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- PDB-7qod: Native structure of a small alarmone hydrolase (RelH) from Coryne... -

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Basic information

Entry
Database: PDB / ID: 7qod
TitleNative 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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 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
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / 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)45,2595
Polymers44,9552
Non-polymers3043
Water1,928107
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering, SEC-MALS Measured mass: ~44 kDa Predicted monomer mass: 22.4 kda
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3260 Å2
ΔGint-30 kcal/mol
Surface area17280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.332, 94.332, 80.561
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/2
#3: y,-x+y,z+1/2
#4: -y,x-y,z
#5: -x+y,-x,z
#6: -x,-y,z+1/2

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Components

#1: Protein Guanosine polyphosphate pyrophosphohydrolases/synthetases


Mass: 22477.506 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-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.31 Å3/Da / Density % sol: 46.83 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1 M imidazole, 12% (w/v) PEG 20000

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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: 1.85→40.703 Å / Num. obs: 67471 / % possible obs: 98.5 % / Redundancy: 4.185 % / Biso Wilson estimate: 38.01 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.084 / Rrim(I) all: 0.096 / Χ2: 0.812 / Net I/σ(I): 8.82 / Num. measured all: 282347
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
1.85-1.964.1551.4750.894483411064107900.3771.69197.5
1.96-2.14.1350.7371.864237710421102490.7340.84698.3
2.1-2.264.1460.3733.4839045962294180.9050.42797.9
2.26-2.484.1350.2065.8436471894188210.9660.23698.7
2.48-2.774.30.1249.6734322806379820.9860.14299
2.77-3.24.230.08714.2629957712970820.9910.199.3
3.2-3.914.1540.06320.3424718598759500.9940.07299.4
3.91-5.54.2680.0542519706466046170.9950.06299.1
5.5-40.7034.2610.05326.3510917260825620.9950.06198.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation6.09 Å40.72 Å
Translation6.09 Å40.72 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: 1.85→36.43 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2063 3380 5.01 %
Rwork0.1766 64051 -
obs0.178 67431 98.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 144.36 Å2 / Biso mean: 51.7307 Å2 / Biso min: 24.12 Å2
Refinement stepCycle: final / Resolution: 1.85→36.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3003 0 15 107 3125
Biso mean--57.88 47.23 -
Num. residues----373
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 24

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.85-1.880.35181370.32792587272496
1.88-1.90.32791370.29992651278898
1.9-1.930.30721380.30362638277698
1.93-1.970.29351430.27982686282998
1.97-20.32331410.27912653279498
2-2.040.30611430.26892653279698
2.04-2.070.24121370.23042654279198
2.08-2.120.27591460.21242683282998
2.12-2.160.25291400.20392637277799
2.16-2.210.21831450.18272686283199
2.21-2.270.24041340.18682607274197
2.27-2.330.19311410.18522683282498
2.33-2.40.25431420.18862660280299
2.4-2.480.27081380.17762714285299
2.48-2.560.19891400.18332648278899
2.56-2.670.22991420.17272696283899
2.67-2.790.21721440.18292691283599
2.79-2.940.18891400.17662688282899
2.94-3.120.24041400.19052677281799
3.12-3.360.2291450.17642724286999
3.36-3.70.20031440.17582677282199
3.7-4.230.18621420.14752693283599
4.23-5.320.15551420.13392685282799
5.33-36.430.16161390.16552680281998
Refinement TLS params.

