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- PDB-5btx: Structure of the N-terminal domain of lpg1496 from Legionella pne... -

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Basic information

Entry
Database: PDB / ID: 5btx
TitleStructure of the N-terminal domain of lpg1496 from Legionella pneumophila in complex with nucleotide
Componentslpg1496
KeywordsUNKNOWN FUNCTION / bacterial effector / alpha-beta fold / nucleotide-binding / complex / Structural Genomics / Montreal-Kingston Bacterial Structural Genomics Initiative / BSGI
Function / homologyADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE / :
Function and homology information
Biological speciesLegionella pneumophila subsp. pneumophila ATCC 43290 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsWong, K. / Kozlov, G. / Gehring, K. / Montreal-Kingston Bacterial Structural Genomics Initiative (BSGI)
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)GSP-48370 Canada
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Structure of the Legionella Effector, lpg1496, Suggests a Role in Nucleotide Metabolism.
Authors: Wong, K. / Kozlov, G. / Zhang, Y. / Gehring, K.
History
DepositionJun 3, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 2, 2015Group: Database references
Revision 1.2Oct 21, 2015Group: Database references
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: lpg1496
B: lpg1496
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,3404
Polymers32,6822
Non-polymers6582
Water1,928107
1
A: lpg1496
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,6702
Polymers16,3411
Non-polymers3291
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: lpg1496
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,6702
Polymers16,3411
Non-polymers3291
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)32.622, 57.446, 63.779
Angle α, β, γ (deg.)90.00, 93.32, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein lpg1496


Mass: 16340.897 Da / Num. of mol.: 2 / Fragment: UNP residues 1-138
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila subsp. pneumophila ATCC 43290 (bacteria)
Gene: lp12_1434 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: G8UY02
#2: Chemical ChemComp-CMP / ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE / CYCLIC AMP / CAMP


Mass: 329.206 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H12N5O6P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.83 Å3/Da / Density % sol: 32.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M sodium chloride, 0.1 M Bis-Tris pH6.5, 25% (w/v) PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.977 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 6, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. all: 14063 / Num. obs: 12544 / % possible obs: 89.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Rsym value: 0.076 / Net I/σ(I): 39
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.497 / Mean I/σ(I) obs: 5.3 / % possible all: 92.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
PHASERphasing
Cootmodel building
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5BTW

5btw


Resolution: 2.1→30 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.878 / SU B: 16.764 / SU ML: 0.233 / Cross valid method: THROUGHOUT / ESU R: 0.407 / ESU R Free: 0.267 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.29159 654 5 %RANDOM
Rwork0.23763 ---
obs0.2404 12544 94.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 33.276 Å2
Baniso -1Baniso -2Baniso -3
1--2.8 Å20 Å20.38 Å2
2---1.7 Å20 Å2
3---4.43 Å2
Refinement stepCycle: 1 / Resolution: 2.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2057 0 44 107 2208
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0192198
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6431.9922991
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.6655275
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.225.76585
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.83915389
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1040.2333
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211614
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4092.0681064
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.1263.0911330
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.6482.2341134
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined4.54318.1153314
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.095→2.15 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.337 46 -
Rwork0.292 901 -
obs--92.39 %
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)
11.17110.40730.45860.4982-0.12912.17790.031-0.1120.19580.05130.01790.13310.0555-0.1206-0.0490.14940.0003-0.0140.15890.00470.052516.559435.783845.3781
22.1234-0.9625-0.18933.8309-0.19590.1970.03790.06930.072-0.0314-0.01640.10820.0609-0.1044-0.02150.1286-0.0151-0.03480.1685-0.01020.033810.971625.407835.619
34.759-2.35671.46734.412-1.60431.2059-0.0337-0.2046-0.0450.210.1280.2186-0.071-0.1454-0.09430.1303-0.0098-0.02130.155-0.00860.026412.863128.932646.1166
40.5180.83-0.05052.04590.2521.42530.11360.0043-0.07580.02460.021-0.09370.1053-0.0149-0.13470.10030.007-0.0480.16070.00510.039822.511923.611942.6666
55.23112.53550.15352.78682.74034.5699-0.0580.3745-0.0467-0.04480.2401-0.1409-0.01720.1073-0.1820.11810.00960.00740.18210.01060.109830.850229.419837.354
62.43431.54380.39571.7386-0.91331.9766-0.07460.0283-0.0593-0.08730.0331-0.14240.08140.10270.04150.12420.0145-0.0180.1991-0.04340.159529.321825.801143.0861
70.29050.4634-0.11112.4812-1.75411.4760.08670.00690.09930.123-0.04820.1555-0.03790.0231-0.03840.17550.02690.01090.19230.01230.044525.818642.256940.3905
81.65180.1778-0.82472.32730.10030.45950.003-0.1902-0.08380.16780.0023-0.09860.02970.1684-0.00530.13570.0084-0.03520.2114-0.04390.060529.136523.506872.929
90.65680.1431-0.36082.12880.0941.2627-0.018-0.03430.12280.17890.05110.00650.05550.0631-0.03310.132-0.0063-0.01830.1565-0.01240.026627.87833.682776.8826
100.05880.0614-0.2272.8989-0.04831.56960.07320.039-0.007-0.1309-0.03040.2014-0.1252-0.1088-0.04280.13710.0117-0.04210.1627-0.00510.046619.294931.418869.6195
110.61430.8970.41581.35390.66881.53790.0414-0.00420.06350.0287-0.01770.13550.1074-0.0383-0.02380.0994-0.0141-0.00740.1641-0.0130.077515.560523.684373.4413
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 23
2X-RAY DIFFRACTION2A24 - 44
3X-RAY DIFFRACTION3A45 - 61
4X-RAY DIFFRACTION4A62 - 93
5X-RAY DIFFRACTION5A94 - 104
6X-RAY DIFFRACTION6A105 - 113
7X-RAY DIFFRACTION7A114 - 132
8X-RAY DIFFRACTION8B1 - 33
9X-RAY DIFFRACTION9B34 - 74
10X-RAY DIFFRACTION10B75 - 100
11X-RAY DIFFRACTION11B101 - 131

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