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- PDB-3q9v: Crystal structure of rra c-terminal domain(123-221) from Deinococ... -

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Entry
Database: PDB / ID: 3q9v
TitleCrystal structure of rra c-terminal domain(123-221) from Deinococcus radiodurans
ComponentsDNA-binding response regulator
KeywordsDNA BINDING PROTEIN / response regulator protein
Function / homology
Function and homology information


phosphorelay response regulator activity / protein-DNA complex / transcription cis-regulatory region binding / regulation of DNA-templated transcription / cytosol
Similarity search - Function
OmpR/PhoB-type DNA-binding domain profile. / OmpR/PhoB-type DNA-binding domain / Transcriptional regulatory protein, C terminal / Transcriptional regulatory protein, C terminal / Transcriptional regulatory protein WalR-like / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily ...OmpR/PhoB-type DNA-binding domain profile. / OmpR/PhoB-type DNA-binding domain / Transcriptional regulatory protein, C terminal / Transcriptional regulatory protein, C terminal / Transcriptional regulatory protein WalR-like / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA-binding response regulator
Similarity search - Component
Biological speciesDeinococcus radiodurans (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.60174363532 Å
AuthorsLiu, Y. / Gao, Z.Q. / Dong, Y.H. / Ji, C.N.
Funding support China, 1items
OrganizationGrant numberCountry
National Basic Research Program of China (973 Program)2009CB918600 China
CitationJournal: To be Published
Title: Crystal structure of rra c-terminal domain (123-221) from Deinococcus radiodurans.
Authors: Liu, Y. / Gao, Z.Q. / Dong, Y.H. / Ji, C.N.
History
DepositionJan 10, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 11, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Feb 23, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _struct_ref_seq_dif.details
Revision 1.3Jul 27, 2022Group: Advisory / Author supporting evidence ...Advisory / Author supporting evidence / Data collection / Database references / Other / Refinement description / Source and taxonomy / Structure summary
Category: diffrn / entity ...diffrn / entity / entity_src_gen / pdbx_audit_support / pdbx_contact_author / pdbx_database_status / pdbx_distant_solvent_atoms / refine / refine_ls_shell / reflns / reflns_shell / struct / struct_ref_seq_dif
Item: _diffrn.pdbx_serial_crystal_experiment / _entity.details ..._diffrn.pdbx_serial_crystal_experiment / _entity.details / _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_seq_type / _pdbx_contact_author.id / _pdbx_contact_author.identifier_ORCID / _pdbx_contact_author.name_salutation / _pdbx_database_status.SG_entry / _refine.occupancy_max / _refine.occupancy_min / _refine.overall_FOM_work_R_set / _refine.pdbx_ls_cross_valid_method / _refine_ls_shell.d_res_high / _refine_ls_shell.d_res_low / _refine_ls_shell.number_reflns_all / _refine_ls_shell.pdbx_total_number_of_bins_used / _reflns.number_all / _reflns.pdbx_netI_over_sigmaI / _reflns_shell.number_unique_all / _reflns_shell.number_unique_obs / _struct.pdbx_CASP_flag / _struct_ref_seq_dif.details
Revision 2.0Aug 3, 2022Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Experimental preparation / Other / Refinement description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / atom_sites / cell / entity / exptl_crystal_grow / pdbx_distant_solvent_atoms / pdbx_nonpoly_scheme / pdbx_refine_tls / pdbx_refine_tls_group / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_sheet_hbond / pdbx_struct_special_symmetry / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_symm_contact / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / reflns / software / struct_conf / struct_mon_prot_cis / struct_sheet / struct_sheet_order / struct_sheet_range / symmetry
Item: _atom_sites.fract_transf_matrix[1][3] / _cell.volume ..._atom_sites.fract_transf_matrix[1][3] / _cell.volume / _entity.pdbx_number_of_molecules / _exptl_crystal_grow.pdbx_details / _refine.B_iso_max / _refine.B_iso_mean / _refine.B_iso_min / _refine.aniso_B[1][1] / _refine.aniso_B[1][2] / _refine.aniso_B[1][3] / _refine.aniso_B[2][2] / _refine.aniso_B[2][3] / _refine.aniso_B[3][3] / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_all / _refine.ls_R_factor_obs / _refine.ls_d_res_high / _refine.ls_d_res_low / _refine.ls_number_reflns_R_work / _refine.ls_number_reflns_all / _refine.ls_percent_reflns_R_free / _refine.ls_percent_reflns_obs / _refine.overall_SU_ML / _refine.pdbx_ls_sigma_F / _refine.pdbx_overall_phase_error / _refine.pdbx_stereochemistry_target_values / _refine.solvent_model_param_bsol / _refine.solvent_model_param_ksol / _refine_hist.d_res_high / _refine_hist.d_res_low / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_ls_restr.dev_ideal / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work / _refine_ls_shell.d_res_high / _refine_ls_shell.d_res_low / _refine_ls_shell.number_reflns_R_work / _refine_ls_shell.percent_reflns_obs / _reflns.B_iso_Wilson_estimate / _struct_conf.beg_auth_comp_id / _struct_conf.beg_auth_seq_id / _struct_conf.beg_label_comp_id / _struct_conf.beg_label_seq_id / _struct_conf.end_auth_comp_id / _struct_conf.end_auth_seq_id / _struct_conf.end_label_comp_id / _struct_conf.end_label_seq_id / _struct_conf.pdbx_PDB_helix_id / _struct_conf.pdbx_PDB_helix_length / _symmetry.space_group_name_Hall
Revision 2.1Aug 17, 2022Group: Database references / Category: citation / Item: _citation.title
Revision 2.2Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA-binding response regulator
B: DNA-binding response regulator


