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- PDB-4u64: Structure of the periplasmic output domain of the Legionella pneu... -

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Basic information

Entry
Database: PDB / ID: 4u64
TitleStructure of the periplasmic output domain of the Legionella pneumophila LapD ortholog CdgS9 in the apo state
ComponentsTwo component histidine kinase, GGDEF domain protein/EAL domain protein
KeywordsTRANSFERASE / signalling / PAS-like fold
Function / homology
Function and homology information


kinase activity / phosphorylation / signal transduction / membrane
Similarity search - Function
LapD/MoxY periplasmic domain, C-terminal / LapD/MoxY, periplasmic domain / LapD/MoxY periplasmic domain / Putative diguanylate phosphodiesterase / EAL domain / EAL domain superfamily / EAL domain / EAL domain profile. / Diguanylate cyclase, GGDEF domain / diguanylate cyclase ...LapD/MoxY periplasmic domain, C-terminal / LapD/MoxY, periplasmic domain / LapD/MoxY periplasmic domain / Putative diguanylate phosphodiesterase / EAL domain / EAL domain superfamily / EAL domain / EAL domain profile. / Diguanylate cyclase, GGDEF domain / diguanylate cyclase / HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain / GGDEF domain profile. / GGDEF domain / HAMP domain profile. / HAMP domain / Nucleotide cyclase / Reverse transcriptase/Diguanylate cyclase domain
Similarity search - Domain/homology
Two component histidine kinase, GGDEF domain protein/EAL domain protein
Similarity search - Component
Biological speciesLegionella pneumophila subsp. pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.141 Å
AuthorsChatterjee, D. / Cooley, R.B. / Boyd, C.D. / Mehl, R.A. / O'Toole, G.A. / Sondermann, H.S.
Funding support United States, 6items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)DMR-1332208 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM-103485 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01- RAI097307 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)F32-GM108440 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32-GM08704 United States
National Science Foundation (NSF, United States)MCB9984521 United States
CitationJournal: Elife / Year: 2014
Title: Mechanistic insight into the conserved allosteric regulation of periplasmic proteolysis by the signaling molecule cyclic-di-GMP.
Authors: Chatterjee, D. / Cooley, R.B. / Boyd, C.D. / Mehl, R.A. / O'Toole, G.A. / Sondermann, H.
History
DepositionJul 27, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 13, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 17, 2014Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Derived calculations ...Author supporting evidence / Derived calculations / Other / Source and taxonomy
Category: entity_src_gen / pdbx_audit_support ...entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_oper_list
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine_hist
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: Two component histidine kinase, GGDEF domain protein/EAL domain protein


Theoretical massNumber of molelcules
Total (without water)15,1181
Polymers15,1181
Non-polymers00
Water1,62190
1
A: Two component histidine kinase, GGDEF domain protein/EAL domain protein

A: Two component histidine kinase, GGDEF domain protein/EAL domain protein


Theoretical massNumber of molelcules
Total (without water)30,2372
Polymers30,2372
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_444-y-1,-x-1,-z-1/61
Buried area3030 Å2
ΔGint-21 kcal/mol
Surface area14050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.581, 61.581, 147.528
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-233-

HOH

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Components

#1: Protein Two component histidine kinase, GGDEF domain protein/EAL domain protein


Mass: 15118.335 Da / Num. of mol.: 1 / Fragment: Periplasmic output domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila subsp. pneumophila (bacteria)
Strain: Philadelphia 1 / ATCC 33152 / DSM 7513 / Gene: lpg0829 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): T7 Express / References: UniProt: Q5ZXA3
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 90 / 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: 2.67 Å3/Da / Density % sol: 53.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.1 M Bis-Tris (pH=5.0), 14% PEG3350 and 4% v/v 2,2,2-trifluoroethanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.976 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 1, 2012
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.14→30.79 Å / Num. obs: 9611 / % possible obs: 98.6 % / Redundancy: 21.9 % / Net I/σ(I): 35.4

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.4_1496) / Classification: refinement
RefinementResolution: 2.141→30.79 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 0.55 / Phase error: 22.8 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.243 961 10 %
Rwork0.2194 --
obs0.2217 9611 98.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.141→30.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1042 0 0 90 1132
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031096
X-RAY DIFFRACTIONf_angle_d0.5981493
X-RAY DIFFRACTIONf_dihedral_angle_d14.249405
X-RAY DIFFRACTIONf_chiral_restr0.034169
X-RAY DIFFRACTIONf_plane_restr0.004188
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1412-2.25410.29271310.23951176X-RAY DIFFRACTION97
2.2541-2.39530.28061320.24691198X-RAY DIFFRACTION98
2.3953-2.58010.26921340.23051195X-RAY DIFFRACTION98
2.5801-2.83960.27771330.2461205X-RAY DIFFRACTION98
2.8396-3.25010.26261380.23651237X-RAY DIFFRACTION99
3.2501-4.09330.23381410.20921268X-RAY DIFFRACTION100
4.0933-30.79370.2121520.19951371X-RAY DIFFRACTION99
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)
15.585-2.183-0.72851.3113-0.06542.61220.29890.31420.2232-0.173-0.191-0.1536-0.22140.3243-0.09540.2556-0.01950.00130.2210.00780.3184-13.6581-18.2418-11.1126
22.5059-1.05240.79882.8656-0.98571.8666-0.0032-0.11920.00430.02690.13930.2098-0.3145-0.0393-0.12620.24310.01770.06320.2456-0.02480.208-20.5589-11.6302-9.2614
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 22:100)
2X-RAY DIFFRACTION2(chain A and resid 101:152)

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