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- PDB-7szs: Crystal Structure of Probable GTP-binding protein EngB bound to G... -

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Basic information

Entry
Database: PDB / ID: 7szs
TitleCrystal Structure of Probable GTP-binding protein EngB bound to GDP from Klebsiella pneumoniae subsp. pneumoniae
ComponentsProbable GTP-binding protein EngB
KeywordsCELL CYCLE / SSGCID / Cell division / Septation / GTP-Binding / Metal-binding / Nucleotide-binding / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


division septum assembly / GTP binding / metal ion binding
Similarity search - Function
GTP-binding protein, ribosome biogenesis, YsxC / EngB-type guanine nucleotide-binding (G) domain profile. / EngB-type guanine nucleotide-binding (G) domain / 50S ribosome-binding GTPase / GTP binding domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
1,4-BUTANEDIOL / GUANOSINE-5'-DIPHOSPHATE / R-1,2-PROPANEDIOL / Probable GTP-binding protein EngB
Similarity search - Component
Biological speciesKlebsiella pneumoniae subsp. pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: to be published
Title: Crystal Structure of Probable GTP-binding protein EngB bound to GDP from Klebsiella pneumoniae subsp. pneumoniae
Authors: DeBouver, N.D. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.
History
DepositionNov 29, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 15, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: 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: Probable GTP-binding protein EngB
B: Probable GTP-binding protein EngB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,5577
Polymers49,4132
Non-polymers1,1455
Water8,521473
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4620 Å2
ΔGint-6 kcal/mol
Surface area18130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.470, 94.070, 56.590
Angle α, β, γ (deg.)90.000, 108.600, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Probable GTP-binding protein EngB


Mass: 24706.305 Da / Num. of mol.: 2 / Fragment: KlpnC.00252.a.B1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae subsp. pneumoniae (strain HS11286) (bacteria)
Strain: HS11286 / Gene: engB, KPHS_00220 / Plasmid: KlpnC.00252.a.B1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0H3GG62

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Non-polymers , 5 types, 478 molecules

#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: GDP, energy-carrying molecule*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-BU1 / 1,4-BUTANEDIOL


Mass: 90.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2
#5: Chemical ChemComp-PGR / R-1,2-PROPANEDIOL


Mass: 76.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 473 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.69 Å3/Da / Density % sol: 54.31 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: KlpnC.00252.a.B1.PW38989 [Barcode: 321927d12, PuckID: nyh1-5, Cryo: Direct, BEAMLINE: APS21idf, Collected date: 07292021, Concentration: 20 mg/mL] 100 mM Bicine/Trizma base pH 8.5, 12.5% ...Details: KlpnC.00252.a.B1.PW38989 [Barcode: 321927d12, PuckID: nyh1-5, Cryo: Direct, BEAMLINE: APS21idf, Collected date: 07292021, Concentration: 20 mg/mL] 100 mM Bicine/Trizma base pH 8.5, 12.5% (w/v) PEG 1000, 12.5% (w/v) PEG 3350, 12.5% (w/v) MPD, 0.02 M each of [1,6-hexandiol, 1-butanol, 1,2-propanediol, 2-propanol, 1,4-butanediol, 1,3-propanediol]

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Oct 21, 2021 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.5→47.04 Å / Num. obs: 83437 / % possible obs: 99.8 % / Redundancy: 4.164 % / Biso Wilson estimate: 15.23 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.054 / Rrim(I) all: 0.062 / Χ2: 0.937 / Net I/σ(I): 14.87 / Num. measured all: 347458 / Scaling rejects: 4
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
1.5-1.544.1250.5052.8225338615261420.8610.58199.8
1.54-1.584.1390.4043.5624844601360030.9110.46599.8
1.58-1.634.1420.344.1524135583058270.9370.39199.9
1.63-1.684.1570.2854.9723660570356920.950.32899.8
1.68-1.734.1650.2286.1222834549254830.9650.26299.8
1.73-1.794.1740.1837.5122189532353160.9760.21199.9
1.79-1.864.1830.149.3721545516551510.9860.16199.7
1.86-1.944.1740.10512.2620647494649460.9920.121100
1.94-2.024.1810.08914.5719797474247350.9930.10299.9
2.02-2.124.1830.07317.5218856452045080.9950.08399.7
2.12-2.244.1890.06220.0818074432543150.9960.07199.8
2.24-2.374.1760.05522.3217041409240810.9960.06399.7
2.37-2.544.1810.04924.6716039384838360.9970.05699.7
2.54-2.744.1830.04426.7914933358635700.9970.05199.6
2.74-34.1760.04128.5413703328932810.9970.04799.8
3-3.354.1820.03731.5912567301930050.9980.04399.5
3.35-3.874.1630.03533.9710898262326180.9980.0499.8
3.87-4.744.1670.03235.659322225122370.9980.03799.4
4.74-6.714.1620.03234.877183173117260.9980.03799.7
6.71-47.043.9930.03135.1538539839650.9980.03698.2

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX1.20rc3-4406refinement
PDB_EXTRACT3.27data extraction
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PUI

