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- PDB-3e6c: CprK OCPA DNA Complex -

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Basic information

Entry
Database: PDB / ID: 3e6c
TitleCprK OCPA DNA Complex
Components
  • Cyclic nucleotide-binding protein
  • DNA (5'-D(P*DGP*DCP*DAP*DTP*DTP*DAP*DAP*DCP*DAP*DTP*DGP*DCP*DC)-3')
  • DNA (5'-D(P*DGP*DGP*DCP*DAP*DTP*DGP*DTP*DTP*DAP*DAP*DTP*DGP*DC)-3')
KeywordsTRANSCRIPTION REGULATION/DNA / CprK / Halorespiration / transcriptional regulator / TRANSCRIPTION REGULATION-DNA COMPLEX
Function / homology
Function and homology information


regulation of DNA-templated transcription / DNA binding
Similarity search - Function
Crp-type HTH domain profile. / Crp-like helix-turn-helix domain / Crp-type HTH domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain / Cyclic nucleotide-binding domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain ...Crp-type HTH domain profile. / Crp-like helix-turn-helix domain / Crp-type HTH domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain / Cyclic nucleotide-binding domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Jelly Rolls / Winged helix-like DNA-binding domain superfamily / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
(3-CHLORO-4-HYDROXYPHENYL)ACETIC ACID / DNA / DNA (> 10) / Cyclic nucleotide-binding protein / :
Similarity search - Component
Biological speciesDesulfitobacterium hafniense (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsLevy, C.
CitationJournal: Mol.Microbiol. / Year: 2008
Title: Molecular basis of halorespiration control by CprK, a CRP-FNR type transcriptional regulator
Authors: Levy, C. / Pike, K. / Heyes, D.J. / Joyce, M.G. / Gabor, K. / Smidt, H. / van der Oost, J. / Leys, D.
History
DepositionAug 15, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Cyclic nucleotide-binding protein
B: DNA (5'-D(P*DGP*DCP*DAP*DTP*DTP*DAP*DAP*DCP*DAP*DTP*DGP*DCP*DC)-3')
A: DNA (5'-D(P*DGP*DGP*DCP*DAP*DTP*DGP*DTP*DTP*DAP*DAP*DTP*DGP*DC)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,5084
Polymers36,3223
Non-polymers1871
Water2,738152
1
C: Cyclic nucleotide-binding protein
B: DNA (5'-D(P*DGP*DCP*DAP*DTP*DTP*DAP*DAP*DCP*DAP*DTP*DGP*DCP*DC)-3')
A: DNA (5'-D(P*DGP*DGP*DCP*DAP*DTP*DGP*DTP*DTP*DAP*DAP*DTP*DGP*DC)-3')
hetero molecules

C: Cyclic nucleotide-binding protein
B: DNA (5'-D(P*DGP*DCP*DAP*DTP*DTP*DAP*DAP*DCP*DAP*DTP*DGP*DCP*DC)-3')
A: DNA (5'-D(P*DGP*DGP*DCP*DAP*DTP*DGP*DTP*DTP*DAP*DAP*DTP*DGP*DC)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,0178
Polymers72,6446
Non-polymers3732
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_555-x+y,y,-z1
Buried area11370 Å2
ΔGint-85 kcal/mol
Surface area25810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.600, 100.600, 149.660
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222

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Components

#1: Protein Cyclic nucleotide-binding protein / CprK


Mass: 28379.617 Da / Num. of mol.: 1 / Mutation: C200S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desulfitobacterium hafniense (bacteria)
Strain: DCB-2 / Gene: Dhaf_0678 / Plasmid: pTrc99 / Production host: Escherichia coli (E. coli) / References: UniProt: Q18R04, UniProt: B8FW11*PLUS
#2: DNA chain DNA (5'-D(P*DGP*DCP*DAP*DTP*DTP*DAP*DAP*DCP*DAP*DTP*DGP*DCP*DC)-3')


Mass: 3935.587 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain DNA (5'-D(P*DGP*DGP*DCP*DAP*DTP*DGP*DTP*DTP*DAP*DAP*DTP*DGP*DC)-3')


Mass: 4006.621 Da / Num. of mol.: 1 / Source method: obtained synthetically
#4: Chemical ChemComp-3C4 / (3-CHLORO-4-HYDROXYPHENYL)ACETIC ACID


Mass: 186.592 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H7ClO3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 152 / 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: 3.01 Å3/Da / Density % sol: 59.13 %

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.8→27.48 Å / Num. all: 39695 / Num. obs: 35026

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Processing

SoftwareName: REFMAC / Version: 5.2 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→27.48 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.932 / SU B: 7.986 / SU ML: 0.123 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.116 / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24956 2108 5 %RANDOM
Rwork0.21699 ---
obs0.21867 35026 99.37 %-
all-39695 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.792 Å2
Baniso -1Baniso -2Baniso -3
1--0.33 Å2-0.16 Å20 Å2
2---0.33 Å20 Å2
3---0.49 Å2
Refinement stepCycle: LAST / Resolution: 1.8→27.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1807 533 12 152 2504
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0222453
X-RAY DIFFRACTIONr_bond_other_d0.0030.021510
X-RAY DIFFRACTIONr_angle_refined_deg2.3742.2513423
X-RAY DIFFRACTIONr_angle_other_deg1.19633708
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5065224
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.82623.7882
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.48715339
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1311511
X-RAY DIFFRACTIONr_chiral_restr0.1380.2385
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022305
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02440
X-RAY DIFFRACTIONr_nbd_refined0.2160.2464
X-RAY DIFFRACTIONr_nbd_other0.2170.21545
X-RAY DIFFRACTIONr_nbtor_refined0.2020.21090
X-RAY DIFFRACTIONr_nbtor_other0.0970.21098
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1840.2132
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.5530.214
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2870.250
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3430.213
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5321.51253
X-RAY DIFFRACTIONr_mcbond_other0.4081.5457
X-RAY DIFFRACTIONr_mcangle_it2.01221817
X-RAY DIFFRACTIONr_scbond_it2.48531677
X-RAY DIFFRACTIONr_scangle_it3.5734.51604
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.398 146 -
Rwork0.371 2838 -
obs--99.14 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
17.0397-0.10721.36071.68180.08932.346-0.08040.0743-1.208-0.06740.19450.2771-0.0095-0.3512-0.1141-0.3055-0.04720.0735-0.2685-0.00410.1196-17.96428.229-4.276
21.63710.07690.24732.3830.11212.3569-0.12550.2388-0.0832-0.33190.1020.047-0.2562-0.04540.0235-0.2711-0.03130.0234-0.2418-0.0132-0.4265-2.37651.53-10.892
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1CA145 - 233145 - 233
2X-RAY DIFFRACTION2CA9 - 1409 - 140

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