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- PDB-1nxt: MicArec pH 4.0 -

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Basic information

Entry
Database: PDB / ID: 1nxt
TitleMicArec pH 4.0
ComponentsDNA-binding response regulator
KeywordsSIGNALING PROTEIN / doubly wound 5 alpha / 5 beta fold
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
XENON / Transcriptional regulatory protein WalR
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD Xenon/Sulphur / Resolution: 2.34 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

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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)13,8122
Polymers13,6811
Non-polymers1311
Water54030
1
A: DNA-binding response regulator
hetero molecules

A: DNA-binding response regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6244
Polymers27,3612
Non-polymers2632
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
Unit cell
Length a, b, c (Å)79.673, 92.829, 36.789
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Detailshe 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: 13680.710 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-XE / XENON


Mass: 131.293 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Xe
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / 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: 2.54 Å3/Da / Density % sol: 51.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 40%v/v PEG 300, 100mM Phosphate Citrate, pH 4.0, 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: ELETTRA / Beamline: 5.2R / Wavelength: 1.8 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 29, 2002
RadiationMonochromator: 1.8 / Protocol: SAD using Sulphur and Xenon / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.8 Å / Relative weight: 1
ReflectionResolution: 2.34→30.86 Å / Num. obs: 5398 / % possible obs: 98.96 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 39.55 Å2 / Rsym value: 0.052 / Net I/σ(I): 11.6
Reflection shellResolution: 2.342→2.402 Å / Mean I/σ(I) obs: 5.1 / Rsym value: 0.116 / % possible all: 97.3
Reflection
*PLUS
Num. measured all: 110950 / Rmerge(I) obs: 0.052
Reflection shell
*PLUS
Rmerge(I) obs: 0.116

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Processing

Software
NameVersionClassification
REFMAC5.1.27refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
SHARPphasing
RefinementMethod to determine structure: SAD Xenon/Sulphur / Resolution: 2.34→30.86 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.911 / SU B: 11.526 / SU ML: 0.259 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R: 0.396 / ESU R Free: 0.239 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23556 579 9.7 %RANDOM
Rwork0.2141 ---
obs0.21614 5398 98.96 %-
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: 39.556 Å2
Baniso -1Baniso -2Baniso -3
1-2.61 Å20 Å20 Å2
2---1.28 Å20 Å2
3----1.33 Å2
Refinement stepCycle: LAST / Resolution: 2.34→30.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms922 0 1 30 953
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.022921
X-RAY DIFFRACTIONr_bond_other_d00.02889
X-RAY DIFFRACTIONr_angle_refined_deg1.8382.0131239
X-RAY DIFFRACTIONr_angle_other_deg3.78832068
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4765114
X-RAY DIFFRACTIONr_chiral_restr0.1120.2147
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02983
X-RAY DIFFRACTIONr_gen_planes_other0.0130.02167
X-RAY DIFFRACTIONr_nbd_refined0.2220.2198
X-RAY DIFFRACTIONr_nbd_other0.2790.2906
X-RAY DIFFRACTIONr_nbtor_other0.110.2473
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.3310.225
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2160.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3030.251
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2350.25
X-RAY DIFFRACTIONr_mcbond_it1.0581.5575
X-RAY DIFFRACTIONr_mcangle_it1.9722931
X-RAY DIFFRACTIONr_scbond_it2.9283346
X-RAY DIFFRACTIONr_scangle_it5.3684.5308
LS refinement shellResolution: 2.342→2.402 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.247 41
Rwork0.301 357
Refinement TLS params.Method: refined / Origin x: 64.7686 Å / Origin y: 57.3347 Å / Origin z: 5.4721 Å
111213212223313233
T0.0151 Å20.0112 Å2-0.0047 Å2-0.0109 Å2-0.0006 Å2--0.0047 Å2
L0.3313 °2-0.2105 °2-0.059 °2-1.0424 °20.2223 °2--0.1837 °2
S-0.006 Å °0.0129 Å °0.0078 Å °0.032 Å °0.0128 Å °-0.0424 Å °0.0015 Å °-0.0309 Å °-0.0067 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 DIFFRACTION1AA59 - 7059 - 70
5X-RAY DIFFRACTION1AA71 - 9471 - 94
6X-RAY DIFFRACTION1AA95 - 11995 - 119
Refinement
*PLUS
Rfactor Rfree: 0.2376 / Rfactor Rwork: 0.1899
Solvent computation
*PLUS
Displacement parameters
*PLUS

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