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- PDB-3goz: Crystal structure of the leucine-rich repeat-containing protein L... -

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Basic information

Entry
Database: PDB / ID: 3goz
TitleCrystal structure of the leucine-rich repeat-containing protein LegL7 from Legionella pneumophila. Northeast Structural Genomics Consortium target LgR148
ComponentsLeucine-rich repeat-containing protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Leucine-rich repeat-containing protein / legL7 / NESG / LgR148 / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium
Function / homology
Function and homology information


nucleocytoplasmic transport / GTPase activator activity / small GTPase binding / perinuclear region of cytoplasm / cytosol
Similarity search - Function
: / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Alpha-Beta Horseshoe / Leucine-rich repeat domain superfamily / Alpha Beta
Similarity search - Domain/homology
Leucine-rich repeat-containing protein
Similarity search - Component
Biological speciesLegionella pneumophila subsp. pneumophila str. Philadelphia 1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.099 Å
AuthorsVorobiev, S.M. / Abashidze, M. / Seetharaman, J. / Belote, R.L. / Foote, E.L. / Ciccosanti, C. / Janjua, H. / Xiao, R. / Acton, T.B. / Montelione, G.T. ...Vorobiev, S.M. / Abashidze, M. / Seetharaman, J. / Belote, R.L. / Foote, E.L. / Ciccosanti, C. / Janjua, H. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal structure of the leucine-rich repeat-containing protein LegL7 from Legionella pneumophila. Northeast Structural Genomics Consortium target LgR148.
Authors: Vorobiev, S.M. / Abashidze, M. / Seetharaman, J. / Belote, R.L. / Foote, E.L. / Ciccosanti, C. / Janjua, H. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L.
History
DepositionMar 20, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 31, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Leucine-rich repeat-containing protein


Theoretical massNumber of molelcules
Total (without water)39,5261
Polymers39,5261
Non-polymers00
Water2,450136
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)67.196, 67.196, 155.420
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
DetailsMonomer according to gel filtration

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Components

#1: Protein Leucine-rich repeat-containing protein


Mass: 39525.664 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila subsp. pneumophila str. Philadelphia 1 (bacteria)
Strain: Philadelphia 1 / DSM 7513 / Gene: leg7, legL7, lpg2400 / Plasmid: pET21-23C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: Q5ZSW6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 136 / Source method: isolated from a natural source / Formula: H2O
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: 2.56 Å3/Da / Density % sol: 52 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 18% PEG 3350, 4% Ethylene glycol, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 11, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.099→50 Å / Num. all: 91532 / Num. obs: 91532 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 27.69
Reflection shellResolution: 2.099→2.18 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.529 / Mean I/σ(I) obs: 1.98 / Num. unique all: 9155 / % possible all: 99

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Processing

Software
NameClassification
HKL-2000data collection
SHELXDEphasing
RESOLVEmodel building
PHENIXrefinement
DENZOdata reduction
SCALEPACKdata scaling
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.099→33.598 Å / SU ML: 0.18 / σ(F): 1 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: The Friedel pairs were used in phasing
RfactorNum. reflection% reflection
Rfree0.262 2343 5.13 %
Rwork0.2055 --
obs0.2084 45714 99.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.934 Å2 / ksol: 0.338 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-6.3641 Å2-0 Å2-0 Å2
2--6.3641 Å2-0 Å2
Refinement stepCycle: LAST / Resolution: 2.099→33.598 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2401 0 0 136 2537
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.006
X-RAY DIFFRACTIONf_angle_deg0.93
X-RAY DIFFRACTIONf_dihedral_angle_d17.712
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.099-2.14170.32551230.26912594100
2.1417-2.18820.30671660.26012499100
2.1882-2.23910.30581510.26522588100
2.2391-2.29510.42231280.3204248699
2.2951-2.35720.31941380.2362558100
2.3572-2.42650.2511440.20892565100
2.4265-2.50480.30851490.20572542100
2.5048-2.59430.24551270.20922607100
2.5943-2.69810.32721030.20862586100
2.6981-2.82090.27971200.21162602100
2.8209-2.96950.26861620.21842477100
2.9695-3.15540.2831400.21732570100
3.1554-3.39880.31761440.21212547100
3.3988-3.74050.26251310.18732600100
3.7405-4.28080.19851470.16882514100
4.2808-5.38970.22451420.17442565100
5.3897-33.60230.21831280.1975247196

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