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- PDB-4ynl: Crystal structure of the hood domain of Anabaena HetR in complex ... -

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Basic information

Entry
Database: PDB / ID: 4ynl
TitleCrystal structure of the hood domain of Anabaena HetR in complex with the hexapeptide ERGSGR derived from PatS
Components
  • Heterocyst differentiation control protein
  • Heterocyst inhibition-signaling peptide
KeywordsTRANSCRIPTION / Heterocyst differentiation / Transcription factor
Function / homology
Function and homology information


heterocyst development / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / periplasmic space / serine-type endopeptidase activity / proteolysis / DNA binding / identical protein binding
Similarity search - Function
Peptidase S48, DNA-binding transcriptional activator HetR / HetR, C-terminal Hood domain / HetR, flap domain / HetR, N-terminal DNA-binding domain / Peptidase family S48 / Heterocyst differentiation regulator C-terminal Hood domain
Similarity search - Domain/homology
Heterocyst inhibition-signaling peptide / DNA-binding transcriptional activator HetR
Similarity search - Component
Biological speciesNostoc sp. PCC 7120 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsHu, H.X. / Jiang, Y.L. / Zhao, M.X. / Zhang, C.C. / Chen, Y. / Zhou, C.Z.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China31370757 China
National Natural Science Foundation of China31070652 China
CitationJournal: Sci Rep / Year: 2015
Title: Structural insights into HetR-PatS interaction involved in cyanobacterial pattern formation
Authors: Hu, H.X. / Jiang, Y.L. / Zhao, M.X. / Cai, K. / Liu, S. / Wen, B. / Lv, P. / Zhang, Y. / Peng, J. / Zhong, H. / Yu, H.M. / Ren, Y.M. / Zhang, Z. / Tian, C. / Wu, Q. / Oliveberg, M. / Zhang, ...Authors: Hu, H.X. / Jiang, Y.L. / Zhao, M.X. / Cai, K. / Liu, S. / Wen, B. / Lv, P. / Zhang, Y. / Peng, J. / Zhong, H. / Yu, H.M. / Ren, Y.M. / Zhang, Z. / Tian, C. / Wu, Q. / Oliveberg, M. / Zhang, C.C. / Chen, Y. / Zhou, C.Z.
History
DepositionMar 10, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 2, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Heterocyst differentiation control protein
A: Heterocyst differentiation control protein
D: Heterocyst inhibition-signaling peptide
C: Heterocyst inhibition-signaling peptide
N: Heterocyst differentiation control protein
M: Heterocyst differentiation control protein
P: Heterocyst inhibition-signaling peptide
R: Heterocyst inhibition-signaling peptide


Theoretical massNumber of molelcules
Total (without water)46,6418
Polymers46,6418
Non-polymers00
Water3,099172
1
B: Heterocyst differentiation control protein
A: Heterocyst differentiation control protein
D: Heterocyst inhibition-signaling peptide
C: Heterocyst inhibition-signaling peptide


Theoretical massNumber of molelcules
Total (without water)23,3204
Polymers23,3204
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
N: Heterocyst differentiation control protein
M: Heterocyst differentiation control protein
P: Heterocyst inhibition-signaling peptide
R: Heterocyst inhibition-signaling peptide


Theoretical massNumber of molelcules
Total (without water)23,3204
Polymers23,3204
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)218.215, 43.463, 55.113
Angle α, β, γ (deg.)90.00, 97.54, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Heterocyst differentiation control protein


Mass: 10997.505 Da / Num. of mol.: 4 / Fragment: UNP residues 219-299
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nostoc sp. PCC 7120 (bacteria) / Strain: PCC 7120 / Gene: hetR, alr2339 / Production host: Escherichia coli (E. coli) / References: UniProt: P27709
#2: Protein/peptide
Heterocyst inhibition-signaling peptide


Mass: 662.698 Da / Num. of mol.: 4 / Fragment: UNP residues 12-17 / Source method: obtained synthetically / Source: (synth.) Nostoc sp. PCC 7120 (bacteria) / References: UniProt: O52748
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 172 / 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: 2.8 Å3/Da / Density % sol: 56.11 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 25% PEG 4000, 0.1 M sodium citrate, 0.2 M ammonium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 10, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 29699 / % possible obs: 97.5 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.138 / Net I/σ(I): 7.81
Reflection shellResolution: 2.1→2.15 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.517 / Mean I/σ(I) obs: 2.413 / % possible all: 95.1

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4K1M

4k1m
PDB Unreleased entry


Resolution: 2.1→42.65 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.904 / SU B: 4.811 / SU ML: 0.128 / Cross valid method: THROUGHOUT / ESU R: 0.195 / ESU R Free: 0.179 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2557 1506 5.1 %RANDOM
Rwork0.21197 ---
obs0.21425 28079 96.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 72.776 Å2
Baniso -1Baniso -2Baniso -3
1-3.5 Å2-0 Å2-0.07 Å2
2---1.57 Å2-0 Å2
3----1.85 Å2
Refinement stepCycle: 1 / Resolution: 2.1→42.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2778 0 0 172 2950
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0192844
X-RAY DIFFRACTIONr_bond_other_d0.0010.022720
X-RAY DIFFRACTIONr_angle_refined_deg1.3781.9533814
X-RAY DIFFRACTIONr_angle_other_deg0.78136244
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6155326
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.25222.658158
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.72715546
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4751540
X-RAY DIFFRACTIONr_chiral_restr0.080.2378
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213140
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02676
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.2387.1041316
X-RAY DIFFRACTIONr_mcbond_other3.2377.1041315
X-RAY DIFFRACTIONr_mcangle_it5.2810.6281632
X-RAY DIFFRACTIONr_mcangle_other5.27910.6291633
X-RAY DIFFRACTIONr_scbond_it3.1727.591528
X-RAY DIFFRACTIONr_scbond_other3.1717.5911529
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.34411.2712181
X-RAY DIFFRACTIONr_long_range_B_refined9.13256.1523551
X-RAY DIFFRACTIONr_long_range_B_other8.90756.523452
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.093→2.147 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 98 -
Rwork0.261 1822 -
obs--84.32 %

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