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- PDB-5bu2: Structure of the C-terminal domain of lpg1496 from Legionella pne... -

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Basic information

Entry
Database: PDB / ID: 5bu2
TitleStructure of the C-terminal domain of lpg1496 from Legionella pneumophila in complex with nucleotide
Componentslpg1496
KeywordsUNKNOWN FUNCTION / bacterial effector / nucleotide-binding / complex / Structural Genomics / Montreal-Kingston Bacterial Structural Genomics Initiative / BSGI
Function / homologyADENOSINE-5'-DIPHOSPHATE / ADENOSINE MONOPHOSPHATE / alpha-D-ribofuranose / :
Function and homology information
Biological speciesLegionella pneumophila subsp. pneumophila ATCC 43290 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.11 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 ...Author supporting evidence / Database references / Derived calculations / Refinement description
Category: citation / pdbx_audit_support ...citation / pdbx_audit_support / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization ..._citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.4Jan 8, 2020Group: Author supporting evidence / Data collection / Category: chem_comp / pdbx_audit_support
Item: _chem_comp.type / _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: lpg1496
B: lpg1496
C: lpg1496
D: lpg1496
hetero molecules


Theoretical massNumber of molelcules
Total (without water)207,11710
Polymers204,9114
Non-polymers2,2066
Water2,180121
1
A: lpg1496
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,0823
Polymers51,2281
Non-polymers8542
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: lpg1496
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,0023
Polymers51,2281
Non-polymers7742
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: lpg1496
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,6552
Polymers51,2281
Non-polymers4271
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: lpg1496
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,3782
Polymers51,2281
Non-polymers1501
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.867, 69.707, 77.027
Angle α, β, γ (deg.)89.87, 72.30, 70.31
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: 0 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / Refine code: 0

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRAA298 - 590146 - 438
21THRTHRBB298 - 590146 - 438
12THRTHRAA298 - 590146 - 438
22THRTHRCC298 - 590146 - 438
13THRTHRAA298 - 590146 - 438
23THRTHRDD298 - 590146 - 438
14THRTHRBB298 - 591146 - 439
24THRTHRCC298 - 591146 - 439
15GLUGLUBB298 - 589146 - 437
25GLUGLUDD298 - 589146 - 437
16GLUGLUCC298 - 589146 - 437
26GLUGLUDD298 - 589146 - 437

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
lpg1496


Mass: 51227.770 Da / Num. of mol.: 4 / Fragment: UNP residues 154-598
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-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#4: Sugar ChemComp-RIB / alpha-D-ribofuranose / alpha-D-ribose / D-ribose / ribose / Ribose


Type: D-saccharide, alpha linking / Mass: 150.130 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C5H10O5
IdentifierTypeProgram
DRibfaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-ribofuranoseCOMMON NAMEGMML 1.0
a-D-RibfIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
RibSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 121 / 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

Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1 M HEPES, 25% (w/v) PEG3350, 5 mM ADP

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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: Mar 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 57062 / Num. obs: 54209 / % possible obs: 95 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Rsym value: 0.098 / Net I/σ(I): 11.3
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.435 / Mean I/σ(I) obs: 1.7 / % possible all: 78.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
ARPmodel building
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5BU1

5bu1


Resolution: 2.11→34 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.9 / SU B: 9.239 / SU ML: 0.236 / Cross valid method: THROUGHOUT / ESU R: 0.384 / ESU R Free: 0.25 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.27307 2884 5.1 %RANDOM
Rwork0.22898 ---
obs0.23123 54209 94.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.641 Å2
Baniso -1Baniso -2Baniso -3
1-4.75 Å2-1.13 Å2-1.43 Å2
2---1.88 Å2-0.5 Å2
3----3.15 Å2
Refinement stepCycle: 1 / Resolution: 2.11→34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9218 0 141 121 9480
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0199634
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2121.95913073
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.12651159
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.21325.263456
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.308151626
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.3391524
X-RAY DIFFRACTIONr_chiral_restr0.0840.21371
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0217315
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_it1.5113.6164630
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.4155.4135776
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.8973.8745004
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined4.83931.42415414
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A3910.07
12B3910.07
21A3980.08
22C3980.08
31A3920.09
32D3920.09
41B3990.08
42C3990.08
51B3850.08
52D3850.08
61C3960.11
62D3960.11
LS refinement shellResolution: 2.11→2.166 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 179 -
Rwork0.28 3047 -
obs--72.48 %

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