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- PDB-3ulq: Crystal Structure of the Anti-Activator RapF Complexed with the R... -

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Basic information

Entry
Database: PDB / ID: 3ulq
TitleCrystal Structure of the Anti-Activator RapF Complexed with the Response Regulator ComA DNA Binding Domain
Components
  • Response regulator aspartate phosphatase F
  • Transcriptional regulatory protein ComA
KeywordsGENE REGULATION/TRANSCRIPTION ACTIVATOR / TETRATRICOPEPTIDE REPEAT / RESPONSE REGULATOR HELIX-TURN-HELX DNA BINDING / 3-HELIX BUNDLE / HYDROLASE-TRANSCRIPTION ACTIVATOR complex / GENE REGULATION-TRANSCRIPTION ACTIVATOR complex
Function / homology
Function and homology information


establishment of competence for transformation / phosphorelay signal transduction system / regulation of DNA-templated transcription / DNA binding / metal ion binding / cytoplasm
Similarity search - Function
response regulator aspartate phosphatase H, N terminal / Anaphase-promoting complex, cyclosome, subunit 3 / LuxR-type HTH domain signature. / LuxR-type HTH domain profile. / Transcription regulator LuxR, C-terminal / Bacterial regulatory proteins, luxR family / helix_turn_helix, Lux Regulon / Transcriptional regulatory protein WalR-like / Tetratricopeptide repeat / Signal transduction response regulator, C-terminal effector ...response regulator aspartate phosphatase H, N terminal / Anaphase-promoting complex, cyclosome, subunit 3 / LuxR-type HTH domain signature. / LuxR-type HTH domain profile. / Transcription regulator LuxR, C-terminal / Bacterial regulatory proteins, luxR family / helix_turn_helix, Lux Regulon / Transcriptional regulatory protein WalR-like / Tetratricopeptide repeat / Signal transduction response regulator, C-terminal effector / Tetratricopeptide repeat domain / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Arc Repressor Mutant, subunit A / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
: / Transcriptional regulatory protein ComA / Regulatory protein RapF
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsBaker, M.D. / Neiditch, M.B.
CitationJournal: Plos Biol. / Year: 2011
Title: Structural basis of response regulator inhibition by a bacterial anti-activator protein.
Authors: Baker, M.D. / Neiditch, M.B.
History
DepositionNov 11, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 4, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 25, 2012Group: Database references
Revision 1.2Sep 13, 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_initial_refinement_model / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_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: Response regulator aspartate phosphatase F
B: Transcriptional regulatory protein ComA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,8063
Polymers55,7512
Non-polymers551
Water1,62190
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1970 Å2
ΔGint-10 kcal/mol
Surface area22390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.304, 81.437, 78.346
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-407-

HOH

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Components

#1: Protein Response regulator aspartate phosphatase F


Mass: 45777.035 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: rapF, ywhJ, BSU37460 / Production host: Escherichia coli (E. coli)
References: UniProt: P71002, Hydrolases; Acting on ester bonds
#2: Protein Transcriptional regulatory protein ComA / Competence protein A


Mass: 9974.232 Da / Num. of mol.: 1 / Fragment: DNA Binding Domain, UNP residues 146-214
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: comA, comA1, comAA, BSU31680 / Production host: Escherichia coli (E. coli) / References: UniProt: P14204
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 90 / 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: 3.3 Å3/Da / Density % sol: 62.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 6% [w/v] PEG 8,000, 240 mM calcium acetate, 80 mM sodium cacodylate pH 6.5, and 20% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 18, 2009
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. obs: 33622 / Observed criterion σ(I): 3.28
Reflection shellResolution: 2.3→2.34 Å / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3Q15

3q15


Resolution: 2.3→19.762 Å / SU ML: 0.34 / σ(F): 1.34 / Phase error: 23.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2241 1686 5.08 %
Rwork0.1888 --
obs0.1906 33197 99.33 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.937 Å2 / ksol: 0.353 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.7364 Å2-0 Å20 Å2
2---2.1235 Å2-0 Å2
3---2.8599 Å2
Refinement stepCycle: LAST / Resolution: 2.3→19.762 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3641 0 1 90 3732
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083726
X-RAY DIFFRACTIONf_angle_d1.0335005
X-RAY DIFFRACTIONf_dihedral_angle_d14.4211413
X-RAY DIFFRACTIONf_chiral_restr0.07520
X-RAY DIFFRACTIONf_plane_restr0.003640
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.36760.311280.2542609X-RAY DIFFRACTION100
2.3676-2.44390.29631380.24152619X-RAY DIFFRACTION100
2.4439-2.53110.25841160.23982619X-RAY DIFFRACTION100
2.5311-2.63220.2841380.22012617X-RAY DIFFRACTION100
2.6322-2.75170.25871390.22862602X-RAY DIFFRACTION100
2.7517-2.89640.26611660.23362606X-RAY DIFFRACTION100
2.8964-3.07720.26761210.22242613X-RAY DIFFRACTION100
3.0772-3.31380.30981480.2112643X-RAY DIFFRACTION100
3.3138-3.64540.2171290.20052652X-RAY DIFFRACTION100
3.6454-4.16850.21141610.17082642X-RAY DIFFRACTION100
4.1685-5.23570.16931450.1442697X-RAY DIFFRACTION100
5.2357-19.7630.20381570.17662592X-RAY DIFFRACTION93
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)
14.822.0031-0.32646.5588-0.88552.83060.1247-0.35940.0880.295-0.23240.344-0.1386-0.0274-0.00050.3347-0.03840.03170.39220.00540.340530.1409-4.80519.1091
22.65580.25051.9241.96131.1081.7852-0.0381-0.2523-0.25040.19470.11450.01060.1582-0.15370.00030.3901-0.08180.00290.45270.07670.374245.1516-2.408517.023
32.4985-0.3221.61321.74041.5192.762-0.19940.15810.1461-0.08190.29270.1125-0.8495-0.14380.00050.5238-0.06490.02360.45230.04910.428352.16679.528922.5069
41.22720.952-0.7581.77890.47741.4712-0.235-0.2290.5339-0.13180.26280.2817-0.9906-0.17040.00020.73630.05980.010.3989-0.02820.483352.896519.346432.2885
51.80190.6769-1.54271.6560.02261.54830.2863-0.26360.2297-0.30110.23440.546-0.47670.1241-0.00030.70220.13270.03050.6566-0.12190.632546.783222.203543.6955
60.91860.029-0.41322.1136-0.73370.99060.0038-0.289-0.2630.1634-0.14811.1381-0.0956-0.89220.00010.56330.15330.08660.7352-0.09550.795538.317418.219352.5816
70.50670.16740.05150.95560.16080.0413-0.16380.0978-0.65090.4009-0.19261.17710.3668-0.6136-0.00040.67250.08860.16180.7699-0.07050.900239.07263.972755.0864
82.77240.30920.19411.999-0.44950.6509-0.2148-0.2192-0.09970.2733-0.05320.5337-0.4696-0.26550.00040.6740.13850.07760.63350.04780.485451.51821.730457.3592
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 6:72)
2X-RAY DIFFRACTION2(chain A and resid 94:133)
3X-RAY DIFFRACTION3(chain A and resid 137:173)
4X-RAY DIFFRACTION4(chain A and resid 178:215)
5X-RAY DIFFRACTION5(chain A and resid 218:254)
6X-RAY DIFFRACTION6(chain A and resid 258:295)
7X-RAY DIFFRACTION7(chain A and resid 298:330)
8X-RAY DIFFRACTION8(chain A and resid 333:368)

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