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- PDB-6z3n: Apo Structure of a Hydrolase from Pseudomonas aeruginosa PAO1 -

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Basic information

Entry
Database: PDB / ID: 6z3n
TitleApo Structure of a Hydrolase from Pseudomonas aeruginosa PAO1
ComponentsHydrolase
KeywordsHYDROLASE / Guanosine pentaphosphate phosphohydrolase / small alarmone / ppGpp
Function / homology: / guanosine-3',5'-bis(diphosphate) 3'-diphosphatase activity / HD domain / metal ion binding / ACETATE ION / NICKEL (II) ION / Bifunctional (P)ppGpp synthetase/guanosine-3',5'-bis(Diphosphate) 3'-pyrophosphohydrolase
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.58 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 1.0Jun 9, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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 / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)93,63111
Polymers93,1864
Non-polymers4457
Water10,196566
1
CCC: Hydrolase
hetero molecules

AAA: Hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,9207
Polymers46,5932
Non-polymers3285
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_545x+1/2,y-1/2,z1
Buried area3350 Å2
ΔGint-33 kcal/mol
Surface area16230 Å2
2
BBB: Hydrolase
DDD: Hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,7104
Polymers46,5932
Non-polymers1172
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2870 Å2
ΔGint-34 kcal/mol
Surface area16030 Å2
Unit cell
Length a, b, c (Å)85.310, 85.900, 122.640
Angle α, β, γ (deg.)90.000, 102.340, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11BBB-422-

HOH

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Components

#1: Protein
Hydrolase


Mass: 23296.412 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Gene: PA0431 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9I686
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C2H3O2
#3: Chemical
ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ni
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 566 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.74 Å3/Da / Density % sol: 55.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 12 mg/mL of PaSpo2 protein stock in the buffer of 25 mM Tris pH 8.0, 200 mM NaCl, and 10 mM MgCl2 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: 1.58→59.9 Å / Num. obs: 95945 / % possible obs: 81.3 % / Redundancy: 5.9 % / CC1/2: 0.999 / Net I/σ(I): 23.2
Reflection shellResolution: 1.58→1.61 Å / Num. unique obs: 1474 / CC1/2: 0.573

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
xia2data reduction
Aimlessdata scaling
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 1.58→59.9 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.961 / SU B: 5.847 / SU ML: 0.08 / Cross valid method: FREE R-VALUE / ESU R: 0.1 / ESU R Free: 0.09
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2004 4868 5.074 %
Rwork0.1374 91077 -
all0.141 --
obs-95945 81.169 %
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: 33.78 Å2
Baniso -1Baniso -2Baniso -3
1--0.32 Å2-0 Å2-1.978 Å2
2--2.023 Å20 Å2
3----0.764 Å2
Refinement stepCycle: LAST / Resolution: 1.58→59.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5632 0 18 566 6216
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0135777
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175234
X-RAY DIFFRACTIONr_angle_refined_deg1.6761.6467850
X-RAY DIFFRACTIONr_angle_other_deg1.5131.57312106
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3925706
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.55921.709357
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.96215926
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6751552
X-RAY DIFFRACTIONr_chiral_restr0.0840.2729
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.026622
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021242
X-RAY DIFFRACTIONr_nbd_refined0.2230.21357
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1810.24702
X-RAY DIFFRACTIONr_nbtor_refined0.1680.22831
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0860.22339
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.2377
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0580.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1540.228
X-RAY DIFFRACTIONr_nbd_other0.1970.287
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1660.228
X-RAY DIFFRACTIONr_mcbond_it5.9613.1942835
X-RAY DIFFRACTIONr_mcbond_other5.9613.1932834
X-RAY DIFFRACTIONr_mcangle_it6.8584.7923536
X-RAY DIFFRACTIONr_mcangle_other6.8574.7923537
X-RAY DIFFRACTIONr_scbond_it7.6153.8922942
X-RAY DIFFRACTIONr_scbond_other7.6153.8922942
X-RAY DIFFRACTIONr_scangle_it8.9955.5984314
X-RAY DIFFRACTIONr_scangle_other8.9965.5984314
X-RAY DIFFRACTIONr_lrange_it8.44239.536813
X-RAY DIFFRACTIONr_lrange_other8.34839.1166711
X-RAY DIFFRACTIONr_rigid_bond_restr3.864311011
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.58-1.6210.3781040.3782240X-RAY DIFFRACTION26.8499
1.621-1.6660.3411660.3513005X-RAY DIFFRACTION37.3939
1.666-1.7140.3132270.323812X-RAY DIFFRACTION49.0468
1.714-1.7670.3332050.3154740X-RAY DIFFRACTION61.5816
1.767-1.8240.33160.2985454X-RAY DIFFRACTION73.9744
1.824-1.8880.2563480.1986207X-RAY DIFFRACTION87.0056
1.888-1.960.2213670.1446698X-RAY DIFFRACTION97.5829
1.96-2.040.2053570.1196623X-RAY DIFFRACTION99.9141
2.04-2.130.1843350.1126352X-RAY DIFFRACTION99.9552
2.13-2.2340.1773380.0996097X-RAY DIFFRACTION99.8448
2.234-2.3550.2043060.1055766X-RAY DIFFRACTION100
2.355-2.4980.1793070.1045470X-RAY DIFFRACTION99.9654
2.498-2.670.1712840.1025161X-RAY DIFFRACTION99.9633
2.67-2.8840.1962440.1174821X-RAY DIFFRACTION99.9211
2.884-3.1590.1982230.1314432X-RAY DIFFRACTION99.9356
3.159-3.5320.2112230.1433992X-RAY DIFFRACTION99.8342
3.532-4.0780.1641810.1193555X-RAY DIFFRACTION99.8397
4.078-4.9930.1631380.1183022X-RAY DIFFRACTION99.842
4.993-7.0550.2541280.1842325X-RAY DIFFRACTION99.756

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