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- PDB-2h6c: Crystal structure of reduced CprK in absence of any ligand -

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Basic information

Entry
Database: PDB / ID: 2h6c
TitleCrystal structure of reduced CprK in absence of any ligand
ComponentsChloroPhenol Reduction gene K
KeywordsDNA BINDING PROTEIN / DNA binding / helix-turn-helix / chlorophenol / halorespiration / CprK
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 / 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 ...Crp-type HTH domain profile. / Crp-like helix-turn-helix domain / Crp-type HTH 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
Putative transcription regulator
Similarity search - Component
Biological speciesDesulfitobacterium dehalogenans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsLevy, 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: Advisory / Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id
Remark 999SEQUENCE THE SEQUENCE OF THE PROTEIN WAS NOT AVAILABLE IN ANY UNIPROT SEQUENCE DATABASE AT THE TIME ...SEQUENCE THE SEQUENCE OF THE PROTEIN WAS NOT AVAILABLE IN ANY UNIPROT 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


Theoretical massNumber of molelcules
Total (without water)53,3552
Polymers53,3552
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5550 Å2
ΔGint-34 kcal/mol
Surface area19620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.637, 50.030, 76.415
Angle α, β, γ (deg.)90.00, 105.54, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B
13A
23B
14A
24B
15A
25B

NCS domain segments:

Component-ID: 1 / Refine code: 6

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PHEPHEGLYGLYAA20 - 4020 - 40
21PHEPHEGLYGLYBB20 - 4020 - 40
12THRTHRILEILEAA50 - 8450 - 84
22THRTHRILEILEBB50 - 8450 - 84
13ASNASNTRPTRPAA93 - 10693 - 106
23ASNASNTRPTRPBB93 - 10693 - 106
14LEULEUALAALAAA112 - 135112 - 135
24LEULEUALAALABB112 - 135112 - 135
15ILEILEILEILEAA153 - 215153 - 215
25ILEILEILEILEBB153 - 215153 - 215

NCS ensembles :
ID
1
2
3
4
5

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Components

#1: Protein ChloroPhenol Reduction gene K / CprK


Mass: 26677.727 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desulfitobacterium dehalogenans (bacteria)
Gene: cprK / Production host: Escherichia coli (E. coli) / References: UniProt: Q9LAS2

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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: 2.51 Å3/Da / Density % sol: 50.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 8% PEG 3350, 115mM MgCl2, 10mM DTT, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 1, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.9→30 Å / Num. obs: 16387 / % possible obs: 99 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 10.6
Reflection shellResolution: 2.9→2.97 Å / Rmerge(I) obs: 0.257 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
CrystalClear(MSC/RIGAKU)data reduction
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2H6B

2h6b


Resolution: 2.9→29.63 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.888 / SU B: 30.826 / SU ML: 0.275 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.493 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30723 582 4.9 %RANDOM
Rwork0.23181 ---
all0.2354 ---
obs0.2354 11256 98.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 75.205 Å2
Baniso -1Baniso -2Baniso -3
1--0.62 Å20 Å2-0.24 Å2
2---0.26 Å20 Å2
3---0.75 Å2
Refinement stepCycle: LAST / Resolution: 2.9→29.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3281 0 0 0 3281
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0223365
X-RAY DIFFRACTIONr_bond_other_d0.0020.023098
X-RAY DIFFRACTIONr_angle_refined_deg2.0751.9644546
X-RAY DIFFRACTIONr_angle_other_deg0.96337172
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.9555417
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.37323.724145
X-RAY DIFFRACTIONr_dihedral_angle_3_deg24.27415592
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.6111519
X-RAY DIFFRACTIONr_chiral_restr0.1070.2520
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023710
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02707
X-RAY DIFFRACTIONr_nbd_refined0.2640.2911
X-RAY DIFFRACTIONr_nbd_other0.2260.23389
X-RAY DIFFRACTIONr_nbtor_refined0.2160.21686
X-RAY DIFFRACTIONr_nbtor_other0.1080.22140
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2240.299
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0670.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2390.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2490.241
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1260.22
X-RAY DIFFRACTIONr_mcbond_it0.5471.52160
X-RAY DIFFRACTIONr_mcbond_other0.0981.5861
X-RAY DIFFRACTIONr_mcangle_it0.92723348
X-RAY DIFFRACTIONr_scbond_it1.47731406
X-RAY DIFFRACTIONr_scangle_it2.2994.51198
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-IDNumberTypeRms dev position (Å)Weight position
1331loose positional0.135
2517loose positional0.155
3215loose positional0.155
4387loose positional0.545
5884loose positional0.215
1331loose thermal0.9110
2517loose thermal1.1710
3215loose thermal0.9110
4387loose thermal1.1410
5884loose thermal0.9710
LS refinement shellResolution: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.437 39 -
Rwork0.337 832 -
obs--100 %
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)
15.8450.4135.00981.0443-0.93376.6189-0.1922-0.7566-0.28730.4880.18790.1626-0.0355-0.22010.00430.07460.12550.01830.03850.0942-0.116944.7169-20.077830.1483
23.76452.52560.36341.7470.50731.3546-0.22550.11630.12230.13910.0457-0.5433-0.67350.42670.17980.2056-0.0764-0.12760.27050.0295-0.034557.6133-9.362622.3074
38.4577-0.78922.62953.26610.12463.2528-0.2058-0.21830.61340.3420.0139-0.0219-0.2024-0.10160.192-0.20250.02750.0584-0.26790.038-0.144421.7009-3.12752.1532
45.9504-0.00290.63143.0812-0.30781.0446-0.0221-0.3346-0.77590.53380.2494-0.0990.2398-0.058-0.2273-0.0467-0.03280.09-0.11030.068-0.202816.8477-31.762812.2682
55.2136-0.72170.9753.19310.41240.27920.1196-0.27-0.03040.13550.12250.36290.0679-0.2644-0.2421-0.2127-0.00980.1463-0.08760.09-0.36699.4195-16.94163.7806
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA140 - 222140 - 222
2X-RAY DIFFRACTION2BB140 - 222140 - 222
3X-RAY DIFFRACTION3AA19 - 10819 - 108
4X-RAY DIFFRACTION4BB19 - 10819 - 108
5X-RAY DIFFRACTION5BB109 - 136109 - 136
6X-RAY DIFFRACTION5AA109 - 136109 - 136

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