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- PDB-4nic: Crystal structure of Klebsiella pneumoniae RstA BeF3-activated N-... -

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Basic information

Entry
Database: PDB / ID: 4nic
TitleCrystal structure of Klebsiella pneumoniae RstA BeF3-activated N-terminal receiver domain
ComponentsDNA-binding transcriptional regulator RstA
KeywordsTRANSCRIPTION REGULATOR / Two-Component System / response regulator
Function / homologyResponse regulator / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / BERYLLIUM TRIFLUORIDE ION / :
Function and homology information
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.18 Å
AuthorsLi, Y.C. / Hsiao, C.D.
CitationJournal: Nucleic Acids Res. / Year: 2014
Title: Structural dynamics of the two-component response regulator RstA in recognition of promoter DNA element.
Authors: Li, Y.C. / Chang, C.K. / Chang, C.F. / Cheng, Y.H. / Fang, P.J. / Yu, T. / Chen, S.C. / Li, Y.C. / Hsiao, C.D. / Huang, T.H.
History
DepositionNov 6, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 16, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 13, 2014Group: Database references
Revision 1.2Feb 28, 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_label_asym_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: DNA-binding transcriptional regulator RstA
B: DNA-binding transcriptional regulator RstA
C: DNA-binding transcriptional regulator RstA
D: DNA-binding transcriptional regulator RstA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,08412
Polymers57,7234
Non-polymers3618
Water68538
1
A: DNA-binding transcriptional regulator RstA
B: DNA-binding transcriptional regulator RstA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0426
Polymers28,8612
Non-polymers1814
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1980 Å2
ΔGint-18 kcal/mol
Surface area10930 Å2
MethodPISA
2
C: DNA-binding transcriptional regulator RstA
D: DNA-binding transcriptional regulator RstA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0426
Polymers28,8612
Non-polymers1814
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2040 Å2
ΔGint-18 kcal/mol
Surface area11090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.475, 113.475, 243.685
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein
DNA-binding transcriptional regulator RstA / RstA protein


Mass: 14430.747 Da / Num. of mol.: 4 / Fragment: N-terminal receiver domain (UNP residues 2-119)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: rstA, KPN2242_10390, KPR_2822 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: G0GNT0
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 38 / 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: 3.92 Å3/Da / Density % sol: 68.65 %
Crystal growTemperature: 299 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 100 mM Bis-Tris, 25% PEG3350, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 299K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 0.97891 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 17, 2011
RadiationMonochromator: LN2-cooled, fixed-exit double crystal Si(111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97891 Å / Relative weight: 1
ReflectionResolution: 3.1→30 Å / Num. all: 16342 / Num. obs: 15850 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6 % / Rmerge(I) obs: 0.116 / Rsym value: 0.116 / Net I/σ(I): 15.689
Reflection shellResolution: 3.1→3.21 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.354 / Mean I/σ(I) obs: 6.8 / % possible all: 99.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 3.18→26.598 Å / SU ML: 0.31 / σ(F): 0.32 / Phase error: 21.52 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2227 1584 10 %RANDOM
Rwork0.187 ---
obs0.1906 15845 97.23 %-
all-15845 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.18→26.598 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3652 0 20 38 3710
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013720
X-RAY DIFFRACTIONf_angle_d1.3695040
X-RAY DIFFRACTIONf_dihedral_angle_d18.7671432
X-RAY DIFFRACTIONf_chiral_restr0.089600
X-RAY DIFFRACTIONf_plane_restr0.007648
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.18-3.28270.29411360.26381230X-RAY DIFFRACTION95
3.2827-3.39980.36011410.22851268X-RAY DIFFRACTION97
3.3998-3.53570.26331390.22121254X-RAY DIFFRACTION96
3.5357-3.69620.23171390.21051253X-RAY DIFFRACTION97
3.6962-3.89050.2421410.19631263X-RAY DIFFRACTION97
3.8905-4.13340.22851430.18171288X-RAY DIFFRACTION97
4.1334-4.45120.22721450.1711302X-RAY DIFFRACTION99
4.4512-4.89660.18011440.15061300X-RAY DIFFRACTION98
4.8966-5.59940.21161480.18091334X-RAY DIFFRACTION99
5.5994-7.0330.23371510.20171357X-RAY DIFFRACTION99
7.033-26.59940.17351570.16821412X-RAY DIFFRACTION96

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