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- PDB-3vv4: Crystal structure of cyanobacteriochrome TePixJ GAF domain -

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Basic information

Entry
Database: PDB / ID: 3vv4
TitleCrystal structure of cyanobacteriochrome TePixJ GAF domain
ComponentsMethyl-accepting chemotaxis proteinMethyl-accepting chemotaxis proteins
KeywordsSIGNALING PROTEIN / cyanobacteriochrome / phycoviolobilin binding
Function / homology
Function and homology information


chemotaxis / lysozyme activity / signal transduction / metal ion binding / plasma membrane
Similarity search - Function
Double Cache domain 1 / Cache domain / Phytochrome chromophore attachment domain / Phytochrome chromophore attachment site domain profile. / Methyl-accepting chemotaxis protein (MCP) signalling domain / Methyl-accepting chemotaxis protein (MCP) signalling domain / Bacterial chemotaxis sensory transducers domain profile. / Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer). / GAF domain / HAMP domain ...Double Cache domain 1 / Cache domain / Phytochrome chromophore attachment domain / Phytochrome chromophore attachment site domain profile. / Methyl-accepting chemotaxis protein (MCP) signalling domain / Methyl-accepting chemotaxis protein (MCP) signalling domain / Bacterial chemotaxis sensory transducers domain profile. / Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer). / GAF domain / HAMP domain / HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain / HAMP domain profile. / HAMP domain / GAF domain / Domain present in phytochromes and cGMP-specific phosphodiesterases. / GAF domain / GAF-like domain superfamily / Beta-Lactamase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Phycoviolobilin, green light-absorbing form / Methyl-accepting chemotaxis protein
Similarity search - Component
Biological speciesThermosynechococcus elongatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsIshizuka, T. / Narikawa, R. / Muraki, N. / Shiba, T. / Kurisu, G. / Ikeuchi, M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Structures of cyanobacteriochromes from phototaxis regulators AnPixJ and TePixJ reveal general and specific photoconversion mechanism
Authors: Narikawa, R. / Ishizuka, T. / Muraki, N. / Shiba, T. / Kurisu, G. / Ikeuchi, M.
History
DepositionJul 14, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 30, 2013Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Methyl-accepting chemotaxis protein
B: Methyl-accepting chemotaxis protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,1448
Polymers44,5822
Non-polymers1,5626
Water2,000111
1
A: Methyl-accepting chemotaxis protein
hetero molecules

B: Methyl-accepting chemotaxis protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,1448
Polymers44,5822
Non-polymers1,5626
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_545-x+y,-x-1,z+1/31
Buried area1630 Å2
ΔGint-9 kcal/mol
Surface area16050 Å2
MethodPISA
2
B: Methyl-accepting chemotaxis protein
hetero molecules

A: Methyl-accepting chemotaxis protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,1448
Polymers44,5822
Non-polymers1,5626
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_444-y-1,x-y-1,z-1/31
Unit cell
Length a, b, c (Å)72.868, 72.868, 166.667
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1113A6 - 201
2113B6 - 201

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Components

#1: Protein Methyl-accepting chemotaxis protein / Methyl-accepting chemotaxis proteins / TePixJ


Mass: 22291.098 Da / Num. of mol.: 2 / Fragment: GAF domain, UNP residues 430-591
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermosynechococcus elongatus (bacteria)
Strain: BP-1 / Gene: tll0569 / Production host: Synechocystis (bacteria) / Strain (production host): PCC6803 / References: UniProt: Q8DLC7
#2: Chemical ChemComp-PVG / Phycoviolobilin, green light-absorbing form


Mass: 588.694 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C33H40N4O6
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 111 / 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: 2.87 Å3/Da / Density % sol: 57.07 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: 1.15M ammonium sulfate, 100mM MES buffer, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 11, 2011
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→100 Å / Num. all: 39334 / Num. obs: 36534 / % possible obs: 92.88 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2
Reflection shellResolution: 1.95→2.02 Å / Rmerge(I) obs: 0.566 / Mean I/σ(I) obs: 2.2 / % possible all: 71

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→59.02 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.95 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 6.994 / SU ML: 0.097 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.144 / ESU R Free: 0.139 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2232 1606 5 %RANDOM
Rwork0.1855 30434 --
obs0.1874 32040 94.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 138.52 Å2 / Biso mean: 45.75 Å2 / Biso min: 17.87 Å2
Baniso -1Baniso -2Baniso -3
1--0.13 Å2-0.06 Å20 Å2
2---0.13 Å20 Å2
3---0.19 Å2
Refinement stepCycle: LAST / Resolution: 2→59.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2522 0 106 111 2739
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.022680
X-RAY DIFFRACTIONr_angle_refined_deg1.4951.9883650
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1735311
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.2923.942137
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.52215438
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6231524
X-RAY DIFFRACTIONr_chiral_restr0.120.2400
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.0212060
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
655MEDIUM POSITIONAL0.140.5
623LOOSE POSITIONAL0.475
655MEDIUM THERMAL3.292
623LOOSE THERMAL6.2210
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 95 -
Rwork0.26 1898 -
all-1993 -
obs--79.56 %
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)
11.3597-0.2149-0.14380.93440.04242.4442-0.06550.0616-0.1102-0.0774-0.02590.0020.2378-0.25460.09140.0796-0.06350.01110.0839-0.0310.0391-7.225-20.79-15.415
21.27450.16850.44251.840.48052.38960.0568-0.03650.06970.3076-0.0975-0.044-0.20040.03160.04070.1235-0.0587-0.01770.0449-0.00610.0802-13.273-44.21-41.248
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 158
2X-RAY DIFFRACTION1A201
3X-RAY DIFFRACTION2B-1 - 158
4X-RAY DIFFRACTION2B201

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