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- PDB-2h6b: Crystal structure of oxidized CprK in complex with o-chlorophenol... -

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Basic information

Entry
Database: PDB / ID: 2h6b
TitleCrystal structure of oxidized CprK in complex with o-chlorophenolacetic acid
ComponentsChloroPhenol Reduction gene K
KeywordsDNA BINDING PROTEIN / halorespiration / DNA binding / chlorinated ligand / chlorophenol / CprK / helix-turn-helix
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 / : / Putative transcription regulatory protein
Similarity search - Component
Biological speciesDesulfitobacterium hafniense (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.2 Å
AuthorsJoyce, M.G. / Levy, C. / Leys, D.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: CprK Crystal Structures Reveal Mechanism for Transcriptional Control of Halorespiration.
Authors: Joyce, M.G. / Levy, C. / Pop, S.M. / Biehl, B.D. / Doukov, T.I. / Ryter, J.M. / Mazon, H. / Smidt, H. / van den Heuvel, R.H. / Ragsdale, S.W. / van der Oost, J. / Leys, D.
History
DepositionMay 31, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 4, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Remark 999SEQUENCE THE SEQUENCE OF THE PROTEIN WAS NOT AVAILABLE IN ANY UNIPROT REFERENCE SEQUENCE DATABASE ...SEQUENCE THE SEQUENCE OF THE PROTEIN WAS NOT AVAILABLE IN ANY UNIPROT REFERENCE SEQUENCE DATABASE AT THE TIME OF PROCESSING.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ChloroPhenol Reduction gene K
B: ChloroPhenol Reduction gene K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,3576
Polymers56,7912
Non-polymers5654
Water4,107228
1
A: ChloroPhenol Reduction gene K
B: ChloroPhenol Reduction gene K
hetero molecules

A: ChloroPhenol Reduction gene K
B: ChloroPhenol Reduction gene K
hetero molecules

A: ChloroPhenol Reduction gene K
B: ChloroPhenol Reduction gene K
hetero molecules

A: ChloroPhenol Reduction gene K
B: ChloroPhenol Reduction gene K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)229,42724
Polymers227,1658
Non-polymers2,26116
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_675-x+1,-y+2,z1
crystal symmetry operation3_655-x+1,y,-z1
crystal symmetry operation4_575x,-y+2,-z1
Buried area43480 Å2
ΔGint-431 kcal/mol
Surface area75940 Å2
MethodPISA
2
A: ChloroPhenol Reduction gene K
B: ChloroPhenol Reduction gene K
hetero molecules

A: ChloroPhenol Reduction gene K
B: ChloroPhenol Reduction gene K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,71312
Polymers113,5834
Non-polymers1,1318
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_675-x+1,-y+2,z1
MethodPQS
Unit cell
Length a, b, c (Å)104.437, 112.185, 119.495
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11B-391-

HOH

DetailsThe second part of the biological assembly is generated by the two fold axis: -x,-y,z

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Components

#1: Protein ChloroPhenol Reduction gene K / CprK


Mass: 28395.684 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desulfitobacterium hafniense (bacteria)
Production host: Escherichia coli (E. coli) / References: UniProt: Q18R04, UniProt: Q8RPJ2*PLUS
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-3C4 / (3-CHLORO-4-HYDROXYPHENYL)ACETIC ACID


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


Mass: 18.015 Da / Num. of mol.: 228 / 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: 3.08 Å3/Da / Density % sol: 60.07 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 1.8 M Ammonium sulphate, 1mM orthochlorophenol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, Hamburg / Beamline: X11 / Wavelength: 0.9 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Mar 1, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. obs: 35512 / % possible obs: 99.2 % / Biso Wilson estimate: 40 Å2 / Rmerge(I) obs: 0.102 / Net I/σ(I): 16.6
Reflection shellResolution: 2.2→2.25 Å / Rmerge(I) obs: 0.573 / Mean I/σ(I) obs: 2.5 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
RefinementMethod to determine structure: MIR / Resolution: 2.2→19.92 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.946 / SU B: 6.111 / SU ML: 0.147 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.2 / ESU R Free: 0.179 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22945 1760 5 %RANDOM
Rwork0.18346 ---
all0.18579 33350 --
obs0.18579 33350 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 39.915 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20 Å20 Å2
2---0.09 Å20 Å2
3---0.04 Å2
Refinement stepCycle: LAST / Resolution: 2.2→19.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3772 0 34 228 4034
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0223905
X-RAY DIFFRACTIONr_bond_other_d0.0010.023584
X-RAY DIFFRACTIONr_angle_refined_deg1.9891.9815276
X-RAY DIFFRACTIONr_angle_other_deg0.9738346
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4295471
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.23524.035171
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.35815716
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5841522
X-RAY DIFFRACTIONr_chiral_restr0.1120.2595
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024252
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02796
X-RAY DIFFRACTIONr_nbd_refined0.2170.2798
X-RAY DIFFRACTIONr_nbd_other0.1960.23447
X-RAY DIFFRACTIONr_nbtor_refined0.1860.21866
X-RAY DIFFRACTIONr_nbtor_other0.0930.22225
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1590.2218
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0970.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1950.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2610.270
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0720.212
X-RAY DIFFRACTIONr_mcbond_it1.241.52618
X-RAY DIFFRACTIONr_mcbond_other0.2751.5969
X-RAY DIFFRACTIONr_mcangle_it1.80523829
X-RAY DIFFRACTIONr_scbond_it2.69931723
X-RAY DIFFRACTIONr_scangle_it4.0394.51443
LS refinement shellResolution: 2.2→2.258 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.536 93 -
Rwork0.415 2043 -
obs--100 %

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