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- PDB-7qpr: Structure of full length SpoT -

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Basic information

Entry
Database: PDB / ID: 7qpr
TitleStructure of full length SpoT
ComponentsACT domain protein
KeywordsHYDROLASE / (p)ppGpp hydrolase bound to ppGpp
Function / homology
Function and homology information


guanosine-3',5'-bis(diphosphate) 3'-diphosphatase / guanosine-3',5'-bis(diphosphate) 3'-diphosphatase activity / GTP diphosphokinase activity / guanosine tetraphosphate biosynthetic process / response to starvation / kinase activity / nucleotide binding / metal ion binding / plasma membrane
Similarity search - Function
HD domain / RelA/SpoT / Region found in RelA / SpoT proteins / TGS domain / Hypothetical protein af1432 / Hypothetical protein af1432 / HD domain profile. / TGS-like / TGS domain profile. / TGS ...HD domain / RelA/SpoT / Region found in RelA / SpoT proteins / TGS domain / Hypothetical protein af1432 / Hypothetical protein af1432 / HD domain profile. / TGS-like / TGS domain profile. / TGS / HD domain / Beta Polymerase, domain 2 / Beta-grasp domain superfamily / Metal dependent phosphohydrolases with conserved 'HD' motif. / HD/PDEase domain / Beta Polymerase; domain 2 / Nucleotidyltransferase superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
CITRATE ANION / GUANOSINE-5',3'-TETRAPHOSPHATE / : / guanosine-3',5'-bis(diphosphate) 3'-diphosphatase
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.513 Å
AuthorsGarcia-Pino, A. / Tamman, H.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structure of full length SpoT
Authors: Garcia-Pino, A. / Tamman, H.
History
DepositionJan 5, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 18, 2023Provider: 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: ACT domain protein
B: ACT domain protein
C: ACT domain protein
D: ACT domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)322,96027
Polymers319,1654
Non-polymers3,79623
Water15,709872
1
A: ACT domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,8317
Polymers79,7911
Non-polymers1,0406
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ACT domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,6075
Polymers79,7911
Non-polymers8164
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: ACT domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,9489
Polymers79,7911
Non-polymers1,1578
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: ACT domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,5746
Polymers79,7911
Non-polymers7835
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)128.791, 133.761, 211.328
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
ACT domain protein / Bifunctional (P)ppGpp synthetase/guanosine-3' / 5'-bis(Diphosphate) 3'-pyrophosphohydrolase / ...Bifunctional (P)ppGpp synthetase/guanosine-3' / 5'-bis(Diphosphate) 3'-pyrophosphohydrolase / Bifunctional protein SpoT / GTP pyrophosphokinase(ATP:GTP 3'-pyrophosphotransferase)(PpGpp synthetase I) / Guanosine-3' / 5'-bis(Diphosphate) 3'-pyrophosphohydrolase / pyrophosphokinase / (P)ppGpp synthetase II / Guanosine-3 / 5-bis(Diphosphate) 3-pyrophosphohydrolase / HD domain-containing protein / Putative GTP pyrophosphokinase RelA (ATP:GTP 3'-pyrophosphotransferase) (PPGPP synthetase I) ((P)PPGPP synthetase) (GTP diphosphokinase) / RelA/SpoT family protein


