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- PDB-9b8d: Structure of Legionella pneumophila Ceg10 -

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Basic information

Entry
Database: PDB / ID: 9b8d
TitleStructure of Legionella pneumophila Ceg10
ComponentsCeg10
KeywordsHYDROLASE / Bacterial / Effector / Pathogen
Function / homologyPHOSPHATE ION / Type IV secretion protein Dot
Function and homology information
Biological speciesLegionella pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.72 Å
AuthorsTomchick, D.R. / Heisler, D.B. / Alto, N.M.
Funding support United States, 6items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R35GM137978-0 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1R21AI169558-01 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI083359 United States
Robert A. Welch FoundationI-1704 United States
Burroughs Wellcome Fund1011019 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)T32 AI007520 United States
CitationJournal: Plos Pathog. / Year: 2024
Title: Exploiting bacterial effector proteins to uncover evolutionarily conserved antiviral host machinery.
Authors: Embry, A. / Baggett, N.S. / Heisler, D.B. / White, A. / de Jong, M.F. / Kocsis, B.L. / Tomchick, D.R. / Alto, N.M. / Gammon, D.B.
History
DepositionMar 29, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2024Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ceg10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1526
Polymers26,8081
Non-polymers3435
Water1,26170
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)85.947, 112.322, 55.189
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein Ceg10


Mass: 26808.359 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila (bacteria) / Gene: C3927_00720 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / References: UniProt: A0AA44XLE0
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.48 Å3/Da / Density % sol: 50.49 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 1.5 M sodium phosphate monobasic, 0.5 M potassium phosphate dibasic, 10 mM sodium phosphate dibasic/citrate, 25% ethylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97911 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 4, 2020
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97911 Å / Relative weight: 1
ReflectionResolution: 1.71→50 Å / Num. obs: 28293 / % possible obs: 96.1 % / Redundancy: 6.4 % / Biso Wilson estimate: 12.71 Å2 / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.022 / Rrim(I) all: 0.058 / Χ2: 0.919 / Net I/σ(I): 9.5 / Num. measured all: 180331
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.71-1.744.10.5829060.7420.9230.2830.6530.94162.6
1.74-1.774.50.54712910.8510.9590.2550.6070.86487.5
1.77-1.814.70.51712830.9060.9750.2410.5740.8790.2
1.81-1.8450.38313530.9570.9890.1730.4230.92293.1
1.84-1.885.20.38613850.9590.9890.1710.4240.86495.8
1.88-1.935.60.31914390.9720.9930.140.350.99497
1.93-1.975.40.25514130.9830.9960.1130.280.90498.8
1.97-2.036.10.2214510.9890.9970.0930.2390.91699
2.03-2.096.70.18214460.9950.9990.0740.1971.01599.2
2.09-2.1570.15314560.9970.9990.0610.1640.88599.7
2.15-2.237.10.11614400.9970.9990.0460.1250.89599.9
2.23-2.327.10.11414730.9970.9990.0460.1231.04199.9
2.32-2.436.70.08414680.9970.9990.0340.0910.9299.7
2.43-2.557.50.07814670.9970.9990.030.0840.885100
2.55-2.717.50.06514680.9970.9990.0260.070.893100
2.71-2.927.40.05614840.9970.9990.0220.0610.9100
2.92-3.226.90.04714900.9970.9990.0190.0510.92599.8
3.22-3.687.60.04114770.99810.0160.0440.97899.9
3.68-4.646.90.03815110.99810.0160.0410.89999.9
4.64-5070.03915920.9970.9990.0160.0420.84999.7