1pui


Resolution: 1.5→47.04 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1821 2021 2.42 %
Rwork0.1642 81402 -
obs0.1646 83423 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 72.09 Å2 / Biso mean: 21.2786 Å2 / Biso min: 8.26 Å2
Refinement stepCycle: final / Resolution: 1.5→47.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3147 0 73 477 3697
Biso mean--19.76 30.74 -
Num. residues----406
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.5-1.540.25761450.232457835928
1.54-1.580.22741370.204658135950
1.58-1.630.22791280.194157955923
1.63-1.680.22641730.185357935966
1.68-1.740.16631600.174357585918
1.74-1.810.1981330.174558305963
1.81-1.890.19761300.172258435973
1.89-1.990.19771450.16157855930
1.99-2.110.19341440.154958125956
2.11-2.280.18321470.154658355982
2.28-2.510.15911470.161457865933
2.51-2.870.17851450.166258235968
2.87-3.610.19531500.157258395989
3.62-47.040.14981370.153659076044
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)
12.61570.12750.8923.8948-0.43091.4074-0.06070.2589-0.2702-0.51440.0997-0.01410.1168-0.0995-0.01370.16710.0009-0.01520.0903-0.02460.124810.59418.66441.4845
21.3399-0.2254-0.56750.884-0.44062.5168-0.00940.106-0.1653-0.06690.04740.160.4307-0.3-0.03740.1424-0.0374-0.01040.1180.00020.14548.7999-6.5189.8168
33.4399-1.40310.04582.29810.96841.8902-0.0003-0.0572-0.1427-0.01530.11610.28220.333-0.4921-0.06010.1065-0.0503-0.00160.15250.02430.12951.05842.730614.1156
42.85850.03780.35222.76520.44911.7496-0.0164-0.1058-0.21980.04280.05650.31780.3058-0.2902-0.0630.0948-0.00310.01720.0804-0.00760.14196.5832-4.700611.2912
56.10250.9826-1.07375.588-2.70916.9294-0.042-0.4642-0.62990.2033-0.14230.39060.9068-0.38380.20050.2948-0.03870.02660.15220.01810.249610.8811-16.312715.832
61.0153-0.2328-0.12254.70773.72822.95650.02620.0198-0.0475-0.10330.0609-0.1094-0.12480.1364-0.11310.06760.01930.00340.10160.01360.107615.4843-3.109612.4723
71.1655-0.7905-0.6083.20060.95972.91050.0081-0.0818-0.04270.1283-0.0319-0.0040.08490.07070.01750.0749-0.001-0.01730.10280.01770.09117.399-2.301822.4175
83.3594-3.2427-2.29627.2653.81615.4291-0.2161-0.40490.27250.43830.2629-0.4158-0.0630.3341-0.06060.1646-0.0167-0.0550.17490.00760.162423.64475.392228.3512
93.9357-2.3332-0.25075.30230.25333.4451-0.0558-0.00430.22220.0987-0.0305-0.1733-0.08720.08460.05630.0976-0.0243-0.00830.0730.00780.049716.56216.870920.2601
103.6769-2.6336-2.8126.27474.46193.82350.19070.25580.0278-0.3814-0.0888-0.3799-0.31610.0206-0.170.11110.01540.00850.10770.02290.1318.23325.9374.8292
112.0852-0.5070.46983.8236-2.562.9355-0.2045-0.2503-0.01110.55780.06340.1272-0.2227-0.2410.11840.14530.0081-0.00180.1226-0.0360.11735.798624.932415.057
122.361-0.2427-2.28990.88430.8894.79340.07860.09960.2663-0.1175-0.00650.0723-0.3402-0.187-0.0630.13250.0004-0.02230.11920.00960.148310.154939.33548.3464
133.7139-0.8197-0.5012.00660.1372.8771-0.1050.26470.2045-0.35290.12620.0701-0.3377-0.1817-0.06350.1346-0.0004-0.05180.10490.01630.10376.87229.864-0.1602
143.11940.5665-0.24982.3880.63521.78710.06590.23070.3805-0.2987-0.04590.1561-0.5031-0.1549-0.06130.22370.0418-0.01220.11690.0170.131511.478941.77916.4514
151.08550.0016-0.38221.48510.55481.9932-0.01120.0173-0.0428-0.05550.0191-0.1772-0.03750.1662-0.02080.0812-0.01480.00490.09850.00950.09824.437631.62344.8391
162.4354-1.5799-1.94375.68394.55224.0667-0.0096-0.27270.0130.46540.0048-0.18560.31790.0741-0.03730.1372-0.02-0.0310.12190.00830.114214.13226.650518.0494
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -2 through 16 )A-2 - 16
2X-RAY DIFFRACTION2chain 'A' and (resid 17 through 39 )A17 - 39
3X-RAY DIFFRACTION3chain 'A' and (resid 40 through 65 )A40 - 65
4X-RAY DIFFRACTION4chain 'A' and (resid 66 through 89 )A66 - 89
5X-RAY DIFFRACTION5chain 'A' and (resid 90 through 106 )A90 - 106
6X-RAY DIFFRACTION6chain 'A' and (resid 107 through 118 )A107 - 118
7X-RAY DIFFRACTION7chain 'A' and (resid 119 through 152 )A119 - 152
8X-RAY DIFFRACTION8chain 'A' and (resid 153 through 169 )A153 - 169
9X-RAY DIFFRACTION9chain 'A' and (resid 170 through 186 )A170 - 186
10X-RAY DIFFRACTION10chain 'A' and (resid 187 through 206 )A187 - 206
11X-RAY DIFFRACTION11chain 'B' and (resid -1 through 16 )B-1 - 16
12X-RAY DIFFRACTION12chain 'B' and (resid 17 through 39 )B17 - 39
13X-RAY DIFFRACTION13chain 'B' and (resid 40 through 65 )B40 - 65
14X-RAY DIFFRACTION14chain 'B' and (resid 66 through 106 )B66 - 106
15X-RAY DIFFRACTION15chain 'B' and (resid 107 through 186 )B107 - 186
16X-RAY DIFFRACTION16chain 'B' and (resid 187 through 206 )B187 - 206

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