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- PDB-3sy8: Crystal structure of the response regulator RocR -

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Basic information

Entry
Database: PDB / ID: 3sy8
TitleCrystal structure of the response regulator RocR
ComponentsRocR
KeywordsTRANSCRIPTION REGULATOR / TIM barrel phosphodiesterase-A
Function / homology
Function and homology information


cyclic-guanylate-specific phosphodiesterase activity / phosphorelay signal transduction system / negative regulation of DNA-templated transcription / metal ion binding
Similarity search - Function
EAL domain / Putative diguanylate phosphodiesterase / EAL domain / EAL domain superfamily / EAL domain / EAL domain profile. / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. ...EAL domain / Putative diguanylate phosphodiesterase / EAL domain / EAL domain superfamily / EAL domain / EAL domain profile. / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Response regulator / TIM Barrel / Alpha-Beta Barrel / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsChen, M.W. / Kotaka, M. / Vonrhein, C. / Bricogne, G. / Lescar, J.
CitationJournal: J.Bacteriol. / Year: 2012
Title: Structural insights into the regulatory mechanism of the response regulator RocR from Pseudomonas aeruginosa in cyclic Di-GMP signaling.
Authors: Chen, M.W. / Kotaka, M. / Vonrhein, C. / Bricogne, G. / Rao, F. / Chuah, M.L.C. / Svergun, D. / Schneider, G. / Liang, Z.X. / Lescar, J.
History
DepositionJul 16, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 18, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 21, 2013Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
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_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_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.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

Downloads & links

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Assembly

Deposited unit
A: RocR
B: RocR
C: RocR
D: RocR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)176,2469
Polymers175,9104
Non-polymers3365
Water3,027168
1
A: RocR
B: RocR
C: RocR
D: RocR
hetero molecules

A: RocR
B: RocR
C: RocR
D: RocR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)352,49118
Polymers351,8208
Non-polymers67110
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555x,x-y,-z+1/61
Buried area30620 Å2
ΔGint-188 kcal/mol
Surface area117460 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14000 Å2
ΔGint-87 kcal/mol
Surface area60040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.795, 118.795, 495.100
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein
RocR


Mass: 43977.516 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Gene: PA3947, rocR / Plasmid: pET26b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9HX69
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 168 / 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: 2.87 Å3/Da / Density % sol: 57.09 % / Mosaicity: 0.22 °
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 15-20% PEG 3350, 5% glycerol, 0.2M sodium tartrate, 0.1M sodium HEPES, pH 7.5, vapor diffusion, hanging drop, temperature 291K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 60623 / % possible obs: 82.9 % / Redundancy: 12 % / Rmerge(I) obs: 0.042 / Χ2: 1.187 / Net I/σ(I): 24.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.5-2.5990.62528880.97140.3
2.59-2.69100.46435261.135149.4
2.69-2.8210.80.30543540.983160.7
2.82-2.9611.30.20957031.043179.2
2.96-3.1512.90.14271031.113198.7
3.15-3.39130.08772021.21199.4
3.39-3.7312.70.05972531.348199.6
3.73-4.2712.70.03773221.269199.7
4.27-5.3812.50.0374321.171199.6
5.38-3011.40.02678401.296199

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.5.0102refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: SAD / Resolution: 2.5→19.96 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.901 / Occupancy max: 1 / Occupancy min: 1 / SU B: 23.76 / SU ML: 0.242 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.331 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2853 3044 5 %RANDOM
Rwork0.2162 ---
obs0.2197 60309 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 148.74 Å2 / Biso mean: 66.4872 Å2 / Biso min: 21.69 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å2-0.01 Å20 Å2
2---0.02 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.5→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11699 0 19 168 11886
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.02211933
X-RAY DIFFRACTIONr_angle_refined_deg1.6351.98116185
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.80551522
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.12424.04495
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.161152011
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.3271575
X-RAY DIFFRACTIONr_chiral_restr0.1090.21883
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0218899
X-RAY DIFFRACTIONr_mcbond_it0.7891.57608
X-RAY DIFFRACTIONr_mcangle_it1.518212196
X-RAY DIFFRACTIONr_scbond_it2.13734325
X-RAY DIFFRACTIONr_scangle_it3.5934.53989
LS refinement shellResolution: 2.503→2.567 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 94 -
Rwork0.31 1983 -
all-2077 -
obs--100 %
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)
11.30690.2772-0.96360.18510.06441.3094-0.05030.2427-0.0801-0.06710.0437-0.0324-0.1229-0.18710.00650.1132-0.029-0.0190.13040.01490.035751.097352.6499-15.8064
20.54720.2765-0.04190.8622-0.12730.2865-0.0340.0013-0.0665-0.08140.0092-0.0845-0.00580.0130.02480.07780.00720.00140.0339-0.01540.057958.298228.977314.2285
30.58130.1849-0.1610.2165-0.46211.5885-0.056-0.15960.0267-0.0144-0.0619-0.0508-0.35380.17290.11780.3416-0.0787-0.0190.07090.00160.048264.980670.613823.1401
40.91460.04020.10230.8975-0.48920.4923-0.1118-0.10280.2226-0.01920.05030.0055-0.1015-0.11010.06150.11550.0775-0.05440.0604-0.04920.07532.636563.875521.7834
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 392
2X-RAY DIFFRACTION2B1 - 392
3X-RAY DIFFRACTION3C2 - 392
4X-RAY DIFFRACTION4D3 - 398

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