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- PDB-3e6b: OCPA complexed CprK (C200S) -

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Basic information

Entry
Database: PDB / ID: 3e6b
TitleOCPA complexed CprK (C200S)
ComponentsCyclic nucleotide-binding protein
KeywordsTRANSCRIPTION REGULATION / CprK / Halorespiration / transcriptional regulator
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 / Cyclic nucleotide-binding protein / :
Similarity search - Component
Biological speciesDesulfitobacterium hafniense (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 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: 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

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Assembly

Deposited unit
A: Cyclic nucleotide-binding protein
B: Cyclic nucleotide-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,1324
Polymers56,7592
Non-polymers3732
Water4,954275
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6620 Å2
ΔGint-60 kcal/mol
Surface area18870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.500, 86.510, 125.230
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Cyclic nucleotide-binding protein / CprK


Mass: 28379.617 Da / Num. of mol.: 2 / 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: Chemical ChemComp-3C4 / (3-CHLORO-4-HYDROXYPHENYL)ACETIC ACID


Mass: 186.592 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H7ClO3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 275 / 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: 2.03 Å3/Da / Density % sol: 39.35 %
Crystal growTemperature: 294 K / pH: 6
Details: 100mM MES, 10% MPD, pH 6, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.012→40.26 Å / Num. obs: 29505

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Processing

SoftwareName: REFMAC / Version: 5.2 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.01→40.26 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.933 / SU B: 4.516 / SU ML: 0.124 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.191 / ESU R Free: 0.167 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.232 1561 5 %RANDOM
Rwork0.189 ---
obs0.191 29505 98.7 %-
all-29505 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.22 Å2
Baniso -1Baniso -2Baniso -3
1--1.09 Å20 Å20 Å2
2--0.94 Å20 Å2
3---0.14 Å2
Refinement stepCycle: LAST / Resolution: 2.01→40.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3340 0 24 275 3639
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0223424
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9131.9814611
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1545412
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.46123.63146
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.64615644
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.531521
X-RAY DIFFRACTIONr_chiral_restr0.1190.2521
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022503
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.230.21447
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3140.22289
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2240.2236
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.210.230
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2820.225
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2431.52177
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.9523343
X-RAY DIFFRACTIONr_scbond_it3.12231488
X-RAY DIFFRACTIONr_scangle_it4.7054.51264
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.01→2.06 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.377 95 -
Rwork0.27 1878 -
obs--87.07 %

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