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- PDB-7qoc: Se-Met derivative structure of a small alarmone hydrolase (RelH) ... -

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Basic information

Entry
Database: PDB / ID: 7qoc
TitleSe-Met derivative structure of a small alarmone hydrolase (RelH) from Corynebacterium glutamicum
ComponentsGuanosine polyphosphate pyrophosphohydrolases/synthetases
KeywordsHYDROLASE / Alarmone / Stress response / HD domain
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 / Metal dependent phosphohydrolases with conserved 'HD' motif. / HD/PDEase domain / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Guanosine polyphosphate pyrophosphohydrolases/synthetases
Similarity search - Component
Biological speciesCorynebacterium glutamicum ATCC 13032 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 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 1.2Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Guanosine polyphosphate pyrophosphohydrolases/synthetases
B: Guanosine polyphosphate pyrophosphohydrolases/synthetases
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3794
Polymers45,3302
Non-polymers492
Water27015
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering, SEC-MALS Measured mass across peak: ~44 kDa Predicted monomer mass from sequence: 22.4 kDa, SAXS, Estimated mass in solution corresponds to homodimer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2630 Å2
ΔGint-41 kcal/mol
Surface area17070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.010, 96.010, 80.470
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63

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Components

#1: Protein Guanosine polyphosphate pyrophosphohydrolases/synthetases


Mass: 22665.086 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium glutamicum ATCC 13032 (bacteria)
Gene: Cgl1313 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Lemo21
References: UniProt: Q8NQV9, guanosine-3',5'-bis(diphosphate) 3'-diphosphatase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / 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: 2.39 Å3/Da / Density % sol: 48.5 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 1 M ammonium phosphate dibasic, 0.1 M Sodium acetate pH 4.5

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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: P14 (MX2) / Wavelength: 0.97624 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 28, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97624 Å / Relative weight: 1
ReflectionResolution: 2.3→48.004 Å / Num. obs: 36896 / % possible obs: 99.9 % / Redundancy: 5.943 % / Biso Wilson estimate: 76.69 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.052 / Rrim(I) all: 0.057 / Χ2: 1.1 / Net I/σ(I): 15.1 / Num. measured all: 219291
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
2.3-2.445.9351.5820.8535332595959530.4891.73599.9
2.44-2.615.9040.8331.7333242563056300.7390.915100
2.61-2.815.9730.4533.3730928518151780.9040.49799.9
2.81-3.085.9770.2286.8728851482748270.9770.25100
3.08-3.445.9180.10714.2725526431643130.9940.11899.9
3.44-3.975.8450.05726.2922363382738260.9980.062100
3.97-4.866.0030.03441.4819505325032490.9990.037100
4.86-6.845.9720.03344.2215079252525250.9990.036100
6.84-48.0046.0680.02659.558465140113950.9990.02899.6