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
HKL-3000data scaling
HKL-3000data reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.72→42.92 Å / SU ML: 0.1951 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.3114
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2542 1991 8.75 %
Rwork0.2198 20761 -
obs0.2228 22752 79.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.97 Å2
Refinement stepCycle: LAST / Resolution: 1.72→42.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1789 0 21 70 1880
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00661871
X-RAY DIFFRACTIONf_angle_d0.76082534
X-RAY DIFFRACTIONf_chiral_restr0.0415283
X-RAY DIFFRACTIONf_plane_restr0.0069327
X-RAY DIFFRACTIONf_dihedral_angle_d14.4211690
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.72-1.760.2779690.243722X-RAY DIFFRACTION39.31
1.76-1.810.2933810.225844X-RAY DIFFRACTION45.95
1.81-1.860.2755940.2232984X-RAY DIFFRACTION52.71
1.86-1.920.2771050.22851090X-RAY DIFFRACTION59.1
1.92-1.990.25191140.22641197X-RAY DIFFRACTION64.87
1.99-2.070.2361300.23321353X-RAY DIFFRACTION72.98
2.07-2.170.28931470.23321531X-RAY DIFFRACTION82.54
2.17-2.280.25891610.23571675X-RAY DIFFRACTION89.6
2.28-2.420.2791740.23971818X-RAY DIFFRACTION97.03
2.42-2.610.25881800.23221874X-RAY DIFFRACTION99.9
2.61-2.870.26191790.2411871X-RAY DIFFRACTION100
2.87-3.290.2761820.23081896X-RAY DIFFRACTION99.86
3.29-4.140.24041840.19691910X-RAY DIFFRACTION99.95
4.15-42.920.21681910.19031996X-RAY DIFFRACTION99.73
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)
10.8265916560270.7985088854080.6087834257651.26844692740.2157308906660.7281263850270.01575997404170.142056933955-0.0354257404659-0.357142098140.0391181010943-0.443993100890.2190004826550.369540445007-0.1252060239850.3435785193370.1521727999840.1478669778940.47097024976-0.07972783485060.43307381540535.594407376118.76169344443.17168025119
20.689413457173-0.228044684-0.09773287893070.836791075056-0.5787346359291.503110966420.07679427186230.0101344304085-0.0120703161535-0.07999026066890.0776166985112-0.0109114559130.1497133466370.008942373787420.1304714137810.0185427300080.0220594799183-0.01396863173640.07472738487080.00469676067920.052966936739721.918214661623.351148883816.0472696261
30.7169707179390.131543426035-0.4298413231312.572640571750.176760139981.86019103950.02332267588480.12272914334-0.198017985584-0.3345278370370.0407328657614-0.2442607808820.6382069343280.122190164341-0.0445332009270.3275414344070.0716801177641-0.03087949917850.0800730824306-0.01277843051740.08260915664325.178724515112.06000231829.78689136446
40.8808482942950.154183077452-0.5370889955582.36189626868-1.93143805832.71533783688-0.07899048210730.103733407925-0.127772102516-0.3992950836570.15812872920.1513804193790.580067085342-0.197550412378-0.08686702896820.535640702779-0.0260411922937-0.0419957010250.1373520864130.007886032017310.13482574019619.76860735785.1848156828118.3754154071
51.99128330156-0.852908918022-1.247824382046.59125701353-3.363563301884.15057282835-0.101708484213-0.231603681517-0.1692641893910.20882917759-0.065961979711-0.12718651270.06050880976070.1853989107610.1919149850060.463298513506-0.098823892187-0.07078555521110.2029433722440.06941053430490.17819770218216.55820999865.1065413160925.7554135606
60.0956029831504-0.000104430371338-0.06129368320930.526301709479-0.2936300454180.2510993274090.0389030602387-0.06744141335590.0266485008312-0.1085170589570.02198732897630.2801046520010.0334901349837-0.477770558476-0.1327269172170.2052533912570.00949366750006-0.1020320534590.5446722999880.09286975841670.3293804556867.6805658579820.260713608114.1372269573
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 58 through 86 )58 - 861 - 29
22chain 'A' and (resid 87 through 158 )87 - 15830 - 101
33chain 'A' and (resid 159 through 231 )159 - 231102 - 174
44chain 'A' and (resid 232 through 246 )232 - 246175 - 189
55chain 'A' and (resid 247 through 264 )247 - 264190 - 201
66chain 'A' and (resid 265 through 283 )265 - 283202 - 220

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