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- PDB-1nxw: MicArec pH 5.1 -

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Basic information

Entry
Database: PDB / ID: 1nxw
TitleMicArec pH 5.1
ComponentsDNA-binding response regulator
KeywordsSIGNALING PROTEIN / doubly wound 5 alpha - 5 beta structure
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
ACETIC ACID / Transcriptional regulatory protein WalR
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 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: Advisory / Source and taxonomy / Version format compliance
Revision 1.3Aug 16, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: DNA-binding response regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,6612
Polymers13,6011
Non-polymers601
Water1,00956
1
A: DNA-binding response regulator
hetero molecules

A: DNA-binding response regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,3224
Polymers27,2012
Non-polymers1202
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Unit cell
Length a, b, c (Å)78.353, 92.622, 36.892
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-154-

HOH

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: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 2.4 Å3/Da / Density % sol: 48.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.1
Details: PEG 300, Sodium acetate, pH 5.1, 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: ESRF / Beamline: BM14 / Wavelength: 1.024 Å
DetectorType: MACSCIENCE / Detector: CCD / Date: Dec 5, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.024 Å / Relative weight: 1
ReflectionResolution: 1.92→28.87 Å / Num. obs: 10522 / % possible obs: 99.04 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 28.02 Å2
Reflection shellResolution: 1.919→1.969 Å / % possible all: 98.6
Reflection
*PLUS
Num. measured all: 345059 / Rmerge(I) obs: 0.045
Reflection shell
*PLUS
% possible obs: 99 % / Rmerge(I) obs: 0.211 / Mean I/σ(I) obs: 3.6

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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: 1.92→28.87 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.94 / SU B: 3.686 / SU ML: 0.105 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.155 / ESU R Free: 0.144 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22382 1018 9.7 %RANDOM
Rwork0.1846 ---
obs0.18839 9519 99.04 %-
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: 28.022 Å2
Baniso -1Baniso -2Baniso -3
1-3.61 Å20 Å20 Å2
2---2.21 Å20 Å2
3----1.39 Å2
Refinement stepCycle: LAST / Resolution: 1.92→28.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms935 0 4 56 995
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.022941
X-RAY DIFFRACTIONr_bond_other_d0.0020.02913
X-RAY DIFFRACTIONr_angle_refined_deg1.662.0021265
X-RAY DIFFRACTIONr_angle_other_deg0.90232129
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1415117
X-RAY DIFFRACTIONr_chiral_restr0.1070.2150
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021013
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02169
X-RAY DIFFRACTIONr_nbd_refined0.2480.2203
X-RAY DIFFRACTIONr_nbd_other0.250.21054
X-RAY DIFFRACTIONr_nbtor_other0.0930.2606
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2420.236
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2610.215
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3330.255
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4980.210
X-RAY DIFFRACTIONr_mcbond_it1.0041.5591
X-RAY DIFFRACTIONr_mcangle_it1.8792957
X-RAY DIFFRACTIONr_scbond_it2.7973350
X-RAY DIFFRACTIONr_scangle_it4.8754.5308
LS refinement shellResolution: 1.919→1.969 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.193 60
Rwork0.225 656
Refinement TLS params.Method: refined / Origin x: 63.549 Å / Origin y: 10.873 Å / Origin z: 5.444 Å
111213212223313233
T0.0343 Å20.0359 Å2-0.0212 Å2-0.044 Å2-0.0029 Å2--0.0699 Å2
L0.7285 °2-0.7438 °2-0.3426 °2-2.3785 °20.4417 °2--0.7544 °2
S-0.053 Å °-0.0287 Å °0.0214 Å °0.1002 Å °0.0472 Å °-0.0081 Å °0.039 Å °-0.0457 Å °0.0058 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 242 - 24
2X-RAY DIFFRACTION1AA25 - 4425 - 44
3X-RAY DIFFRACTION1AA45 - 5445 - 54
4X-RAY DIFFRACTION1AA58 - 7058 - 70
5X-RAY DIFFRACTION1AA71 - 9471 - 94
6X-RAY DIFFRACTION1AA95 - 11995 - 119
Refinement
*PLUS
Rfactor Rfree: 0.2238
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Rfactor Rfree: 0.194 / Rfactor Rwork: 0.228

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