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- PDB-3nqw: A metazoan ortholog of SpoT hydrolyzes ppGpp and plays a role in ... -

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Basic information

Entry
Database: PDB / ID: 3nqw
TitleA metazoan ortholog of SpoT hydrolyzes ppGpp and plays a role in starvation responses
ComponentsCG11900
KeywordsHYDROLASE / stringent response / pyrophosphohydrolase / HD (Histidine and Aspartic acid) family / ppGpp hydrolase
Function / homology
Function and homology information


guanosine tetraphosphate catabolic process / guanosine-3',5'-bis(diphosphate) 3'-diphosphatase / guanosine-3',5'-bis(diphosphate) 3'-diphosphatase activity / response to starvation / metal ion binding
Similarity search - Function
Hypothetical protein af1432 / Hypothetical protein af1432 / HD domain profile. / HD domain / Metal dependent phosphohydrolases with conserved 'HD' motif. / HD/PDEase domain / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
: / Guanosine-3',5'-bis(diphosphate) 3'-pyrophosphohydrolase MESH1
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.9 Å
AuthorsSun, D.W. / Kim, H.Y. / Kim, K.J. / Jeon, Y.H. / Chung, J.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2010
Title: A metazoan ortholog of SpoT hydrolyzes ppGpp and functions in starvation responses
Authors: Sun, D.W. / Lee, G. / Lee, J.H. / Kim, H.Y. / Rhee, H.W. / Park, S.Y. / Kim, K.J. / Kim, Y. / Kim, B.Y. / Hong, J.I. / Park, C. / Choy, H.E. / Kim, J.H. / Jeon, Y.H. / Chung, J.
History
DepositionJun 30, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 8, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 9, 2013Group: Database references
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CG11900
B: CG11900
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,5016
Polymers41,1992
Non-polymers3024
Water64936
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2710 Å2
ΔGint-17 kcal/mol
Surface area16280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.000, 71.400, 49.900
Angle α, β, γ (deg.)90.000, 101.400, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein CG11900 / IP06614p / Metazoan SpoT Homolog 1 / Mesh1


Mass: 20599.461 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: CG11900, Dmel_CG11900 / Production host: Escherichia coli (E. coli) / Strain (production host): BL23(DE3) / References: UniProt: Q9VAM9
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 36 / Source method: isolated from a natural source / Formula: H2O

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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: 2.12 Å3/Da / Density % sol: 41.96 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 100mM sodium cacodylate (pH 6.5), 1.2-1.5M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 6C1 / Wavelength: 1.23985 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 14, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.23985 Å / Relative weight: 1
ReflectionRedundancy: 3.5 % / Av σ(I) over netI: 20.02 / Number: 26676 / Rmerge(I) obs: 0.071 / Χ2: 1.31 / D res high: 2.9 Å / D res low: 50 Å / Num. obs: 7539 / % possible obs: 96.5
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
6.24509410.0361.8463.5
4.966.2410010.051.4153.7
4.334.9699.510.0541.5223.7
3.944.3399.410.071.4693.7
3.653.9499.710.0911.3463.7
3.443.6510010.1211.2243.7
3.273.4410010.1741.073.7
3.123.2799.210.2361.0613.5
33.1293.410.3020.9673.2
2.9380.410.3660.9532.7
ReflectionResolution: 2.9→50 Å / Num. all: 7811 / Num. obs: 7539 / % possible obs: 96.5 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.071 / Χ2: 1.31 / Net I/σ(I): 10.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.9-32.70.3666280.953180.4
3-3.123.20.3027320.967193.4
3.12-3.273.50.2367351.061199.2
3.27-3.443.70.1747851.071100
3.44-3.653.70.1217751.2241100
3.65-3.943.70.0917741.346199.7
3.94-4.333.70.077771.469199.4
4.33-4.963.70.0547771.522199.5
4.96-6.243.70.057981.4151100
6.24-503.50.0367581.846194

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 49.71 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.89 Å49.03 Å
Translation2.89 Å49.03 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.4phasing
CNSrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→20 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2822 526 6.8 %RANDOM
Rwork0.2129 ---
all-7528 --
obs-7060 91.8 %-
Solvent computationBsol: 25.8118 Å2
Displacement parametersBiso max: 107.31 Å2 / Biso mean: 65.9301 Å2 / Biso min: 16.54 Å2
Baniso -1Baniso -2Baniso -3
1--6.411 Å20 Å22.757 Å2
2--19.39 Å20 Å2
3----12.979 Å2
Refinement stepCycle: LAST / Resolution: 2.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2870 0 12 36 2918
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_d1.19
X-RAY DIFFRACTIONc_mcbond_it1.3521.5
X-RAY DIFFRACTIONc_scbond_it1.6372
X-RAY DIFFRACTIONc_mcangle_it2.3432
X-RAY DIFFRACTIONc_scangle_it2.6022.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5carbohydrate.paramcarbohydrate.top

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