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- PDB-3nr1: A metazoan ortholog of SpoT hydrolyzes ppGpp and plays a role in ... -

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Basic information

Entry
Database: PDB / ID: 3nr1
TitleA metazoan ortholog of SpoT hydrolyzes ppGpp and plays a role in starvation responses
ComponentsHD domain-containing protein 3
KeywordsHYDROLASE / stringent response / pyrophosphohydrolase / HD (Histidine and Aspartic acid) family / ppGpp hydrolase
Function / homology
Function and homology information


guanosine-3',5'-bis(diphosphate) 3'-diphosphatase / guanosine-3',5'-bis(diphosphate) 3'-diphosphatase activity / metal ion binding
Similarity search - Function
HD domain / 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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 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_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_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: HD domain-containing protein 3
B: HD domain-containing protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,5724
Polymers40,4622
Non-polymers1102
Water3,963220
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2440 Å2
ΔGint-13 kcal/mol
Surface area16660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.900, 62.400, 53.900
Angle α, β, γ (deg.)90.000, 95.300, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein HD domain-containing protein 3 / Metazoan SpoT Homolog 1 / Mesh1


Mass: 20230.848 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HDDC3 / Plasmid: pET28(a) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8N4P3
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 220 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.23 Å3/Da / Density % sol: 44.86 % / Mosaicity: 0.37 °
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 20-25% PEG 3350, 0.2M sodium citrate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 296K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12931
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONPAL/PLS 4A10.97953
SYNCHROTRONPAL/PLS 6C120.97955
Detector
TypeIDDetectorDate
ADSC QUANTUM 2101CCDSep 12, 2007
ADSC QUANTUM 2102CCDMar 6, 2008
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SADMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.979531
20.979551
ReflectionRedundancy: 7.4 % / Av σ(I) over netI: 21.87 / Number: 158988 / Rmerge(I) obs: 0.074 / Χ2: 1.25 / D res high: 2.05 Å / D res low: 50 Å / Num. obs: 21527 / % possible obs: 99.7
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.425010010.0492.927.4
3.514.4210010.0441.7057.6
3.063.5110010.0571.3667.6
2.783.0610010.0841.1637.6
2.582.7810010.1151.0497.6
2.432.5810010.1260.9417.6
2.312.4310010.1690.8667.6
2.212.3199.910.2110.7967.4
2.122.2199.310.2540.8097
2.052.1297.510.310.7596.5
ReflectionResolution: 1.9→50 Å / Num. all: 28395 / Num. obs: 28330 / % possible obs: 99.8 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.077 / Χ2: 1.373 / Net I/σ(I): 8.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.9-1.973.50.35428440.7341,299.5
1.97-2.053.70.26627880.7961,299.9
2.05-2.143.80.18928230.9131,2100
2.14-2.253.80.15228290.9931,299.9
2.25-2.393.80.12428041.0811,299.9
2.39-2.583.80.10128471.3511,299.9
2.58-2.843.80.08728341.4421,299.9
2.84-3.253.70.07128101.6941,299.9
3.25-4.093.70.05528512.2671,299.8
4.09-503.50.05129002.4971,299.2

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Phasing

PhasingMethod: SAD
Phasing MADD res high: 2.5 Å / D res low: 50 Å / FOM : 0.43 / Reflection: 11722
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Se19.6360.45300.2190.955
2Se20.8420.2190.6090.4530.924
3Se39.8810.8360.5090.450.419
4Se33.4720.550.6020.1630.363
Phasing MAD shell
Resolution (Å)FOM Reflection
9.04-500.45568
5.69-9.040.5981
4.45-5.690.491249
3.77-4.450.471486
3.33-3.770.441654
3.01-3.330.431819
2.77-3.010.381918
2.58-2.770.352047
Phasing dmFOM : 0.73 / FOM acentric: 0.73 / FOM centric: 0.68 / Reflection: 11722 / Reflection acentric: 11101 / Reflection centric: 621
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
7.1-32.80.90.920.7653345578
4.5-7.10.860.870.8116031483120
3.6-4.50.880.880.7820021883119
3.1-3.60.790.790.712000190694
2.7-3.10.650.650.5834653332133
2.5-2.70.530.530.432119204277

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVE2.13phasing
RESOLVE2.13phasing
CNSrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.9→50 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2302 1890 6.7 %RANDOM
Rwork0.2033 ---
all-28205 --
obs-27178 96.4 %-
Solvent computationBsol: 64.5821 Å2
Displacement parametersBiso max: 69.89 Å2 / Biso mean: 24.3943 Å2 / Biso min: 10.86 Å2
Baniso -1Baniso -2Baniso -3
1-0.177 Å20 Å23.997 Å2
2---0.369 Å20 Å2
3---0.191 Å2
Refinement stepCycle: LAST / Resolution: 1.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2850 0 2 220 3072
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_d1.032
X-RAY DIFFRACTIONc_mcbond_it1.2251.5
X-RAY DIFFRACTIONc_scbond_it2.2962
X-RAY DIFFRACTIONc_mcangle_it1.8382
X-RAY DIFFRACTIONc_scangle_it3.4992.5
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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