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- PDB-7qoe: Structure of a small alarmone hydrolase from Leptospira levettii -

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Basic information

Entry
Database: PDB / ID: 7qoe
TitleStructure of a small alarmone hydrolase from Leptospira levettii
ComponentsHDc domain-containing protein
KeywordsHYDROLASE / Alarmone / Stress response / HD domain
Function / homologyMetal dependent phosphohydrolases with conserved 'HD' motif. / HD/PDEase domain / : / HDc domain-containing protein
Function and homology information
Biological speciesLeptospira levettii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.2 Å
AuthorsBisiak, F. / Brodersen, D.E. / Chrenkova, A.
Funding support Denmark, 1items
OrganizationGrant numberCountry
Novo Nordisk FoundationNNF18OC0030646 Denmark
CitationJournal: J.Biol.Chem. / Year: 2022
Title: Structural variations between small alarmone hydrolase dimers support different modes of regulation of the stringent response.
Authors: Bisiak, F. / Chrenkova, A. / Zhang, S.D. / Pedersen, J.N. / Otzen, D.E. / Zhang, Y.E. / Brodersen, D.E.
History
DepositionDec 23, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 13, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 27, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2May 1, 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: HDc domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,4132
Polymers23,3581
Non-polymers551
Water4,017223
1
A: HDc domain-containing protein
hetero molecules

A: HDc domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,8254
Polymers46,7152
Non-polymers1102
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z1
Buried area3780 Å2
ΔGint-24 kcal/mol
Surface area17500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.708, 98.708, 40.086
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/2
#3: y+1/2,-x+1/2,z+1/2
#4: x+1/2,-y+1/2,-z+1/2
#5: -x+1/2,y+1/2,-z+1/2
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z

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Components

#1: Protein HDc domain-containing protein


Mass: 23357.666 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leptospira levettii (bacteria) / Gene: CH368_08595 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Lemo21 / References: UniProt: A0A2N0AXP5
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 223 / 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: 2.1 Å3/Da / Density % sol: 41.38 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2 M sodium acetate trihydrate pH 7, 20% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.97624 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 30, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97624 Å / Relative weight: 1
ReflectionResolution: 1.2→44.144 Å / Num. obs: 118506 / % possible obs: 100 % / Redundancy: 9.681 % / Biso Wilson estimate: 19.73 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.068 / Rrim(I) all: 0.071 / Χ2: 0.788 / Net I/σ(I): 12.06 / Num. measured all: 1147266
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.2-1.279.5843.9480.4918343519157191390.414.17299.9
1.27-1.369.4272.0870.9916980818012180120.6762.208100
1.36-1.479.7741.0562.0316426416806168060.91.115100
1.47-1.619.590.4324.7814801915434154340.9750.457100
1.61-1.810.010.2389.1413935413922139220.9890.251100
1.8-2.089.680.10919.2111918612313123130.9970.115100
2.08-2.549.8360.06434.110246710418104180.9980.067100
2.54-3.599.6280.04943.8477210801980190.9990.051100
3.59-44.1449.7960.04550.2443523444644430.9990.04799.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation4.63 Å44.14 Å
Translation4.63 Å44.14 Å

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Processing

Software
NameVersionClassification
PHENIX1.19.2refinement
XDS20190315data reduction
XDS20190315data scaling
PHASER2.8.2phasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: SeMet RelH

Resolution: 1.2→44.14 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 23.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1814 5950 5.04 %
Rwork0.1516 112104 -
obs0.1531 118054 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 70.99 Å2 / Biso mean: 30.0279 Å2 / Biso min: 15.96 Å2
Refinement stepCycle: final / Resolution: 1.2→44.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1496 0 1 223 1720
Biso mean--17.09 40.97 -
Num. residues----187
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.2-1.210.4841910.5083518370993
1.21-1.230.48821970.46793639383698
1.23-1.240.39781970.41937203917100
1.24-1.260.45292000.403637563956100
1.26-1.270.35771990.365537483947100
1.27-1.290.35511960.327137313927100
1.29-1.310.35241950.309437813976100
1.31-1.330.27631990.289737393938100
1.33-1.350.29572030.267237503953100
1.35-1.370.29161910.243237173908100
1.37-1.40.26991990.22537623961100
1.4-1.420.25441970.211837383935100
1.42-1.450.22791990.191237533952100
1.45-1.480.20742020.177737753977100
1.48-1.510.1892000.163136913891100
1.51-1.550.18691950.150438043999100
1.55-1.590.172020.134837203922100
1.59-1.630.17681970.119137293926100
1.63-1.680.17642000.11737853985100
1.68-1.730.15632000.115537343934100
1.73-1.790.15052030.118637503953100
1.79-1.860.14431950.110237423937100
1.86-1.950.16312010.121637233924100
1.95-2.050.15912020.119137843986100
2.05-2.180.13991970.112837323929100
2.18-2.350.13451950.114637823977100
2.35-2.580.17031980.130937243922100
2.58-2.960.17092010.140537763977100
2.96-3.730.16872030.144637383941100
3.73-44.140.1911960.163737633959100

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