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- PDB-1nxo: MicArec pH7.0 -

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Basic information

Entry
Database: PDB / ID: 1nxo
TitleMicArec pH7.0
ComponentsDNA-binding response regulator
KeywordsSIGNALING PROTEIN / doubly wound 5 alpha 5 beta fold
Function / homology
Function and homology information


phosphorelay response regulator activity / protein-DNA complex / transcription cis-regulatory region binding / regulation of DNA-templated transcription / metal ion binding / cytosol
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
Transcriptional regulatory protein WalR
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsBent, C.J. / Isaacs, N.W. / Mitchell, T.J. / Riboldi-Tunnicliffe, A.
CitationJournal: J.Bacteriol. / Year: 2004
Title: Crystal structure of the response regulator 02 receiver domain, the essential YycF two-component system of Streptococcus pneumoniae in both complexed and native states.
Authors: Bent, C.J. / Isaacs, N.W. / Mitchell, T.J. / Riboldi-Tunnicliffe, A.
History
DepositionFeb 11, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 17, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA-binding response regulator


Theoretical massNumber of molelcules
Total (without water)13,6011
Polymers13,6011
Non-polymers00
Water1,15364
1
A: DNA-binding response regulator

A: DNA-binding response regulator


Theoretical massNumber of molelcules
Total (without water)27,2012
Polymers27,2012
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
Unit cell
Length a, b, c (Å)80.308, 92.512, 36.520
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsThe second part of the biological assembly is generated by the two fold axis: x, -y, -z

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Components

#1: Protein DNA-binding response regulator


Mass: 13600.730 Da / Num. of mol.: 1 / Fragment: MicA receiver domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Strain: TIGR4 / Plasmid: PET33B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9S1K0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / 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: 2.46 Å3/Da / Density % sol: 49.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 40%v/v PEG 300, 5%w/v PEG 1,000, 100mM Tris, , pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7.5 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
125 mMTris-HCl1drop
2300 mM1droppH7.5NaCl
310 mg/mlprotein1drop
430 %(v/v)PEG3001reservoir
50.1 MTris-HCl1reservoirpH7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 0.978 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 14, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.85→40.16 Å / Num. all: 19291 / Num. obs: 12010 / % possible obs: 99.43 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 28.22 Å2 / Rsym value: 0.084 / Net I/σ(I): 7
Reflection shellResolution: 1.85→1.898 Å / Mean I/σ(I) obs: 2.4 / Rsym value: 0.537 / % possible all: 99.3
Reflection
*PLUS
Num. measured all: 260225 / Rmerge(I) obs: 0.084
Reflection shell
*PLUS
% possible obs: 100 % / Rmerge(I) obs: 0.237

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Processing

Software
NameVersionClassification
REFMAC5.1.27refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1NXT

1nxt


Resolution: 1.85→40.16 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.943 / SU B: 3.43 / SU ML: 0.101 / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R: 0.223 / ESU R Free: 0.127 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22338 1160 9.7 %RANDOM
Rwork0.17594 ---
obs0.18062 10782 99.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 28.222 Å2
Baniso -1Baniso -2Baniso -3
1-3.51 Å20 Å20 Å2
2---2.4 Å20 Å2
3----1.11 Å2
Refinement stepCycle: LAST / Resolution: 1.85→40.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms920 0 0 64 984
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.022899
X-RAY DIFFRACTIONr_bond_other_d0.0020.02865
X-RAY DIFFRACTIONr_angle_refined_deg1.5321.9881210
X-RAY DIFFRACTIONr_angle_other_deg0.8632004
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7625114
X-RAY DIFFRACTIONr_chiral_restr0.0930.2146
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02978
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02163
X-RAY DIFFRACTIONr_nbd_refined0.2370.2164
X-RAY DIFFRACTIONr_nbd_other0.250.2920
X-RAY DIFFRACTIONr_nbtor_other0.0870.2588
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.4150.243
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2670.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.340.244
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4780.216
X-RAY DIFFRACTIONr_mcbond_it1.3581.5573
X-RAY DIFFRACTIONr_mcangle_it2.1752926
X-RAY DIFFRACTIONr_scbond_it3.6153326
X-RAY DIFFRACTIONr_scangle_it5.7144.5284
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.308 86
Rwork0.233 774
Refinement TLS params.Method: refined / Origin x: 15.055 Å / Origin y: 35.368 Å / Origin z: 5.533 Å
111213212223313233
T0.01 Å20.0199 Å20.0114 Å2-0.0697 Å2-0.0031 Å2--0.0347 Å2
L0.468 °2-0.807 °20.1222 °2-2.9696 °2-0.2769 °2--0.5255 °2
S-0.0008 Å °-0.0338 Å °-0.0587 Å °0.0513 Å °0.0067 Å °0.125 Å °-0.0625 Å °0.0072 Å °-0.006 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 222 - 22
2X-RAY DIFFRACTION1AA23 - 4423 - 44
3X-RAY DIFFRACTION1AA43 - 6643 - 66
4X-RAY DIFFRACTION1AA67 - 8867 - 88
5X-RAY DIFFRACTION1AA89 - 11089 - 110
6X-RAY DIFFRACTION1AA111 - 119111 - 119
Refinement
*PLUS
Rfactor Rfree: 0.2181 / Rfactor Rwork: 0.1659
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Rfactor Rfree: 0.314 / Rfactor Rwork: 0.236

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