Theoretical massNumber of molelcules
Total (without water)29,8702
Polymers29,8702
Non-polymers00
Water3,999222
1
A: DNA-binding response regulator

B: DNA-binding response regulator


Theoretical massNumber of molelcules
Total (without water)29,8702
Polymers29,8702
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area3480 Å2
ΔGint-13 kcal/mol
Surface area11000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.251, 37.602, 48.573
Angle α, β, γ (deg.)90.000, 113.920, 90.000
Int Tables number3
Space group name H-MP121
Space group name HallP2y
Components on special symmetry positions
IDModelComponents
11A-7-

HOH

21A-28-

HOH

31A-285-

HOH

41B-288-

HOH

51B-297-

HOH

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Components

#1: Protein DNA-binding response regulator


Mass: 14934.901 Da / Num. of mol.: 2 / Fragment: c-terminal domain
Source method: isolated from a genetically manipulated source
Details: The sequence conflicts of 216-221 are come from the error in database
Source: (gene. exp.) Deinococcus radiodurans (radioresistant)
Strain: ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422
Gene: DR_2418 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9RRR8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 222 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE DEPOSITORS ARE SURE THAT THIS SEQUENCE IS CORRECT, DATABASE SEQUENCE IS WRONG.

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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: 1.85 Å3/Da / Density % sol: 33.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.8 / Details: 0.1 M CH3COONa, 3.1 M NaCl, pH 4.8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BSRF / Beamline: 3W1A / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jul 12, 2010
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 21545 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Biso Wilson estimate: 16.8433553354 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 26.5
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.307 / Num. unique obs: 2158 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
PHASERphasing
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Code 3Q9S

3q9s


Resolution: 1.60174363532→28.8599869657 Å / SU ML: 0.192658065937 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.6579633727
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.23028658528 1107 5.13856008912 %RANDOM
Rwork0.1929616372 20436 --
obs0.194947534671 21543 99.4965823019 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.53712932 Å2
Refinement stepCycle: LAST / Resolution: 1.60174363532→28.8599869657 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1566 0 0 222 1788
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007491181992071595
X-RAY DIFFRACTIONf_angle_d0.9694074933452147
X-RAY DIFFRACTIONf_chiral_restr0.0503283554588236
X-RAY DIFFRACTIONf_plane_restr0.00567977539697281
X-RAY DIFFRACTIONf_dihedral_angle_d16.8655265506629
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6017-1.67460.2492388500961330.1954402364892511X-RAY DIFFRACTION97.6005906238
1.6746-1.76290.2940323758651300.1987228349882548X-RAY DIFFRACTION100
1.7629-1.87330.2449263753231280.2007279672472554X-RAY DIFFRACTION100
1.8733-2.0180.2309197876161450.1878306046792508X-RAY DIFFRACTION99.9623210249
2.018-2.2210.2241192729071260.1829331091392600X-RAY DIFFRACTION100
2.221-2.54220.2230931350911630.1914421156632525X-RAY DIFFRACTION100
2.5422-3.20220.2276965815161340.2008162310172584X-RAY DIFFRACTION99.8897464168
3.2022-28.86470.2240764968781480.1910749300432606X-RAY DIFFRACTION98.5683607731

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