Method: refined / 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)
15.57833.68513.03337.82794.57335.4551-0.24160.21410.2585-0.4480.14790.062-0.24950.00670.03880.30550.00220.01490.2140.05210.212342.833-4.9725-7.9598
22.90160.42310.8822.69270.60715.4766-0.01930.0413-0.205-0.25030.0376-0.01870.123-0.0038-0.02420.3263-0.00090.01280.2260.01910.255244.8182-5.7125-14.5873
33.4918-0.72863.24292.5762-1.8693.6006-0.4258-0.2360.21090.5617-0.3348-1.5374-0.21581.81610.63080.46410.0504-0.05920.53320.01290.541955.2271-3.3374-2.26
47.78430.4372-1.47643.7517-1.4998.0308-0.1818-0.3742-0.64630.2681-0.0031-0.2830.3770.64080.19230.40930.0828-0.00790.2660.05230.349353.6926-14.3222-8.523
57.49510.03395.05422.34850.60753.4959-0.3623-0.03740.59560.4115-0.0762-0.4644-0.62660.18020.54150.5013-0.0434-0.05180.32710.06260.419566.6398-2.1331-18.1947
64.9168-1.9103-1.01625.1131-1.27913.1232-0.133-0.06420.27710.70940.1514-0.1244-0.1102-0.0943-0.03010.3205-0.0113-0.00670.2441-0.00580.228251.6672-1.0054-21.6203
74.70355.58682.44828.7325-0.44056.43-0.13560.25090.90090.39191.0574-0.8114-2.3650.0216-0.9431.2510.04110.11980.9033-0.23211.076452.196819.7905-18.9435
84.5912-0.0098-0.05355.6122-0.4394.26260.1171-0.02050.3812-0.0652-0.0516-0.1063-0.2991-0.0574-0.04340.38180.00690.02860.27250.02740.248554.76853.1508-28.7816
93.95123.77015.74033.61855.50388.3595-0.7253-1.4844-0.9584-0.2820.6886-1.454-2.0674-1.5698-0.01121.08680.27410.0960.8566-0.02970.908955.564621.8394-32.0298
101.80170.57830.10832.5944-1.15624.9951-0.020.1960.0993-0.18610.05950.1675-0.2908-0.3704-0.01770.31520.0488-0.02740.273-0.00010.298733.61032.0057-11.6612
118.96990.7354-2.76664.3217-4.28194.66650.0072-0.68720.72260.14960.09410.8068-0.7311-1.2892-0.15950.64820.11610.00680.5213-0.03750.525430.489511.0951-1.6117
123.66022.4841-2.38678.10051.99584.27510.05680.09880.9216-0.1637-0.03970.6959-0.6338-0.86160.00530.49840.2044-0.07240.47780.04280.537125.265812.9207-12.8215
133.51421.5146-5.49082.211-1.49439.0793-0.777-1.1413.89042.61820.88760.9243-1.8269-0.474-0.17311.19310.2150.02530.9393-0.08381.376116.89977.04650.0543
140.46331.2403-0.21824.84021.76996.0072-0.2112-1.36060.75340.80880.12970.4607-0.19370.00030.09290.55280.25350.07671.0922-0.25090.893512.1297-0.3014-2.3019
153.7179-2.67763.5535.999-3.5985.2795-0.25010.01310.28950.4525-0.1501-0.1173-0.3711-0.16410.40540.3378-0.02220.01040.3945-0.02120.348225.7364-8.1332-6.6338
168.11943.3065-3.44132.6188-4.51788.94361.3539-0.76350.75532.4544-0.94740.09510.2787-1.5131-0.25871.0717-0.10390.07511.0823-0.0730.618225.8339-15.01648.6751
176.269-0.27980.46628.3358-2.8487.7757-0.2893-0.3084-0.07270.23240.06710.70920.1112-0.66890.20670.2921-0.06430.00510.4788-0.09780.490917.9681-12.5877-8.8873
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 27 )A1 - 27
2X-RAY DIFFRACTION2chain 'A' and (resid 28 through 61 )A28 - 61
3X-RAY DIFFRACTION3chain 'A' and (resid 62 through 67 )A62 - 67
4X-RAY DIFFRACTION4chain 'A' and (resid 68 through 90 )A68 - 90
5X-RAY DIFFRACTION5chain 'A' and (resid 91 through 107 )A91 - 107
6X-RAY DIFFRACTION6chain 'A' and (resid 108 through 134 )A108 - 134
7X-RAY DIFFRACTION7chain 'A' and (resid 135 through 145 )A135 - 145
8X-RAY DIFFRACTION8chain 'A' and (resid 146 through 187 )A146 - 187
9X-RAY DIFFRACTION9chain 'A' and (resid 188 through 192 )A188 - 192
10X-RAY DIFFRACTION10chain 'B' and (resid 1 through 61 )B1 - 61
11X-RAY DIFFRACTION11chain 'B' and (resid 62 through 68 )B62 - 68
12X-RAY DIFFRACTION12chain 'B' and (resid 69 through 88 )B69 - 88
13X-RAY DIFFRACTION13chain 'B' and (resid 89 through 93 )B89 - 93
14X-RAY DIFFRACTION14chain 'B' and (resid 94 through 110 )B94 - 110
15X-RAY DIFFRACTION15chain 'B' and (resid 111 through 137 )B111 - 137
16X-RAY DIFFRACTION16chain 'B' and (resid 138 through 149 )B138 - 149
17X-RAY DIFFRACTION17chain 'B' and (resid 150 through 185 )B150 - 185

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