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- PDB-1mzu: Crystal Structure of the Photoactive Yellow Protein Domain from t... -

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Basic information

Entry
Database: PDB / ID: 1mzu
TitleCrystal Structure of the Photoactive Yellow Protein Domain from the Sensor Histidine Kinase Ppr from Rhodospirillum centenum
ComponentsPPR
KeywordsSIGNALING PROTEIN / photoactive yellow protein / PAS / PYP / Ppr
Function / homology
Function and homology information


detection of visible light / : / photoreceptor activity / phosphorelay sensor kinase activity / phototransduction / regulation of DNA-templated transcription
Similarity search - Function
Phytochrome / Photoactive yellow-protein / Phytochrome, PHY domain superfamily / PAS fold-2 / PAS fold / Phytochrome, central region / Phytochrome region / Phytochrome chromophore attachment domain / Phytochrome chromophore attachment site domain profile. / His Kinase A (phospho-acceptor) domain ...Phytochrome / Photoactive yellow-protein / Phytochrome, PHY domain superfamily / PAS fold-2 / PAS fold / Phytochrome, central region / Phytochrome region / Phytochrome chromophore attachment domain / Phytochrome chromophore attachment site domain profile. / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / PAS domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / Histidine kinase domain / Histidine kinase domain profile. / GAF domain / Domain present in phytochromes and cGMP-specific phosphodiesterases. / GAF domain / GAF-like domain superfamily / Beta-Lactamase / PAS repeat profile. / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / PAS domain / PAS domain superfamily / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
4'-HYDROXYCINNAMIC ACID / PPH
Similarity search - Component
Biological speciesRhodospirillum centenum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsRajagopal, S. / Moffat, K.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2003
Title: Crystal Structure of a Photoactive Yellow Protein from a Sensor Histidine Kinase: Conformational Variability and Signal Transduction
Authors: Rajagopal, S. / Moffat, K.
History
DepositionOct 9, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 25, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 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: PPR
B: PPR
C: PPR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,0366
Polymers43,5433
Non-polymers4923
Water2,054114
1
A: PPR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6792
Polymers14,5141
Non-polymers1641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PPR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6792
Polymers14,5141
Non-polymers1641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: PPR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6792
Polymers14,5141
Non-polymers1641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.560, 143.070, 36.450
Angle α, β, γ (deg.)90.00, 117.96, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein PPR


Mass: 14514.385 Da / Num. of mol.: 3 / Fragment: N-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodospirillum centenum (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9X2W8
#2: Chemical ChemComp-HC4 / 4'-HYDROXYCINNAMIC ACID / PARA-COUMARIC ACID / P-Coumaric acid


Mass: 164.158 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C9H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 114 / 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: 3

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Sample preparation

CrystalDensity Matthews: 1.83 Å3/Da / Density % sol: 32.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 36% PEG 6K, 10 mM Tris, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
112 mg/mlprotein1drop
236 %PEG60001reservoir
310 mMMES1reservoirpH7.0

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 5, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→29.86 Å / Num. all: 19081 / Num. obs: 19081 / % possible obs: 93.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2→2.13 Å / Mean I/σ(I) obs: 3.7 / Rsym value: 0.359 / % possible all: 62.1
Reflection
*PLUS
Highest resolution: 2 Å / Lowest resolution: 40 Å / Num. obs: 19047 / Redundancy: 4.2 % / Rmerge(I) obs: 0.08
Reflection shell
*PLUS
Lowest resolution: 2.04 Å / % possible obs: 78.9 % / Rmerge(I) obs: 0.379 / Mean I/σ(I) obs: 3.2

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→29.86 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.269 1835 Random
Rwork0.245 --
obs0.247 19047 -
all-19081 -
Displacement parametersBiso mean: 43.1 Å2
Baniso -1Baniso -2Baniso -3
1--6.987 Å20 Å20.641 Å2
2--5.779 Å20 Å2
3---1.208 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.42 Å0.32 Å
Refinement stepCycle: LAST / Resolution: 2→29.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2559 0 33 114 2706
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.015
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_deg26.2
X-RAY DIFFRACTIONc_improper_angle_deg1.64
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.03
RfactorNum. reflection% reflection
Rfree0.429 211 -
Rwork0.358 --
obs-1966 62.1 %
Xplor fileSerial no: 1 / Param file: water_rep.param
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 40 Å / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_angle_deg / Dev ideal: 1.54

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