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- PDB-5euh: Crystal structure of the c-di-GMP-bound GGDEF domain of P. fluore... -

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Basic information

Entry
Database: PDB / ID: 5euh
TitleCrystal structure of the c-di-GMP-bound GGDEF domain of P. fluorescens GcbC
ComponentsPutative GGDEF domain membrane protein
KeywordsMEMBRANE PROTEIN / diguanylate cyclase / second messenger / biofilm formation / signaling
Function / homology
Function and homology information


membrane => GO:0016020 / nucleotide binding / plasma membrane
Similarity search - Function
Double Cache domain 1 / Cache domain / Diguanylate cyclase, GGDEF domain / diguanylate cyclase / GGDEF domain profile. / GGDEF domain / Nucleotide cyclase / Reverse transcriptase/Diguanylate cyclase domain / Reverse transcriptase/Diguanylate cyclase domain / Alpha-Beta Plaits ...Double Cache domain 1 / Cache domain / Diguanylate cyclase, GGDEF domain / diguanylate cyclase / GGDEF domain profile. / GGDEF domain / Nucleotide cyclase / Reverse transcriptase/Diguanylate cyclase domain / Reverse transcriptase/Diguanylate cyclase domain / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-C2E / Putative GGDEF domain membrane protein
Similarity search - Component
Biological speciesPseudomonas fluorescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.989 Å
AuthorsGiglio, K.M. / Cooley, R.B. / Sondermann, H.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01-AI097307 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM-103485 United States
National Science Foundation (NSF, United States)DMR-1332208 United States
CitationJournal: Mbio / Year: 2015
Title: Contribution of Physical Interactions to Signaling Specificity between a Diguanylate Cyclase and Its Effector.
Authors: Dahlstrom, K.M. / Giglio, K.M. / Collins, A.J. / Sondermann, H. / O'Toole, G.A.
History
DepositionNov 18, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 30, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 10, 2016Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _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 1.4Sep 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
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative GGDEF domain membrane protein
B: Putative GGDEF domain membrane protein
C: Putative GGDEF domain membrane protein
D: Putative GGDEF domain membrane protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,49513
Polymers76,2534
Non-polymers3,2429
Water1448
1
A: Putative GGDEF domain membrane protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9464
Polymers19,0631
Non-polymers8833
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Putative GGDEF domain membrane protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7326
Polymers19,0631
Non-polymers1,6695
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Putative GGDEF domain membrane protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,7542
Polymers19,0631
Non-polymers6901
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Putative GGDEF domain membrane protein


Theoretical massNumber of molelcules
Total (without water)19,0631
Polymers19,0631
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)141.913, 141.913, 106.169
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number171
Space group name H-MP62

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Components

#1: Protein
Putative GGDEF domain membrane protein


Mass: 19063.297 Da / Num. of mol.: 4 / Fragment: UNP residues 339-501
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas fluorescens (strain Pf0-1) (bacteria)
Strain: Pf0-1 / Gene: Pfl01_4666 / Plasmid: pET21a / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q3K751
#2: Chemical
ChemComp-C2E / 9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one) / c-di-GMP / Cyclic diguanosine monophosphate / Cyclic di-GMP


Mass: 690.411 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C20H24N10O14P2
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O

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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: 4.05 Å3/Da / Density % sol: 72.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1.0 M Ammonium Sulfate, 0.1 M HEPES (pH 7.0), and 0.5% w/v PEG8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.9771 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 21, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9771 Å / Relative weight: 1
ReflectionResolution: 2.989→46.5 Å / Num. obs: 24701 / % possible obs: 99.85 % / Redundancy: 10.7 % / Net I/σ(I): 12.92
Reflection shellResolution: 3→3.1 Å / Redundancy: 10.4 % / Rmerge(I) obs: 0.689 / Mean I/σ(I) obs: 3.07 / % possible all: 98.5

