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- PDB-2zfw: Crystal structure of Pex from Synechococcus sp. (strain PCC 7942)... -

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Basic information

Entry
Database: PDB / ID: 2zfw
TitleCrystal structure of Pex from Synechococcus sp. (strain PCC 7942) (Anacystis nidulans R2)
ComponentsPex
KeywordsCIRCADIAN CLOCK PROTEIN / Five alpha-helices + One beta-sheet
Function / homologyTranscription 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 / Pex
Function and homology information
Biological speciesSynechococcus sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.9 Å
AuthorsKouyama, 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
DepositionJan 14, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 20, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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
B: Pex
D: Pex
E: Pex
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,1309
Polymers68,6494
Non-polymers4805
Water1629
1
A: Pex
B: Pex
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6135
Polymers34,3252
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2510 Å2
ΔGint-54 kcal/mol
Surface area13770 Å2
MethodPISA
2
D: Pex
E: Pex
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5174
Polymers34,3252
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2540 Å2
ΔGint-67 kcal/mol
Surface area13590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.978, 117.978, 92.210
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number171
Space group name H-MP62

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Components

#1: Protein
Pex


Mass: 17162.320 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechococcus sp. (bacteria) / Strain: PCC 7942 / Gene: pex / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: O66226
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 54.42 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 2.5M ammonium sulfate, 0.2M Lithium sulfate, 0.1M Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 283K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 22, 2006 / Details: mirrors
RadiationMonochromator: double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→100 Å / Num. all: 16173 / Num. obs: 14969 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.1 % / Biso Wilson estimate: 21.96 Å2 / Rmerge(I) obs: 0.098 / Rsym value: 0.098 / Net I/σ(I): 19
Reflection shellResolution: 2.9→3.06 Å / Redundancy: 12.9 % / Rmerge(I) obs: 0.497 / Mean I/σ(I) obs: 3.7 / Num. unique all: 1260 / Rsym value: 0.497 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
CNSrefinement
MOSFLMdata reduction
SCALAdata scaling
CNSphasing
RefinementMethod to determine structure: MIR
Starting model: PDB ENTRY 2E1N

2e1n


Resolution: 2.9→15 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.276 756 -RANDOM
Rwork0.24 ---
obs0.24 14969 92.6 %-
Displacement parametersBiso mean: 71.2 Å2
Baniso -1Baniso -2Baniso -3
1-0.217 Å20.217 Å2-0.434 Å2
2--0.241 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.45 Å0.38 Å
Luzzati d res low-6 Å
Luzzati sigma a0.51 Å0.48 Å
Refinement stepCycle: LAST / Resolution: 2.9→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3820 0 25 9 3854
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0085
X-RAY DIFFRACTIONc_angle_deg1.26
X-RAY DIFFRACTIONc_dihedral_angle_d22.2
X-RAY DIFFRACTIONc_improper_angle_d0.74
LS refinement shellResolution: 2.9→3 Å
RfactorNum. reflection% reflection
Rfree0.332 64 -
Rwork0.318 --
obs-1427 92 %

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