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- PDB-2a9p: Medium Resolution BeF3 bound RR02-rec -

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Basic information

Entry
Database: PDB / ID: 2a9p
TitleMedium Resolution BeF3 bound RR02-rec
ComponentsResponse regulator
KeywordsSIGNALING PROTEIN / Response regulator / Essential Protein / Phosphate binding / YycF / YycG
Function / homology
Function and homology information


phosphorelay signal transduction system / regulation of DNA-templated transcription / DNA binding / metal ion binding
Similarity search - Function
: / OmpR/PhoB-type DNA-binding domain / Transcriptional regulatory protein, C terminal / OmpR/PhoB-type DNA-binding domain profile. / Transcriptional regulatory protein, C terminal / Transcriptional regulatory protein WalR-like / Signal transduction response regulator, C-terminal effector / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain ...: / OmpR/PhoB-type DNA-binding domain / Transcriptional regulatory protein, C terminal / OmpR/PhoB-type DNA-binding domain profile. / Transcriptional regulatory protein, C terminal / Transcriptional regulatory protein WalR-like / Signal transduction response regulator, C-terminal effector / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Response regulator / Winged helix-like DNA-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
BERYLLIUM TRIFLUORIDE ION / : / Transcriptional regulatory protein WalR
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 Å
AuthorsRiboldi-Tunnicliffe, A. / Isaacs, N.W. / Mitchell, T.J.
CitationJournal: TO BE PUBLISHED
Title: Crystal structures of an activated YycF homologue, the essential response regulator from S.pneumoniae in complex with BeF3 and the effect of pH on BeF3 binding, possible phosphate in the active site.
Authors: Riboldi-Tunnicliffe, A. / Isaacs, N.W. / Mitchell, T.J.
History
DepositionJul 12, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 26, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 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_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_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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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_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_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_conn.ptnr2_label_seq_id / _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: Response regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7223
Polymers13,6011
Non-polymers1212
Water1,24369
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.705, 93.404, 37.611
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Response regulator


Mass: 13600.730 Da / Num. of mol.: 1 / Fragment: N-terminal Domain (RESIDUES 1-120)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9S1K0
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: BeF3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / 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: 2.41 Å3/Da / Density % sol: 49 %
Crystal growMethod: vapor diffusion, sitting drop / Details: VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R
DetectorType: NICOLET / Detector: DIFFRACTOMETER / Date: Jul 20, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.82→58.32 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.944 / SU B: 5.986 / SU ML: 0.082 / Cross valid method: THROUGHOUT / ESU R: 0.195 / ESU R Free: 0.114 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2059 611 5 %RANDOM
Rwork0.15639 ---
all0.159 ---
obs0.15876 11565 99.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.307 Å2
Baniso -1Baniso -2Baniso -3
1-2.05 Å20 Å20 Å2
2---1.72 Å20 Å2
3----0.33 Å2
Refinement stepCycle: LAST / Resolution: 1.82→58.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms970 0 5 69 1044
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.022978
X-RAY DIFFRACTIONr_angle_refined_deg1.8182.011326
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6015126
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.12625.85441
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.27915193
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.139155
X-RAY DIFFRACTIONr_chiral_restr0.170.2158
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02716
X-RAY DIFFRACTIONr_nbd_refined0.2250.2474
X-RAY DIFFRACTIONr_nbtor_refined0.3030.2699
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1490.273
X-RAY DIFFRACTIONr_metal_ion_refined0.1240.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2550.231
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4830.27
X-RAY DIFFRACTIONr_mcbond_it1.711.5636
X-RAY DIFFRACTIONr_mcangle_it2.58221006
X-RAY DIFFRACTIONr_scbond_it4.6063381
X-RAY DIFFRACTIONr_scangle_it6.654.5320
LS refinement shellResolution: 1.816→1.863 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 49 -
Rwork0.198 792 -
obs--95.35 %
Refinement TLS params.Method: refined / Origin x: 14.026 Å / Origin y: 35.2 Å / Origin z: 5.658 Å
111213212223313233
T0.0108 Å20.0127 Å20.003 Å2--0.0504 Å20.0022 Å2---0.0661 Å2
L0.1604 °2-0.3531 °20.1006 °2-3.6903 °2-0.9697 °2--0.4469 °2
S0.0097 Å °0.0218 Å °-0.0149 Å °0.1583 Å °0.0402 Å °0.0878 Å °-0.0236 Å °0.0235 Å °-0.0499 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 122 - 12
2X-RAY DIFFRACTION1AA13 - 2313 - 23
3X-RAY DIFFRACTION1AA24 - 3424 - 34
4X-RAY DIFFRACTION1AA35 - 4535 - 45
5X-RAY DIFFRACTION1AA46 - 5646 - 56
6X-RAY DIFFRACTION1AA57 - 6757 - 67
7X-RAY DIFFRACTION1AA68 - 7868 - 78
8X-RAY DIFFRACTION1AA79 - 8979 - 89
9X-RAY DIFFRACTION1AA90 - 10090 - 100
10X-RAY DIFFRACTION1AA101 - 111101 - 111
11X-RAY DIFFRACTION1AA112 - 118112 - 118

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