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- PDB-6z3o: The E74Q mutant of Small Alarmone Hydrolase SAH from Pseudomonas ... -

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Basic information

Entry
Database: PDB / ID: 6z3o
TitleThe E74Q mutant of Small Alarmone Hydrolase SAH from Pseudomonas aeruginosa PAO1
ComponentsSmall Alarmone Hydrolase
KeywordsHYDROLASE / Guanosine pentaphosphate phosphohydrolase / small alarmone / ppGpp
Function / homology: / guanosine-3',5'-bis(diphosphate) 3'-diphosphatase activity / HD domain / metal ion binding / : / Bifunctional (P)ppGpp synthetase/guanosine-3',5'-bis(Diphosphate) 3'-pyrophosphohydrolase
Function and homology information
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 Å
AuthorsJin, Y. / Rizkallah, P. / Bell, H.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust209057/Z/ 17/Z United Kingdom
CitationJournal: To Be Published
Title: Apo Structure of a Small Alarmone Hydrolase from Pseudomonas aeruginosa PAO1
Authors: Jin, Y. / Rizkallah, P. / Bell, H.
History
DepositionMay 21, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 27, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Small Alarmone Hydrolase
BBB: Small Alarmone Hydrolase
CCC: Small Alarmone Hydrolase
DDD: Small Alarmone Hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,6518
Polymers92,4314
Non-polymers2204
Water9,476526
1
AAA: Small Alarmone Hydrolase
hetero molecules

CCC: Small Alarmone Hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3264
Polymers46,2162
Non-polymers1102
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455x-1/2,y+1/2,z1
Buried area2860 Å2
ΔGint-26 kcal/mol
Surface area15990 Å2
MethodPISA
2
BBB: Small Alarmone Hydrolase
DDD: Small Alarmone Hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3264
Polymers46,2162
Non-polymers1102
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2910 Å2
ΔGint-26 kcal/mol
Surface area15990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.150, 86.050, 122.580
Angle α, β, γ (deg.)90.000, 101.770, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Small Alarmone Hydrolase


Mass: 23107.846 Da / Num. of mol.: 4 / Mutation: E74Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: PA0431 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9I686
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 526 / Source method: isolated from a natural source / Formula: H2O
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: 2.41 Å3/Da / Density % sol: 48.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 14.6 mg/mL of PaSpo2 E74Q variant protein stock in the buffer of 25 mM Tris pH 8.0, 200 mM NaCl, 10 mM ppGpp and 10 mM MnCl2 is mixed 1:1 ratio with the precipitant consisted of 4.0 M ...Details: 14.6 mg/mL of PaSpo2 E74Q variant protein stock in the buffer of 25 mM Tris pH 8.0, 200 mM NaCl, 10 mM ppGpp and 10 mM MnCl2 is mixed 1:1 ratio with the precipitant consisted of 4.0 M NH4OAc, 0.1 M Bis-Tris propane, pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Dec 14, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.74→57.28 Å / Num. obs: 89102 / % possible obs: 89.6 % / Redundancy: 3.8 % / CC1/2: 0.994 / Net I/σ(I): 7.3
Reflection shellResolution: 1.74→1.77 Å / Mean I/σ(I) obs: 1 / Num. unique obs: 4525 / CC1/2: 0.422 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
xia2data reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6Z3N

6z3n


Resolution: 1.74→43.062 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.949 / SU B: 8.306 / SU ML: 0.109 / Cross valid method: FREE R-VALUE / ESU R: 0.126 / ESU R Free: 0.11
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2274 4527 5.081 %
Rwork0.1518 84575 -
all0.156 --
obs-89102 99.254 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 29.11 Å2
Baniso -1Baniso -2Baniso -3
1-1.702 Å20 Å2-0.033 Å2
2--2.318 Å2-0 Å2
3----3.686 Å2
Refinement stepCycle: LAST / Resolution: 1.74→43.062 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5638 0 4 526 6168
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0135840
X-RAY DIFFRACTIONr_bond_other_d0.0030.0175276
X-RAY DIFFRACTIONr_angle_refined_deg1.7661.6457949
X-RAY DIFFRACTIONr_angle_other_deg1.5071.57312213
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0385721
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.73321.667366
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.12115952
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1131554
X-RAY DIFFRACTIONr_chiral_restr0.0870.2737
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.026739
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021267
X-RAY DIFFRACTIONr_nbd_refined0.2230.21330
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1820.24589
X-RAY DIFFRACTIONr_nbtor_refined0.1640.22856
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.22263
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1750.2321
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1130.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1460.215
X-RAY DIFFRACTIONr_nbd_other0.1910.294
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2020.221
X-RAY DIFFRACTIONr_mcbond_it4.5322.82866
X-RAY DIFFRACTIONr_mcbond_other4.5322.82865
X-RAY DIFFRACTIONr_mcangle_it5.3184.2113587
X-RAY DIFFRACTIONr_mcangle_other5.3174.2123588
X-RAY DIFFRACTIONr_scbond_it6.3883.3242974
X-RAY DIFFRACTIONr_scbond_other6.3853.3232974
X-RAY DIFFRACTIONr_scangle_it7.14.824360
X-RAY DIFFRACTIONr_scangle_other7.0994.8194360
X-RAY DIFFRACTIONr_lrange_it6.95334.436812
X-RAY DIFFRACTIONr_lrange_other6.87234.1336728
X-RAY DIFFRACTIONr_rigid_bond_restr4.984311116
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.74-1.7850.3543050.2566273X-RAY DIFFRACTION99.8331
1.785-1.8340.3073650.2456084X-RAY DIFFRACTION99.9225
1.834-1.8870.313220.2235907X-RAY DIFFRACTION99.8077
1.887-1.9450.313430.2045756X-RAY DIFFRACTION99.7547
1.945-2.0090.2632780.1725599X-RAY DIFFRACTION99.915
2.009-2.080.2523170.1655371X-RAY DIFFRACTION99.7545
2.08-2.1580.2452590.1575266X-RAY DIFFRACTION99.5496
2.158-2.2460.2442620.1285006X-RAY DIFFRACTION99.4337
2.246-2.3460.2192350.1214861X-RAY DIFFRACTION99.473
2.346-2.460.1922620.1124563X-RAY DIFFRACTION99.3412
2.46-2.5930.2262250.1244315X-RAY DIFFRACTION98.9538
2.593-2.7510.2162110.134177X-RAY DIFFRACTION99.3434
2.751-2.940.2092060.1243874X-RAY DIFFRACTION98.8612
2.94-3.1760.2441910.153612X-RAY DIFFRACTION98.7023
3.176-3.4790.2241830.1523295X-RAY DIFFRACTION98.3319
3.479-3.8890.2021640.162989X-RAY DIFFRACTION97.9497
3.889-4.490.1691290.1252637X-RAY DIFFRACTION97.463
4.49-5.4970.2051220.1522246X-RAY DIFFRACTION98.1351
5.497-7.7660.248860.1711774X-RAY DIFFRACTION98.9888

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