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- PDB-4yrv: Crystal structure of Anabaena transcription factor HetR complexed... -

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Basic information

Entry
Database: PDB / ID: 4yrv
TitleCrystal structure of Anabaena transcription factor HetR complexed with 21-bp DNA from hetP promoter
Components
  • DNA (5'-D(P*AP*TP*GP*AP*GP*GP*GP*GP*TP*TP*AP*GP*AP*CP*CP*CP*CP*TP*CP*GP*C)-3')
  • DNA (5'-D(P*GP*CP*GP*AP*GP*GP*GP*GP*TP*CP*TP*AP*AP*CP*CP*CP*CP*TP*CP*AP*T)-3')
  • Heterocyst differentiation control protein
KeywordsTRANSCRIPTION/DNA / Heterocyst differentiation / Transcription factor / Complex / TRANSCRIPTION-DNA complex
Function / homology
Function and homology information


heterocyst development / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / serine-type endopeptidase activity / proteolysis / DNA binding / identical protein binding
Similarity search - Function
HetR, flap domain / HetR, N-terminal DNA-binding domain / 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 / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA-binding transcriptional activator HetR
Similarity search - Component
Biological speciesNostoc sp. PCC 7120 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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 16, 2015Deposition site: RCSB / Processing site: PDBJ
SupersessionDec 2, 2015ID: 4K1M
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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Heterocyst differentiation control protein
A: Heterocyst differentiation control protein
C: DNA (5'-D(P*GP*CP*GP*AP*GP*GP*GP*GP*TP*CP*TP*AP*AP*CP*CP*CP*CP*TP*CP*AP*T)-3')
D: DNA (5'-D(P*AP*TP*GP*AP*GP*GP*GP*GP*TP*TP*AP*GP*AP*CP*CP*CP*CP*TP*CP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,1188
Polymers84,9574
Non-polymers1604
Water55831
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19840 Å2
ΔGint-180 kcal/mol
Surface area32600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.559, 90.559, 242.320
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Heterocyst differentiation control protein / HETR


Mass: 36034.445 Da / Num. of mol.: 2
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: DNA chain DNA (5'-D(P*GP*CP*GP*AP*GP*GP*GP*GP*TP*CP*TP*AP*AP*CP*CP*CP*CP*TP*CP*AP*T)-3')


Mass: 6424.147 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Nostoc sp. PCC 7120 (bacteria)
#3: DNA chain DNA (5'-D(P*AP*TP*GP*AP*GP*GP*GP*GP*TP*TP*AP*GP*AP*CP*CP*CP*CP*TP*CP*GP*C)-3')


Mass: 6464.171 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Nostoc sp. PCC 7120 (bacteria)
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / 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: 57.93 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 9 / Details: 0.3M calcium acetate, 0.1M Bicine

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97886 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 26, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97886 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 25553 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 14.1 % / Biso Wilson estimate: 75.4 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 28.7
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 14.6 % / Rmerge(I) obs: 0.535 / Mean I/σ(I) obs: 6.8 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HRI

4hri


Resolution: 2.8→39.95 Å / SU ML: 0.78 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.264 1297 5.1 %RANDOM
Rwork0.203 ---
obs0.206 25442 99.2 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 73.93 Å2 / ksol: 0.34 e/Å3
Displacement parametersBiso mean: 87.22 Å2
Baniso -1Baniso -2Baniso -3
1-6.2891 Å20 Å2-0 Å2
2--6.2891 Å2-0 Å2
3----12.5781 Å2
Refinement stepCycle: LAST / Resolution: 2.8→39.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4752 861 4 31 5648
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075848
X-RAY DIFFRACTIONf_angle_d1.2568071
X-RAY DIFFRACTIONf_dihedral_angle_d20.8312303
X-RAY DIFFRACTIONf_chiral_restr0.078866
X-RAY DIFFRACTIONf_plane_restr0.005888
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8031-2.91530.38011420.30852634X-RAY DIFFRACTION99
2.9153-3.04790.38031340.28092632X-RAY DIFFRACTION100
3.0479-3.20860.3461390.24242645X-RAY DIFFRACTION100
3.2086-3.40950.31151440.20682652X-RAY DIFFRACTION100
3.4095-3.67260.23651580.19552658X-RAY DIFFRACTION100
3.6726-4.04190.26371540.18912679X-RAY DIFFRACTION100
4.0419-4.6260.24271360.16672703X-RAY DIFFRACTION99
4.626-5.82530.25141610.1862735X-RAY DIFFRACTION100
5.8253-39.94920.23411290.21212807X-RAY DIFFRACTION95

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