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- PDB-7qps: Structure of Mn-free SpoT -

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Basic information

Entry
Database: PDB / ID: 7qps
TitleStructure of Mn-free SpoT
ComponentsACT domain protein
KeywordsHYDROLASE / metal-free (p)ppGpp hydrolase SpoT
Function / homology
Function and homology information


guanosine tetraphosphate biosynthetic process / GTP diphosphokinase / kinase activity / hydrolase activity / phosphorylation
Similarity search - Function
RelA/SpoT / Region found in RelA / SpoT proteins / TGS domain / HD domain profile. / TGS domain profile. / TGS / TGS-like / HD domain / Beta-grasp domain superfamily / Metal dependent phosphohydrolases with conserved 'HD' motif. ...RelA/SpoT / Region found in RelA / SpoT proteins / TGS domain / HD domain profile. / TGS domain profile. / TGS / TGS-like / HD domain / Beta-grasp domain superfamily / Metal dependent phosphohydrolases with conserved 'HD' motif. / HD/PDEase domain / Nucleotidyltransferase superfamily
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / ACT domain protein
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.79 Å
AuthorsGarcia-Pino, A. / Tamman, H.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structure of Mn-free 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,4163
Polymers77,0692
Non-polymers3471
Water4,360242
1
A: ACT domain protein


Theoretical massNumber of molelcules
Total (without water)38,5341
Polymers38,5341
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ACT domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,8822
Polymers38,5341
Non-polymers3471
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.887, 90.887, 262.359
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122

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Components

#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: 38534.348 Da / Num. of mol.: 2
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
#2: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 242 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.77 Å3/Da / Density % sol: 67.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.5 M Ammonium sulfate, 1.0 M Lithium sulfate, 0.1 M Sodium citrate, 30 % w/v PEG 1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 9, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 2.79→85.88 Å / Num. obs: 25337 / % possible obs: 94.7 % / Redundancy: 24.8 % / Biso Wilson estimate: 64.82 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.527 / Rpim(I) all: 0.108 / Net I/σ(I): 10.1
Reflection shellResolution: 2.79→2.9 Å / Rmerge(I) obs: 3.457 / Num. unique obs: 1230 / CC1/2: 0.487 / Rpim(I) all: 0.689

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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: 2.79→85.88 Å / Cor.coef. Fo:Fc: 0.858 / Cor.coef. Fo:Fc free: 0.819 / SU R Cruickshank DPI: 0.781 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.975 / SU Rfree Blow DPI: 0.396 / SU Rfree Cruickshank DPI: 0.389
RfactorNum. reflection% reflectionSelection details
Rfree0.2983 1253 4.95 %RANDOM
Rwork0.2582 ---
obs0.2602 25337 89.2 %-
Displacement parametersBiso mean: 49.36 Å2
Baniso -1Baniso -2Baniso -3
1--0.6286 Å20 Å20 Å2
2---0.6286 Å20 Å2
3---1.2573 Å2
Refine analyzeLuzzati coordinate error obs: 0.46 Å
Refinement stepCycle: LAST / Resolution: 2.79→85.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4893 0 23 242 5158
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0094985HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.996744HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1788SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes865HARMONIC5
X-RAY DIFFRACTIONt_it4960HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.82
X-RAY DIFFRACTIONt_other_torsion17.93
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion685SEMIHARMONIC5
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_contact3997SEMIHARMONIC4
LS refinement shellResolution: 2.79→2.84 Å / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.3997 -3.75 %
Rwork0.3065 488 -
all0.31 507 -
obs--34.17 %
Refinement TLS params.

L11: 0 °2 / L12: 0 °2 / L13: 0 °2 / L22: 0 °2 / L23: 0 °2 / L33: 0 °2 / S11: 0 Å ° / S12: 0 Å ° / S13: 0 Å ° / S21: 0 Å ° / S22: 0 Å ° / S23: 0 Å ° / S31: 0 Å ° / S32: 0 Å ° / S33: 0 Å ° / T11: 0 Å2 / T12: 0 Å2 / T13: 0 Å2 / T22: 0 Å2 / T23: 0 Å2 / T33: 0 Å2 / Method: refined / Refine-ID: X-RAY DIFFRACTION

IDOrigin x (Å)Origin y (Å)Origin z (Å)
1-43.8094-33.403115.1449
2-39.89657.221614.1575
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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