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- PDB-2dql: Crystal structure of the circadian clock associated protein Pex f... -

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Basic information

Entry
Database: PDB / ID: 2dql
TitleCrystal structure of the circadian clock associated protein Pex from anabaena
ComponentsPex protein
KeywordsCIRCADIAN CLOCK PROTEIN / circadian clock associated protein
Function / homology
Function and homology information


Transcription regulator PadR, N-terminal / Transcriptional regulator PadR-like family / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PHOSPHATE ION / Pex protein
Similarity search - Component
Biological speciesAnabaena sp. PCC 7120 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.7 Å
AuthorsKurosawa, S. / Kouyama, T.
CitationJournal: Genes Cells / Year: 2009
Title: Functionally important structural elements of the cyanobacterial clock-related protein Pex.
Authors: Kurosawa, S. / Murakami, R. / Onai, K. / Morishita, M. / Hasegawa, D. / Iwase, R. / Uzumaki, T. / Hayashi, F. / Kitajima-Ihara, T. / Sakata, S. / Murakami, M. / Kouyama, T. / Ishiura, M.
History
DepositionMay 29, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 29, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 21, 2016Group: Structure summary
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

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Assembly

Deposited unit
A: Pex protein
B: Pex protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8163
Polymers27,7212
Non-polymers951
Water6,954386
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2180 Å2
ΔGint-33 kcal/mol
Surface area13490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.126, 75.040, 103.705
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Pex protein


Mass: 13860.675 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anabaena sp. PCC 7120 (bacteria) / Genus: Nostoc / Strain: pcc7120 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8YQ56
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 386 / 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: 2

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Sample preparation

CrystalDensity Matthews: 3.52 Å3/Da / Density % sol: 65.02 %
Crystal growTemperature: 282 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: 1M Sodium Phosphate, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 282K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSPring-8 BL38B110.92
SYNCHROTRONSPring-8 BL41XU20.8
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDApr 16, 2006
RIGAKU RAXIS V2IMAGE PLATEMar 23, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.921
20.81
ReflectionResolution: 1.7→38.66 Å / Num. all: 41503 / Num. obs: 41503 / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.2 % / Biso Wilson estimate: 23.5 Å2 / Rmerge(I) obs: 0.065 / Rsym value: 0.065 / Net I/σ(I): 7.5
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.484 / Mean I/σ(I) obs: 1.7 / Rsym value: 0.484 / % possible all: 94.7

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Processing

Software
NameClassification
ADSCdata collection
SCALAdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MIR / Resolution: 1.7→15 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.255 2028 -RANDOM
Rwork0.234 ---
obs0.234 40593 92.8 %-
all-43733 --
Displacement parametersBiso mean: 25.9677 Å2
Baniso -1Baniso -2Baniso -3
1-2.212 Å20 Å20 Å2
2---3.513 Å20 Å2
3---1.301 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.16 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 1.7→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1958 0 5 386 2349
LS refinement shellResolution: 1.7→1.76 Å
RfactorNum. reflection% reflection
Rfree0.2832 218 -
Rwork0.2907 --
obs-4303 1 %

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