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- PDB-4u65: Structure of the periplasmic output domain of the Legionella pneu... -

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Basic information

Entry
Database: PDB / ID: 4u65
TitleStructure of the periplasmic output domain of the Legionella pneumophila LapD ortholog CdgS9 in complex with Pseudomonas fluorescens LapG
Components
  • Putative cystine protease
  • Two component histidine kinase, GGDEF domain protein/EAL domain protein
KeywordsTransferase/Hydrolase / signalling / PAS-like fold / Transferase-Hydrolase complex
Function / homology
Function and homology information


phosphorylation / kinase activity / peptidase activity / signal transduction / membrane / metal ion binding
Similarity search - Function
Transglutaminase-like cysteine peptidase, predicted / Bacterial transglutaminase-like cysteine proteinase BTLCP / LapD/MoxY periplasmic domain, C-terminal / LapD/MoxY, periplasmic domain / LapD/MoxY periplasmic domain / C8orf32 fold - #30 / C8orf32 fold / Putative diguanylate phosphodiesterase / EAL domain / EAL domain superfamily ...Transglutaminase-like cysteine peptidase, predicted / Bacterial transglutaminase-like cysteine proteinase BTLCP / LapD/MoxY periplasmic domain, C-terminal / LapD/MoxY, periplasmic domain / LapD/MoxY periplasmic domain / C8orf32 fold - #30 / C8orf32 fold / 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 / Papain-like cysteine peptidase superfamily / Reverse transcriptase/Diguanylate cyclase domain / Roll / Alpha Beta
Similarity search - Domain/homology
Putative cystine protease / Two component histidine kinase, GGDEF domain protein/EAL domain protein
Similarity search - Component
Biological speciesLegionella pneumophila subsp. pneumophila (bacteria)
Pseudomonas fluorescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.1 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_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / 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_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / refine_hist / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Two component histidine kinase, GGDEF domain protein/EAL domain protein
B: Two component histidine kinase, GGDEF domain protein/EAL domain protein
C: Two component histidine kinase, GGDEF domain protein/EAL domain protein
D: Two component histidine kinase, GGDEF domain protein/EAL domain protein
E: Putative cystine protease
F: Putative cystine protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,51410
Polymers104,3536
Non-polymers1604
Water12,196677
1
A: Two component histidine kinase, GGDEF domain protein/EAL domain protein
B: Two component histidine kinase, GGDEF domain protein/EAL domain protein
E: Putative cystine protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,2575
Polymers52,1773
Non-polymers802
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6540 Å2
ΔGint-55 kcal/mol
Surface area20540 Å2
MethodPISA
2
C: Two component histidine kinase, GGDEF domain protein/EAL domain protein
D: Two component histidine kinase, GGDEF domain protein/EAL domain protein
F: Putative cystine protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,2575
Polymers52,1773
Non-polymers802
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6360 Å2
ΔGint-54 kcal/mol
Surface area20540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.854, 73.674, 88.223
Angle α, β, γ (deg.)90.00, 92.88, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 14836.964 Da / Num. of mol.: 4 / 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: Protein Putative cystine protease


Mass: 22502.791 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas fluorescens (bacteria) / Strain: Pf0-1 / Gene: lapF, Pfl01_0130 / Production host: Escherichia coli (E. coli) / Strain (production host): T7 Express / References: UniProt: Q3KK32
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 677 / 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: 2.36 Å3/Da / Density % sol: 47.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1 M Bis-Tris (pH=6.0) and 0.1 M magnesium formate

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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: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.1→44.06 Å / Num. obs: 55783 / % possible obs: 97.7 % / Redundancy: 4.3 % / Net I/σ(I): 12.4

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.4_1496) / Classification: refinement
RefinementResolution: 2.1→44.056 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2112 1997 3.58 %
Rwork0.17 --
obs0.1714 55727 97.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→44.056 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7095 0 4 677 7776
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037317
X-RAY DIFFRACTIONf_angle_d0.6419938
X-RAY DIFFRACTIONf_dihedral_angle_d12.0022674
X-RAY DIFFRACTIONf_chiral_restr0.0371103
X-RAY DIFFRACTIONf_plane_restr0.0051256
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0971-2.14960.2711170.22113299X-RAY DIFFRACTION84
2.1496-2.20770.26091420.21483688X-RAY DIFFRACTION95
2.2077-2.27260.261380.19993771X-RAY DIFFRACTION97
2.2726-2.3460.26821410.19683797X-RAY DIFFRACTION97
2.346-2.42980.23991400.19883815X-RAY DIFFRACTION98
2.4298-2.52710.26191500.1893883X-RAY DIFFRACTION98
2.5271-2.64210.22681470.1823874X-RAY DIFFRACTION99
2.6421-2.78140.23641430.18543874X-RAY DIFFRACTION100
2.7814-2.95560.21221410.17333951X-RAY DIFFRACTION100
2.9556-3.18380.19871450.1763948X-RAY DIFFRACTION100
3.1838-3.5040.21831460.16973933X-RAY DIFFRACTION100
3.504-4.01080.18391500.15163932X-RAY DIFFRACTION100
4.0108-5.0520.16081490.133966X-RAY DIFFRACTION100
5.052-44.06550.19941480.16363999X-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)
17.94941.31490.2611.04330.06670.45830.0069-0.3133-0.27280.03690.0028-0.19030.05510.0971-0.01040.1810.0349-0.00530.15960.02180.1783104.161916.645548.8584
25.50170.23780.84370.45750.02741.4411-0.1980.8175-0.1074-0.23710.0917-0.14360.0180.14860.12190.28350.00560.04810.2789-0.02540.2122102.954617.667430.5778
37.4530.8101-0.69930.6573-0.16630.4166-0.0199-0.32080.14070.03630.03620.1317-0.0356-0.009-0.00940.19780.0335-0.00640.1281-0.00740.172983.425128.83445.2628
47.02030.7092-0.75670.3650.24071.1054-0.17780.8465-0.0715-0.21960.08490.07950.0221-0.09180.09230.25950.0092-0.0360.24790.01230.190684.038827.999-13.1716
51.350.5044-0.34553.1604-0.70640.71930.00560.0589-0.0381-0.02190.01820.04240.01970.0353-0.0260.13980.0191-0.02760.164-0.00860.192881.035235.795238.1325
61.37640.65860.45214.04160.76370.7295-0.0420.02010.0712-0.05820.0363-0.083-0.0517-0.04510.00280.12610.01850.02310.14230.0090.1559106.34979.7328-6.0901
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 22:152)
2X-RAY DIFFRACTION2(chain B and resid 22:152)
3X-RAY DIFFRACTION3(chain C and resid 22:152)
4X-RAY DIFFRACTION4(chain D and resid 22:152)
5X-RAY DIFFRACTION5(chain E and resid 51:247)
6X-RAY DIFFRACTION6(chain F and resid 51:247)

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