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDS20190315data reduction
XDS20190315data scaling
CRANK22.0.191phasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: SAD / Resolution: 2.3→48.01 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.947 / SU R Cruickshank DPI: 0.311 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.284 / SU Rfree Blow DPI: 0.193 / SU Rfree Cruickshank DPI: 0.202
RfactorNum. reflection% reflectionSelection details
Rfree0.2154 943 -RANDOM
Rwork0.1915 ---
obs0.1928 18848 100 %-
Displacement parametersBiso mean: 90.03 Å2
Baniso -1Baniso -2Baniso -3
1--5.0209 Å20 Å20 Å2
2---5.0209 Å20 Å2
3---10.0418 Å2
Refine analyzeLuzzati coordinate error obs: 0.31 Å
Refinement stepCycle: LAST / Resolution: 2.3→48.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3056 0 2 15 3073
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0083203HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.934346HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1138SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes547HARMONIC5
X-RAY DIFFRACTIONt_it3203HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion393SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies7HARMONIC1
X-RAY DIFFRACTIONt_ideal_dist_contact2532SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.73
X-RAY DIFFRACTIONt_other_torsion21.78
LS refinement shellResolution: 2.3→2.32 Å
RfactorNum. reflection% reflection
Rfree0.2217 20 -
Rwork0.2247 --
obs0.2246 402 100 %
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.94292.5680.27554.52650.25921.6318-0.13090.16090.08910.1609-0.12980.38690.08910.38690.26070.0570.00350.0079-0.09570.0268-0.104653.22827.32135.1694
22.2393-1.63270.32074.3182-0.43354.6798-0.1898-0.08410.0039-0.0841-0.005-0.1030.0039-0.1030.19480.0192-0.02020.0255-0.1553-0.024-0.09547.76825.3171.2291
34.9637-0.29393.03853.43743.14871.5887-0.06370.27710.07720.2771-0.224-0.04970.0772-0.04970.28780.14590.00860.0548-0.1556-0.0363-0.103639.900814.12652.6746
42.0053-1.0546-0.71884.21960.09091.47520.0539-0.08420.0277-0.0842-0.1974-0.08440.0277-0.08440.14350.0816-0.0292-0.0144-0.156-0.0697-0.035937.66331.1982-7.619
514.3468-6.2217-0.044813.6083-2.018314.35780.15080.33451.08030.3345-0.1-0.04181.0803-0.0418-0.05080.0686-0.23630.0026-0.31850.04760.385938.9548-15.0859-5.6616
61.0685-0.42521.66675.2184-0.46222.810.1834-0.53960.1633-0.5396-0.18290.07680.16330.0768-0.00050.12970.0268-0.0514-0.1204-0.1213-0.140641.379-0.3429-16.7214
76.81425.06527.990913.1916-0.730800.2280.36470.3930.3647-0.1922-0.12310.393-0.1231-0.03590.49450.22-0.2383-0.2625-0.09040.131540.2724-20.9547-17.7088
82.0009-0.83811.20022.6403-0.247112.6861-0.0221-0.04520.1474-0.04520.08690.28690.14740.2869-0.06490.04640.04690.1012-0.17730.0206-0.053658.3014-4.9150.7513
92.349-0.874-2.29313.3380.55843.056-0.06330.1522-0.13140.15220.0020.4216-0.13140.42160.0613-0.03950.00560.0825-0.0540.0577-0.052763.39221.38430.7834
1010.451-1.6532-1.73946.60940.09283.6679-0.46440.24031.05210.24030.03591.30071.05211.30070.4285-0.06290.31560.135-0.20460.11750.118868.5552-11.30333.4409
112.22423.37795.72838.21691.496118.3075-0.05151.28081.89491.2808-0.6274-0.05981.8949-0.05980.6789-0.00160.333-0.11140.29840.28590.200381.5132-0.908210.3282
123.5456-2.2196-4.71745.5634.03933.5717-0.18480.543-0.09270.543-0.00550.8174-0.09270.81740.1903-0.0753-0.0091-0.0511-0.01010.1175-0.046168.717710.54768.058
138.0199-0.891-3.97666.53465.74819.0964-0.42370.51070.30290.51070.11851.76310.30291.76310.3052-0.2392-0.0258-0.1717-0.0060.23180.009577.110111.31238.8386
1410.68918.26772.919421.24046.247511.4255-0.37730.5481-0.91370.54810.11680.6599-0.91370.65990.2606-0.1869-0.0371-0.13410.03510.11720.002273.383618.83095.3697
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|1 - 24 }A1 - 24
2X-RAY DIFFRACTION2{ A|25 - 71 }A25 - 71
3X-RAY DIFFRACTION3{ A|72 - 92 }A72 - 92
4X-RAY DIFFRACTION4{ A|93 - 134 }A93 - 134
5X-RAY DIFFRACTION5{ A|135 - 152 }A135 - 152
6X-RAY DIFFRACTION6{ A|153 - 184 }A153 - 184
7X-RAY DIFFRACTION7{ A|185 - 193 }A185 - 193
8X-RAY DIFFRACTION8{ B|1 - 24 }B1 - 24
9X-RAY DIFFRACTION9{ B|25 - 57 }B25 - 57
10X-RAY DIFFRACTION10{ B|58 - 87 }B58 - 87
11X-RAY DIFFRACTION11{ B|88 - 112 }B88 - 112
12X-RAY DIFFRACTION12{ B|113 - 140 }B113 - 140
13X-RAY DIFFRACTION13{ B|141 - 171 }B141 - 171
14X-RAY DIFFRACTION14{ B|172 - 187 }B172 - 187

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