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- PDB-3p01: Crystal structure of two-component response regulator from Nostoc... -

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Basic information

Entry
Database: PDB / ID: 3p01
TitleCrystal structure of two-component response regulator from Nostoc sp. PCC 7120
ComponentsTwo-component response regulator
KeywordsSIGNALING PROTEIN / PSI-2 / Midwest Center for Structural Genomics / Protein Structure Initiative / MCSG / two-component response regulator
Function / homology
Function and homology information


phosphorelay signal transduction system / ATP binding
Similarity search - Function
Beta-Lactamase - #340 / Helix Hairpins - #590 / GAF domain / Transcriptional regulatory protein WalR-like / Helix Hairpins / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / GAF domain ...Beta-Lactamase - #340 / Helix Hairpins - #590 / GAF domain / Transcriptional regulatory protein WalR-like / Helix Hairpins / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / GAF domain / CheY-like superfamily / Domain present in phytochromes and cGMP-specific phosphodiesterases. / GAF domain / Beta-Lactamase / Helix non-globular / Special / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Two-component response regulator
Similarity search - Component
Biological speciesNostoc sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.65 Å
AuthorsChang, C. / Mack, J. / Feldman, B. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of two-component response regulator from Nostoc sp. PCC 7120
Authors: Chang, C. / Mack, J. / Feldman, B. / Joachimiak, A.
History
DepositionSep 27, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 6, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Two-component response regulator
B: Two-component response regulator
C: Two-component response regulator


Theoretical massNumber of molelcules
Total (without water)60,8773
Polymers60,8773
Non-polymers00
Water75742
1
A: Two-component response regulator

A: Two-component response regulator


Theoretical massNumber of molelcules
Total (without water)40,5852
Polymers40,5852
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_675x-y+1,-y+2,-z+1/31
Buried area2890 Å2
ΔGint-24 kcal/mol
Surface area16380 Å2
MethodPISA
2
B: Two-component response regulator
C: Two-component response regulator


Theoretical massNumber of molelcules
Total (without water)40,5852
Polymers40,5852
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2660 Å2
ΔGint-22 kcal/mol
Surface area16010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.876, 111.876, 112.837
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Two-component response regulator


Mass: 20292.484 Da / Num. of mol.: 3 / Fragment: sequence database residues 134-315
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nostoc sp. (bacteria) / Strain: PCC 7120 / Gene: alr5251 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) magic / References: UniProt: Q8YLP5
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 42 / 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: 3.35 Å3/Da / Density % sol: 63.27 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2M calcium acetate, 0.1M HEPES pH 7.5, 10% PEG8000, VAPOR DIFFUSION, SITTING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97935 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 9, 2010
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97935 Å / Relative weight: 1
ReflectionResolution: 2.65→50 Å / Num. all: 24056 / Num. obs: 23979 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 10.2 % / Biso Wilson estimate: 72.4 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 41.8
Reflection shellResolution: 2.65→2.7 Å / Redundancy: 8.4 % / Rmerge(I) obs: 0.545 / Mean I/σ(I) obs: 4.7 / Num. unique all: 1185 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
SHELXDphasing
SHELXEmodel building
MLPHAREphasing
DMphasing
RESOLVEphasing
Cootmodel building
ARP/wARPmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.65→50 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.911 / Occupancy max: 1 / Occupancy min: 0.75 / SU B: 27.283 / SU ML: 0.256 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.305
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2679 1206 5.1 %RANDOM
Rwork0.2283 ---
all0.2303 23627 --
obs0.2303 23627 98.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 233.51 Å2 / Biso mean: 80.749 Å2 / Biso min: 26.02 Å2
Baniso -1Baniso -2Baniso -3
1-2.63 Å21.31 Å20 Å2
2--2.63 Å20 Å2
3----3.94 Å2
Refinement stepCycle: LAST / Resolution: 2.65→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3892 0 0 42 3934
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0223941
X-RAY DIFFRACTIONr_angle_refined_deg1.4561.9485389
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5945519
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.66926.098164
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.70115638
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.51517
X-RAY DIFFRACTIONr_chiral_restr0.0960.2680
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212920
X-RAY DIFFRACTIONr_mcbond_it1.9931.52604
X-RAY DIFFRACTIONr_mcangle_it3.65724171
X-RAY DIFFRACTIONr_scbond_it3.00531337
X-RAY DIFFRACTIONr_scangle_it5.2094.51218
X-RAY DIFFRACTIONr_rigid_bond_restr1.71633941
LS refinement shellResolution: 2.653→2.722 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.396 69 -
Rwork0.308 1593 -
all-1662 -
obs-1275 94.86 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
116.3983-2.74850.77710.79210.58351.71540.35320.2272-0.0327-0.0621-0.12180.02490.1369-0.0829-0.23140.27580.0139-0.10510.1990.04820.48-14.695494.512514.5104
20.3411-0.1584-0.67361.20510.03761.4357-0.0084-0.01430.0265-0.03790.0635-0.1241-0.02540.0895-0.05510.2872-0.01190.01920.2137-0.0050.21538.770189.20753.6404
36.3244-12.65321.835325.3457-3.61980.63790.2758-0.1430.3198-0.8872-0.0911-0.6390.5363-0.2677-0.18461.4791-0.75270.02220.60040.12320.1473-14.807251.286922.8756
42.6447-0.8605-0.99412.0034-1.11621.58910.0921-0.47270.09250.34060.15570.147-0.37590.1777-0.24780.3936-0.11230.08610.2674-0.04690.2415-30.672773.943319.5506
50.34132.6187-1.035420.3095-7.83373.22490.1837-0.0668-0.07711.187-0.4682-0.4844-0.24140.18760.28440.4747-0.1025-0.14210.17790.02540.1909-9.781252.713513.299
60.34020.32470.35020.31190.31640.9290.1317-0.0182-0.02110.1352-0.0302-0.00760.18370.0387-0.10150.3816-0.0211-0.01080.19480.00290.2001-8.872167.0087-5.7423
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A142 - 159
2X-RAY DIFFRACTION2A160 - 313
3X-RAY DIFFRACTION3B142 - 159
4X-RAY DIFFRACTION4B160 - 313
5X-RAY DIFFRACTION5C142 - 159
6X-RAY DIFFRACTION6C160 - 313

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