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- PDB-6dm3: Crystal structure of the SH2 domain from RavO (Lpg1129) from Legi... -

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Basic information

Entry
Database: PDB / ID: 6dm3
TitleCrystal structure of the SH2 domain from RavO (Lpg1129) from Legionella pneumophila, apoprotein
ComponentsRavO
KeywordsPROTEIN BINDING / SH2 domain / Src homolog 2 domain / Shc1 / phosphopeptide binding / LEGIONELLA PNEUMOPHILA / STRUCTURAL GENOMICS / APC108076 / MIDWEST CENTER FOR STRUCTURAL GENOMICS / MCSG / PSI-BIOLOGY
Function / homologyUncharacterized protein
Function and homology information
Biological speciesLegionella pneumophila subsp. pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.95 Å
AuthorsStogios, P.J. / Evdokimova, E. / Di Leo, R. / Kaneko, T. / Li, S. / Savchenko, A. / Midwest Center for Structural Genomics (MCSG)
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM074942 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM094585 United States
CitationJournal: To Be Published
Title: Crystal structure of the SH2 domain from RavO (Lpg1129) from Legionella pneumophila, apoprotein
Authors: Kaneko, T.
History
DepositionJun 4, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 27, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RavO
B: RavO


Theoretical massNumber of molelcules
Total (without water)27,5312
Polymers27,5312
Non-polymers00
Water1,15364
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1340 Å2
ΔGint-9 kcal/mol
Surface area12400 Å2
Unit cell
Length a, b, c (Å)50.037, 72.981, 71.961
Angle α, β, γ (deg.)90.00, 109.89, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-432-

HOH

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Components

#1: Protein RavO


Mass: 13765.521 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513) (bacteria)
Strain: Philadelphia 1 / ATCC 33152 / DSM 7513 / Gene: lpg1129 / Plasmid: p15TV-LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: Q5ZWF6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / Source method: isolated from a natural source / Formula: H2O

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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: 2.24 Å3/Da / Density % sol: 45.18 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.2 M potassium chloride, 20% (w/v) PEG 5K MME

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97924 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 4, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97924 Å / Relative weight: 1
ReflectionResolution: 1.95→25 Å / Num. obs: 16407 / % possible obs: 92.4 % / Redundancy: 2.8 % / CC1/2: 0.928 / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.04 / Rrim(I) all: 0.071 / Net I/σ(I): 28.56
Reflection shellResolution: 1.95→1.98 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.414 / Num. unique obs: 823 / CC1/2: 0.928 / Rpim(I) all: 0.303 / Rrim(I) all: 0.517 / % possible all: 95.8

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Processing

Software
NameVersionClassification
PHENIX(dev_3092: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.95→24.81 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 36.56
RfactorNum. reflection% reflectionSelection details
Rfree0.3179 821 5.02 %RANDOM
Rwork0.261 ---
obs0.2638 16361 91.6 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.95→24.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1755 0 0 64 1819
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071785
X-RAY DIFFRACTIONf_angle_d1.2242398
X-RAY DIFFRACTIONf_dihedral_angle_d17.784660
X-RAY DIFFRACTIONf_chiral_restr0.065269
X-RAY DIFFRACTIONf_plane_restr0.005300
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9475-2.06940.35921400.35222580X-RAY DIFFRACTION92
2.0694-2.22910.3331430.31272679X-RAY DIFFRACTION95
2.2291-2.45330.31641460.30862672X-RAY DIFFRACTION95
2.4533-2.80780.37441320.31152630X-RAY DIFFRACTION93
2.8078-3.53590.33981370.26842589X-RAY DIFFRACTION91
3.5359-24.8120.28451230.21722390X-RAY DIFFRACTION83
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)
13.2472.49534.79173.83051.62059.3155-0.32031.1525-1.05260.65090.4759-1.70940.62550.55740.10030.5685-0.1153-0.04840.5539-0.02540.710932.099810.818716.3617
26.8364-4.7185-1.73643.62650.4412.185-0.0765-0.10430.39490.12630.09040.2886-0.3539-0.91270.06610.4517-0.091-0.02420.40590.0470.303716.811222.075622.0578
31.3622-0.572-0.59758.1072.19360.7820.49820.138-0.539-0.0978-2.15970.8019-0.3379-0.33321.55280.7961-0.1588-0.27221.2920.10111.099528.874416.669333.4405
42.85230.0151-1.25894.57190.72154.6347-0.78260.1089-0.64770.34640.3720.13751.3201-0.59720.28420.6253-0.16540.13430.4074-0.02490.264816.87468.837324.1157
55.1913-1.35410.9016.59660.6055.6680.2041-0.3458-0.1108-0.005-0.354-0.15290.5418-0.07230.11160.2751-0.15950.01260.43790.03950.218931.415221.030611.9971
62.75573.9109-1.9457.93371.4528.89510.19080.8509-0.0054-0.2847-0.10710.21830.51010.5041-0.01680.10060.05240.00480.4779-0.07370.196633.228724.46780.1066
75.15281.8474-1.64815.88050.26934.7660.1481-0.6636-0.25920.3895-0.4968-0.71130.70131.83640.3670.4077-0.00660.05130.9211-0.0670.398542.949723.454210.6635
84.16940.5626-1.32213.7376-1.41093.37970.6451-0.55210.08280.9497-0.4262-0.0334-0.76720.6454-0.05440.5231-0.4940.33790.7306-0.17480.182440.539435.089310.3207
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 225:235)
2X-RAY DIFFRACTION2(chain A and resid 236:271)
3X-RAY DIFFRACTION3(chain A and resid 272:278)
4X-RAY DIFFRACTION4(chain A and resid 279:340)
5X-RAY DIFFRACTION5(chain B and resid 227:251)
6X-RAY DIFFRACTION6(chain B and resid 252:268)
7X-RAY DIFFRACTION7(chain B and resid 269:310)
8X-RAY DIFFRACTION8(chain B and resid 315:344)

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