Mass: 79791.141 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria)
Gene: spoT_1, relA_1, relA_3, spoT, A7M90_14410, AB945B12_01945, Aba9201_15290, ABCAM1_3401, ABKPCSM17A_01292, ABR2091_3374, ABUW_0309, APC21_16100, APD31_02670, AUO97_04875, AYR68_16515, B7L36_ ...Gene: spoT_1, relA_1, relA_3, spoT, A7M90_14410, AB945B12_01945, Aba9201_15290, ABCAM1_3401, ABKPCSM17A_01292, ABR2091_3374, ABUW_0309, APC21_16100, APD31_02670, AUO97_04875, AYR68_16515, B7L36_04505, B7L45_01975, B9X95_19475, BAA1790NC_0315, BS065_01600, C2U32_12605, C5H40_03430, C6N18_18350, CBE85_06420, CBL15_01550, CSB70_3370, CTZ19_01585, DLI71_12465, DLI72_03665, DOL94_17785, E1A86_17370, E2535_18555, E2539_03475, E2540_19450, EA686_01605, EA706_01570, EA720_012255, EA722_01135, EGM95_01775, EKS29_00960, EP550_01655, EP560_16360, EWO96_11255, F2P40_01005, F4T85_13595, F4T91_15305, FDN00_18830, FE003_01590, FJU36_10385, FJU42_02940, FJU59_00430, FJU76_08505, FR761_17725, GNY86_13750, GSE42_18470, H0529_17955, H1058_16860, HBK86_16410, HIN86_01600, IMO23_16495, NCTC13305_02770, NCTC13421_00317, SAMEA104305281_00293, SAMEA104305340_01315, SAMEA104305385_01516, SI89_16095
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: V5V8V7, GTP diphosphokinase

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Non-polymers , 8 types, 895 molecules

#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-G4P / GUANOSINE-5',3'-TETRAPHOSPHATE / guanosine tetraphosphate;ppGpp


Type: RNA linking / Mass: 603.160 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H17N5O17P4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H5O7
#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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#8: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 872 / 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: 2.91 Å3/Da / Density % sol: 57.77 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.85M sodium citrate, 0.1M sodium chloride, 0.1M tris
PH range: 8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9786 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 11, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.513→48.88 Å / Num. obs: 83804 / % possible obs: 95.5 % / Redundancy: 13.8 % / Biso Wilson estimate: 74.68 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.18 / Rpim(I) all: 0.051 / Net I/σ(I): 9.6
Reflection shellResolution: 2.513→2.78 Å / Redundancy: 14 % / Rmerge(I) obs: 1.664 / Num. unique obs: 4191 / CC1/2: 0.712 / Rpim(I) all: 0.459 / % possible all: 72.6

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Processing

Software
NameVersionClassification
BUSTER2.10.4 (20-OCT-2021)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6S2V

6s2v


Resolution: 2.513→48.88 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.918 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.379
RfactorNum. reflection% reflectionSelection details
Rfree0.2581 4287 5.12 %RANDOM
Rwork0.2207 ---
obs0.2227 83804 67.3 %-
Displacement parametersBiso mean: 69.91 Å2
Baniso -1Baniso -2Baniso -3
1-4.8991 Å20 Å20 Å2
2--0.1775 Å20 Å2
3----5.0766 Å2
Refine analyzeLuzzati coordinate error obs: 0.39 Å
Refinement stepCycle: LAST / Resolution: 2.513→48.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21515 0 207 872 22594
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00822116HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0230054HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d7793SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes3860HARMONIC5
X-RAY DIFFRACTIONt_it22116HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.6
X-RAY DIFFRACTIONt_other_torsion19.17
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion2963SEMIHARMONIC5
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_contact16986SEMIHARMONIC4
LS refinement shellResolution: 2.513→2.69 Å
RfactorNum. reflection% reflection
Rfree0.359 -5.19 %
Rwork0.297 1590 -
obs--7.41 %
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)
10.3879-0.01290.111700.39280.51640.04180.0527-0.03470.011-0.0512-0.0502-0.0092-0.10110.00940.07510.01810.0654-0.05240.0047-0.074729.9454-2.961756.4635
20.0013-0.02620.22600.34161.03650.1313-0.03720.0096-0.0061-0.0594-0.1132-0.0069-0.1316-0.07180.09870.0036-0.0022-0.0418-0.0202-0.130532.8164-62.56242.1418
30.38490.15570.045300.40520.85820.0264-0.006-0.1112-0.0582-0.0124-0.0349-0.1368-0.0714-0.0140.02830.00630.0337-0.07390.0138-0.051528.6262-70.389754.0987
40-0.08550.24860.0640.29020.98590.0597-0.07840.0433-0.0344-0.1232-0.02110.0062-0.01680.0635-0.01020.0047-0.01320.0063-0.05-0.073932.14322.91573.5769
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }

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