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- PDB-3du1: The 2.0 Angstrom Resolution Crystal Structure of HetL, a Pentapep... -

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Basic information

Entry
Database: PDB / ID: 3du1
TitleThe 2.0 Angstrom Resolution Crystal Structure of HetL, a Pentapeptide Repeat Protein involved in Heterocyst Differentiation Regulation from the Cyanobacterium Nostoc sp. Strain PCC 7120
ComponentsAll3740 protein
KeywordsSTRUCTURAL PROTEIN / Right-handed Beta Helix / Repeated Five Residue Fold / Pentapeptide Repeat Protein
Function / homologyPentapeptide repeats (8 copies) / Pentapeptide repeat / E3 ubiquitin-protein ligase SopA / Pectate Lyase C-like / 3 Solenoid / Mainly Beta / All3740 protein
Function and homology information
Biological speciesNostoc sp. (bacteria)
MethodX-RAY DIFFRACTION / sulfur anomalous scattering / Resolution: 2 Å
AuthorsKennedy, M.A. / Ni, S. / Sheldrick, G.M.
CitationJournal: J.Struct.Biol. / Year: 2008
Title: The 2A resolution crystal structure of HetL, a pentapeptide repeat protein involved in regulation of heterocyst differentiation in the cyanobacterium Nostoc sp. strain PCC 7120
Authors: Ni, S. / Sheldrick, G.M. / Benning, M.M. / Kennedy, M.A.
History
DepositionJul 16, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 11, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Mar 20, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
X: All3740 protein


Theoretical massNumber of molelcules
Total (without water)27,7781
Polymers27,7781
Non-polymers00
Water4,288238
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)68.200, 93.763, 101.307
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein All3740 protein / HetL


Mass: 27778.268 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The protein adopts the repeated five residue (Rfr) fold comprised of a right-handed quadrilateral beta-helix
Source: (gene. exp.) Nostoc sp. (bacteria) / Strain: PCC 7120 / Gene: HetL / Plasmid: pET-28B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8YQS9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 238 / 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: 2.92 Å3/Da / Density % sol: 57.81 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPES, 0.7M sodium phosphate monobasic, 0.7M potassium phosphate monobasic, 12.5% glycerol, protein concentration 7.5 mg/ml, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54 Å
DetectorType: BRUKER SMART 6000 / Detector: CCD / Date: Feb 13, 2008 / Details: mirrors
RadiationMonochromator: graded thin film multilayer mirror Bragg Diffraction
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.77→68.84 Å / Num. all: 32008 / Num. obs: 28767 / % possible obs: 89.9 % / Observed criterion σ(I): 3 / Redundancy: 38.58 % / Rsym value: 0.041 / Net I/σ(I): 61.22
Reflection shellResolution: 1.77→1.87 Å / Redundancy: 38.58 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 4.63 / Rsym value: 0.3 / % possible all: 58.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
PROTEUM PLUSPLUSdata collection
SAINTdata reduction
SADABSdata scaling
SHELXSphasing
RefinementMethod to determine structure: sulfur anomalous scattering / Resolution: 2→28.41 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.944 / SU B: 2.582 / SU ML: 0.075 / Cross valid method: THROUGHOUT / ESU R: 0.145 / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2042 1101 5 %RANDOM
Rwork0.17586 ---
obs0.1773 20737 97.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.67 Å2
Baniso -1Baniso -2Baniso -3
1--0.33 Å20 Å20 Å2
2--0.49 Å20 Å2
3----0.15 Å2
Refinement stepCycle: LAST / Resolution: 2→28.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1798 0 0 238 2036
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0211821
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3441.9682461
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6545236
X-RAY DIFFRACTIONr_dihedral_angle_2_deg24.09724.16784
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.47215316
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.1691515
X-RAY DIFFRACTIONr_chiral_restr0.0960.2285
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021369
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2190.2867
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3080.21240
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.2180
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.5170.250
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1330.216
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9651.51202
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.51121838
X-RAY DIFFRACTIONr_scbond_it3.0833691
X-RAY DIFFRACTIONr_scangle_it4.764.5623
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.217 81 -
Rwork0.174 1401 -
obs--92.11 %

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