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- PDB-3cg0: Crystal structure of signal receiver domain of modulated diguanyl... -

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Basic information

Entry
Database: PDB / ID: 3cg0
TitleCrystal structure of signal receiver domain of modulated diguanylate cyclase from Desulfovibrio desulfuricans G20, an example of alternate folding
ComponentsResponse regulator receiver modulated diguanylate cyclase with PAS/PAC sensor
KeywordsLYASE / SIGNAL RECEIVER DOMAIN / DIGUANYLATE CYCLASE / PROTEIN STRUCTURE INITIATIVE / PSI-2 / New York SGX Research Center for Structural Genomics / NYSGXRC / STRUCTURAL GENOMICS
Function / homology
Function and homology information


phosphorelay signal transduction system / regulation of DNA-templated transcription
Similarity search - Function
PAS domain / : / Diguanylate cyclase, GGDEF domain / diguanylate cyclase / GGDEF domain profile. / GGDEF domain / PAS-associated, C-terminal / PAC domain profile. / Nucleotide cyclase / Response regulator receiver domain ...PAS domain / : / Diguanylate cyclase, GGDEF domain / diguanylate cyclase / GGDEF domain profile. / GGDEF domain / PAS-associated, C-terminal / PAC domain profile. / Nucleotide cyclase / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Response regulator / PAS fold / PAS fold / PAS domain / PAS repeat profile. / PAS domain / PAS domain superfamily / Reverse transcriptase/Diguanylate cyclase domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Response regulator receiver modulated diguanylate cyclase with PAS/PAC sensor
Similarity search - Component
Biological speciesDesulfovibrio desulfuricans subsp. desulfuricans str. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.15 Å
AuthorsPatskovsky, Y. / Bonanno, J.B. / Romero, R. / Gilmore, M. / Chang, S. / Groshong, C. / Koss, J. / Wasserman, S.R. / Sauder, J.M. / Burley, S.K. ...Patskovsky, Y. / Bonanno, J.B. / Romero, R. / Gilmore, M. / Chang, S. / Groshong, C. / Koss, J. / Wasserman, S.R. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal Structure of Signal Receiver Domain of Modulated Diguanylate Cyclase from Desulfovibrio desulfuricans.
Authors: Patskovsky, Y. / Bonanno, J.B. / Romero, R. / Gilmore, M. / Chang, S. / Groshong, C. / Koss, J. / Wasserman, S.R. / Sauder, J.M. / Burley, S.K. / Almo, S.C.
History
DepositionMar 4, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Nov 14, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.4Feb 3, 2021Group: Database references / Structure summary
Category: audit_author / citation_author / struct_ref_seq_dif
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_ref_seq_dif.details
Revision 1.5Feb 21, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Response regulator receiver modulated diguanylate cyclase with PAS/PAC sensor
B: Response regulator receiver modulated diguanylate cyclase with PAS/PAC sensor
C: Response regulator receiver modulated diguanylate cyclase with PAS/PAC sensor
D: Response regulator receiver modulated diguanylate cyclase with PAS/PAC sensor


Theoretical massNumber of molelcules
Total (without water)60,8944
Polymers60,8944
Non-polymers00
Water1,63991
1
C: Response regulator receiver modulated diguanylate cyclase with PAS/PAC sensor

D: Response regulator receiver modulated diguanylate cyclase with PAS/PAC sensor

A: Response regulator receiver modulated diguanylate cyclase with PAS/PAC sensor
B: Response regulator receiver modulated diguanylate cyclase with PAS/PAC sensor


Theoretical massNumber of molelcules
Total (without water)60,8944
Polymers60,8944
Non-polymers00
Water724
TypeNameSymmetry operationNumber
crystal symmetry operation1_545x,y-1,z1
crystal symmetry operation1_556x,y,z+11
identity operation1_555x,y,z1
Buried area9310 Å2
ΔGint-57.3 kcal/mol
Surface area22570 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)163.021, 51.631, 67.687
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B
13C
23D
14C
24D

NCS domain segments:

Component-ID: 1 / Refine code: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYILEILEAA9 - 8611 - 88
21GLYGLYILEILEBB9 - 8611 - 88
12GLUGLUGLUGLUAA93 - 13195 - 133
22GLUGLUGLUGLUBB93 - 13195 - 133
13GLYGLYILEILECC9 - 8611 - 88
23GLYGLYILEILEDD9 - 8611 - 88
14GLUGLUGLUGLUCC93 - 13195 - 133
24GLUGLUGLUGLUDD93 - 13195 - 133

NCS ensembles :
ID
1
2
3
4
DetailsAUTHORS STATE THAT THE TETRAMERIC ASSEMBLY OF THE BIOLOGICAL UNIT THAT IS SHOWN IN REMARK 350 IS PUTATIVE AT THE TIME OF DEPOSITION.

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Components

#1: Protein
Response regulator receiver modulated diguanylate cyclase with PAS/PAC sensor


Mass: 15223.411 Da / Num. of mol.: 4 / Fragment: Signal receiver domain: Residues 2-130
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desulfovibrio desulfuricans subsp. desulfuricans str. (bacteria)
Species: Desulfovibrio desulfuricans / Strain: G20 / Gene: Dde_1631 / Plasmid: BC-pSGX3(BC) / Production host: Escherichia coli (E. coli) / References: UniProt: Q311G8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / 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: 2.34 Å3/Da / Density % sol: 47.41 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 200mM Potassium tri-citrate pH 7.5, 20% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9796 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Feb 22, 2008
RadiationMonochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. obs: 31995 / % possible obs: 99.6 % / Observed criterion σ(I): -0.5 / Redundancy: 5.7 % / Biso Wilson estimate: 41.58 Å2 / Rmerge(I) obs: 0.097 / Net I/σ(I): 4.5
Reflection shellResolution: 2.15→2.23 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.89 / Mean I/σ(I) obs: 0.6 / % possible all: 99.2

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Processing

Software
NameVersionClassification
SHELXDphasing
REFMAC5.3.0034refinement
MAR345CCDdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.15→20 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.91 / SU B: 7.812 / SU ML: 0.203 / Cross valid method: THROUGHOUT / ESU R: 0.263 / ESU R Free: 0.227 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28842 994 3.1 %RANDOM
Rwork0.23162 ---
obs0.23339 30631 99.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 53.629 Å2
Baniso -1Baniso -2Baniso -3
1--0.92 Å20 Å20 Å2
2--1.92 Å20 Å2
3----1 Å2
Refinement stepCycle: LAST / Resolution: 2.15→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3808 0 0 91 3899
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0223969
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4031.9945406
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6985533
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.64824.08174
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.90315696
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7941535
X-RAY DIFFRACTIONr_chiral_restr0.090.2645
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022989
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1550.31683
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2950.52701
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1780.5242
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1040.367
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2160.516
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.96122609
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it5.86534110
X-RAY DIFFRACTIONr_scbond_it6.70431462
X-RAY DIFFRACTIONr_scangle_it9.40151279
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

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A544tight positional0.560.25
21B301tight positional0.740.25
31C557tight positional0.510.25
41D318tight positional0.510.25
12A544tight thermal4.412.5
22B301tight thermal5.892.5
32C557tight thermal5.412.5
42D318tight thermal6.272.5
LS refinement shellResolution: 2.15→2.205 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.354 69 -
Rwork0.289 2092 -
obs--94.91 %

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