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3I5C

3i5c


Resolution: 2.989→46.452 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2434 1991 8.09 %Random selection
Rwork0.2258 ---
obs0.2273 24616 99.51 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.989→46.452 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4586 0 209 8 4803
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034871
X-RAY DIFFRACTIONf_angle_d0.6996643
X-RAY DIFFRACTIONf_dihedral_angle_d16.2721734
X-RAY DIFFRACTIONf_chiral_restr0.033768
X-RAY DIFFRACTIONf_plane_restr0.002833
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9891-3.06390.36451360.3141601X-RAY DIFFRACTION98
3.0639-3.14670.35021400.28811627X-RAY DIFFRACTION100
3.1467-3.23930.24961390.27481601X-RAY DIFFRACTION100
3.2393-3.34380.32361440.26311608X-RAY DIFFRACTION100
3.3438-3.46330.21781450.25141610X-RAY DIFFRACTION100
3.4633-3.60190.24081360.2271617X-RAY DIFFRACTION100
3.6019-3.76570.24461490.22361604X-RAY DIFFRACTION100
3.7657-3.96420.27811440.21171620X-RAY DIFFRACTION100
3.9642-4.21240.25411400.21291612X-RAY DIFFRACTION100
4.2124-4.53740.24611460.1951629X-RAY DIFFRACTION100
4.5374-4.99350.21571400.19751611X-RAY DIFFRACTION100
4.9935-5.7150.2121410.20461649X-RAY DIFFRACTION100
5.715-7.19590.25281430.2471630X-RAY DIFFRACTION100
7.1959-46.45750.17491480.20321606X-RAY DIFFRACTION96
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)
10.96880.12570.33231.2104-0.2821.3925-0.0949-0.02390.09950.37180.17730.343-0.0445-0.409-0.08620.49740.00510.02970.35050.07170.37670.2553-31.059221.4264
21.43050.3782-0.21851.56340.08142.02120.1303-0.1030.02620.4113-0.13340.2452-0.3887-0.0715-0.04180.6201-0.06690.02220.32070.04250.335777.5227-26.920328.262
31.2840.0622-0.09241.0288-0.55261.53510.17290.3284-0.2293-0.101-0.1420.15790.44-0.1194-0.04490.41310.0515-0.07570.4379-0.00010.369179.1674-46.5492-5.4021
41.6680.1802-0.01051.20450.27071.83060.12210.5212-0.1403-0.1348-0.0816-0.09730.20240.4413-0.02440.33870.1142-0.03640.60260.00980.358386.3754-42.3005-12.2432
50.69170.0848-0.13090.7555-0.20690.6699-0.08510.37970.08550.2467-0.96-0.82450.29470.7199-0.24780.78360.16020.10350.97570.82911.0965102.7793-15.1763-1.0875
60.85690.177-0.30811.89860.34211.8283-0.21990.8283-0.2768-0.3489-0.7669-0.61080.44980.33660.03770.67930.27660.1270.80880.55020.966395.8512-8.9628-10.4414
70.78080.28680.39760.63120.02930.7462-0.6010.51670.39990.85-0.8529-0.3176-0.98780.4582-0.36191.1736-0.1037-1.07640.7440.49560.9831109.1583-25.201617.9299
80.76-0.13380.02580.9768-0.32840.9698-0.4506-0.38230.7550.9074-0.3479-0.0747-0.61870.1321-0.19680.99740.1254-0.80870.51710.17051.0624111.5602-34.274926.7547
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 339:421)
2X-RAY DIFFRACTION2(chain A and resid 422:502)
3X-RAY DIFFRACTION3(chain B and resid 339:421)
4X-RAY DIFFRACTION4(chain B and resid 422:502)
5X-RAY DIFFRACTION5(chain C and resid 340:462)
6X-RAY DIFFRACTION6(chain C and resid 463:502)
7X-RAY DIFFRACTION7(chain D and resid 340:445)
8X-RAY DIFFRACTION8(chain D and resid 446:502)

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