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- PDB-3luf: Structure of probable two-component system response regulator/GGD... -

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Basic information

Entry
Database: PDB / ID: 3luf
TitleStructure of probable two-component system response regulator/GGDEF domain protein
ComponentsTwo-component system response regulator/GGDEF domain proteinTwo-component regulatory system
KeywordsSIGNALING PROTEIN / structural genomics / ASA_2441 / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


diguanylate cyclase / phosphorelay signal transduction system / metal ion binding
Similarity search - Function
Diguanylate cyclase, GGDEF domain / diguanylate cyclase / GGDEF domain profile. / GGDEF domain / Nucleotide cyclase / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily ...Diguanylate cyclase, GGDEF domain / diguanylate cyclase / GGDEF domain profile. / GGDEF domain / 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 / Reverse transcriptase/Diguanylate cyclase domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesAeromonas salmonicida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.76 Å
AuthorsRamagopal, U.A. / Toro, R. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be published
Title: Structure of probable two-component system response regulator/GGDEF domain protein
Authors: Ramagopal, U.A. / Toro, R. / Burley, S.K. / Almo, S.C.
History
DepositionFeb 17, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Two-component system response regulator/GGDEF domain protein
B: Two-component system response regulator/GGDEF domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,0589
Polymers59,7262
Non-polymers3327
Water3,045169
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4000 Å2
ΔGint-39 kcal/mol
Surface area21180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.195, 53.699, 57.887
Angle α, β, γ (deg.)75.390, 80.990, 77.410
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Two-component system response regulator/GGDEF domain protein / Two-component regulatory system


Mass: 29863.020 Da / Num. of mol.: 2 / Fragment: sequence database residues 2-249
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aeromonas salmonicida (bacteria) / Strain: A449 / Gene: ASA_2441 / Plasmid: BC-pSGX4(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A4SNL2
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 169 / 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: 2.01 Å3/Da / Density % sol: 38.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1 M Bis-Tris pH 5.5, 25% PEG 3350, 0.2M MgCl2, Vapor diffusion, Sitting drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 19, 2009
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.76→40 Å / Num. all: 44744 / Num. obs: 44744 / % possible obs: 97.4 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.063 / Rsym value: 0.068 / Net I/σ(I): 56.3
Reflection shellResolution: 1.76→1.79 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.216 / Mean I/σ(I) obs: 6.9 / Num. unique all: 2183 / Rsym value: 0.187 / % possible all: 95.4

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
PDB_EXTRACT3.005data extraction
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling
SHELXEmodel building
SHELXDphasing
CCP4phasing
RefinementMethod to determine structure: SAD / Resolution: 1.76→40 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.931 / WRfactor Rfree: 0.245 / WRfactor Rwork: 0.203 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.859 / SU B: 2.399 / SU ML: 0.079 / SU R Cruickshank DPI: 0.139 / SU Rfree: 0.13 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.139 / ESU R Free: 0.13 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.226 2263 5.1 %RANDOM
Rwork0.187 ---
obs0.189 44744 97.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 53.49 Å2 / Biso mean: 18.852 Å2 / Biso min: 7.94 Å2
Baniso -1Baniso -2Baniso -3
1-0.16 Å20.36 Å2-0.29 Å2
2--0.67 Å2-0.58 Å2
3----0.6 Å2
Refinement stepCycle: LAST / Resolution: 1.76→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4083 0 16 169 4268
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0224169
X-RAY DIFFRACTIONr_angle_refined_deg1.4981.9735665
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5815533
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.80624.129201
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.18215777
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4031538
X-RAY DIFFRACTIONr_chiral_restr0.1070.2654
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213161
X-RAY DIFFRACTIONr_mcbond_it0.9411.52584
X-RAY DIFFRACTIONr_mcangle_it1.73624195
X-RAY DIFFRACTIONr_scbond_it2.88631585
X-RAY DIFFRACTIONr_scangle_it4.724.51470
LS refinement shellResolution: 1.762→1.807 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 167 -
Rwork0.236 2990 -
all-3157 -
obs--93.54 %

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