB-7ohg: Structure of Thermus thermophilus Rel bound to the non-hydrolasab... -

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Basic information

Entry
Database: PDB / ID: 7ohg
TitleStructure of Thermus thermophilus Rel bound to the non-hydrolasable alarmone analogue
ComponentsGuanosine-3',5'-bis(Diphosphate) 3'-pyrophosphohydrolase
KeywordsTRANSFERASE / GTP / GDP pyrophospho-hydrolase / ppGpp / alarmones / Rel
Function / homologyFORMIC ACID / : / Non-hydrolasable alarmone analogue / :
Function and homology information
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.507 Å
AuthorsGarcia-Pino, A.
CitationJournal: To Be Published
Title: Structure of Thermus thermophilus Rel bound to the non-hydrolasable alarmone analogue
Authors: Garcia-Pino, A.
History
DepositionMay 11, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 1, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Guanosine-3',5'-bis(Diphosphate) 3'-pyrophosphohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,82711
Polymers40,7501
Non-polymers1,07710
Water1,838102
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1350 Å2
ΔGint-63 kcal/mol
Surface area16830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.121, 88.121, 182.889
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Guanosine-3',5'-bis(Diphosphate) 3'-pyrophosphohydrolase


Mass: 40750.000 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Gene: TthHC11_17770 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A510IKK7

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Non-polymers , 7 types, 112 molecules

#2: Chemical ChemComp-VE8 / Non-hydrolasable alarmone analogue / ~{N}-[(2~{S},3~{S},4~{R},5~{R})-5-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-4-oxidanyl-2-[[oxidanyl-[oxidanyl(phosphonooxy)phosphoryl]oxy-phosphoryl]oxymethyl]oxolan-3-yl]-phosphonooxy-phosphonamidic acid


Mass: 682.155 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H19N6O19P5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#5: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#7: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 102 / 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: 4.4 Å3/Da / Density % sol: 72.05 % / Description: long rods
Crystal growTemperature: 295.16 K / Method: vapor diffusion, sitting drop
Details: 8 % w/v PEG 20000; 0.05 M Tris 8.5; 1.2 M Sodium formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.97856 Å
DetectorType: DECTRIS PILATUS 12M / Detector: PIXEL / Date: Mar 2, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.507→88.12 Å / Num. obs: 14157 / % possible obs: 94 % / Redundancy: 23 % / Biso Wilson estimate: 74.46 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.156 / Rpim(I) all: 0.033 / Net I/σ(I): 13.2
Reflection shellResolution: 2.507→2.858 Å / Rmerge(I) obs: 1.048 / Num. unique obs: 707 / CC1/2: 0.824 / Rpim(I) all: 0.316

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Processing

Software
NameVersionClassification
BUSTER2.10.3 (20-MAY-2020)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6S2V

6s2v


Resolution: 2.507→88.12 Å / Cor.coef. Fo:Fc: 0.91 / Cor.coef. Fo:Fc free: 0.899 / SU R Cruickshank DPI: 0.689 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.803 / SU Rfree Blow DPI: 0.342 / SU Rfree Cruickshank DPI: 0.339
RfactorNum. reflection% reflectionSelection details
Rfree0.2453 688 4.86 %RANDOM
Rwork0.2068 ---
obs0.2086 14157 55.4 %-
Displacement parametersBiso mean: 65.14 Å2
Baniso -1Baniso -2Baniso -3
1-1.1508 Å20 Å20 Å2
2--1.1508 Å20 Å2
3----2.3015 Å2
Refine analyzeLuzzati coordinate error obs: 0.39 Å
Refinement stepCycle: LAST / Resolution: 2.507→88.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2771 0 56 102 2929
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0082875HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.983906HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1025SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes497HARMONIC5
X-RAY DIFFRACTIONt_it2875HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.02
X-RAY DIFFRACTIONt_other_torsion20.92
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion371SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2409SEMIHARMONIC4
LS refinement shellResolution: 2.51→2.76 Å
RfactorNum. reflection% reflection
Rfree0.3784 -5.52 %
Rwork0.2668 394 -
obs--78.1 %
Refinement TLS params.Method: refined / Origin x: 66.0072 Å / Origin y: 49.4455 Å / Origin z: 19.026 Å
111213212223313233
T-0.1327 Å2-0.039 Å20.0741 Å2-0.0996 Å2-0.0439 Å2---0.047 Å2
L0.5 °2-0.1882 °2-1.0068 °2-0.573 °20.3125 °2--3.0223 °2
S0.2574 Å °0.0734 Å °0.1837 Å °0.0694 Å °-0.004 Å °0.0073 Å °-0.1675 Å °0.1436 Å °-0.2534 Å °
Refinement TLS groupSelection details: { A|* }

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