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- PDB-3e5q: Unbound Oxidised CprK -

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Basic information

Entry
Database: PDB / ID: 3e5q
TitleUnbound Oxidised CprK
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
Cyclic nucleotide-binding protein / :
Similarity search - Component
Biological speciesDesulfitobacterium hafniense (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 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 14, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim / struct_ref_seq_dif
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 / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cyclic nucleotide-binding protein
B: Cyclic nucleotide-binding protein
C: Cyclic nucleotide-binding protein
D: Cyclic nucleotide-binding protein
E: Cyclic nucleotide-binding protein
F: Cyclic nucleotide-binding protein


Theoretical massNumber of molelcules
Total (without water)170,3746
Polymers170,3746
Non-polymers00
Water0
1
A: Cyclic nucleotide-binding protein
B: Cyclic nucleotide-binding protein


Theoretical massNumber of molelcules
Total (without water)56,7912
Polymers56,7912
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4710 Å2
ΔGint-33 kcal/mol
Surface area19580 Å2
MethodPISA
2
C: Cyclic nucleotide-binding protein
D: Cyclic nucleotide-binding protein


Theoretical massNumber of molelcules
Total (without water)56,7912
Polymers56,7912
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4730 Å2
ΔGint-35 kcal/mol
Surface area19900 Å2
MethodPISA
3
E: Cyclic nucleotide-binding protein
F: Cyclic nucleotide-binding protein


Theoretical massNumber of molelcules
Total (without water)56,7912
Polymers56,7912
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4820 Å2
ΔGint-36 kcal/mol
Surface area19880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.405, 64.710, 148.355
Angle α, β, γ (deg.)90.00, 105.29, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12C
22D
13E
23F

NCS domain segments:

Component-ID: 1 / End auth comp-ID: ILE / End label comp-ID: ILE / Refine code: 4

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASNASNAA18 - 12618 - 126
21PHEPHEBB19 - 12619 - 126
12ASNASNCC18 - 12618 - 126
22PHEPHEDD19 - 12619 - 126
13ASNASNEE18 - 12618 - 126
23PHEPHEFF19 - 12619 - 126

NCS ensembles :
ID
1
2
3

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Components

#1: Protein
Cyclic nucleotide-binding protein / CprK


Mass: 28395.684 Da / Num. of mol.: 6
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

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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: 2.16 Å3/Da / Density % sol: 43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 100mM calcium chloride, 100mM Hepes, PEG 2000 MME, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 9, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 3.2→142.86 Å / Num. all: 19900 / Num. obs: 18436

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Processing

SoftwareName: REFMAC / Version: 5.2 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→142.86 Å / Cor.coef. Fo:Fc: 0.888 / Cor.coef. Fo:Fc free: 0.839 / SU B: 69.847 / SU ML: 0.572 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.808 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.3176 1002 5.2 %RANDOM
Rwork0.25774 ---
obs0.26086 18436 79.75 %-
all-18436 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 79.576 Å2
Baniso -1Baniso -2Baniso -3
1--1.79 Å20 Å2-5.1 Å2
2--6.13 Å20 Å2
3----7.03 Å2
Refinement stepCycle: LAST / Resolution: 3.2→142.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9641 0 0 0 9641
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0229844
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.3021.97113271
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.79951202
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.48623.301418
X-RAY DIFFRACTIONr_dihedral_angle_3_deg25.627151800
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2131565
X-RAY DIFFRACTIONr_chiral_restr0.1390.21519
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.027181
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.3240.26070
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3430.26569
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2550.2536
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.4070.2139
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3080.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4911.56225
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.8529718
X-RAY DIFFRACTIONr_scbond_it1.39334179
X-RAY DIFFRACTIONr_scangle_it2.1834.53553
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A977medium positional0.470.5
2C977medium positional0.490.5
3E976medium positional0.480.5
1A977medium thermal0.952
2C977medium thermal0.842
3E976medium thermal0.782
LS refinement shellResolution: 3.2→3.283 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.363 61 -
Rwork0.31 1276 -
obs--74.78 %
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)
11.60540.32050.43561.424-0.32811.9709-0.12390.4473-0.4479-0.36020.0937-0.34420.53420.04350.0303-0.088-0.2130.233-0.155-0.0276-0.08425.2376-13.7271-47.4687
22.6733-0.22410.01671.916-0.08491.4429-0.0104-0.0591-0.18020.18460.00820.63710.1025-0.72720.0022-0.35090.00570.0818-0.3397-0.0694-0.1319-11.0133-1.41567.5668
33.0699-0.54070.61081.75431.34954.97180.0864-0.1810.9726-0.09580.1533-0.5399-1.34950.3474-0.2398-0.0138-0.03640.1198-0.3446-0.06380.187431.96918.903647.405
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA18 - 14118 - 141
2X-RAY DIFFRACTION1BB19 - 14119 - 141
3X-RAY DIFFRACTION1AA149 - 226149 - 226
4X-RAY DIFFRACTION1BB149 - 226149 - 226
5X-RAY DIFFRACTION2CC18 - 14218 - 142
6X-RAY DIFFRACTION2DD19 - 14119 - 141
7X-RAY DIFFRACTION2CC149 - 226149 - 226
8X-RAY DIFFRACTION2DD149 - 226149 - 226
9X-RAY DIFFRACTION3EE18 - 14218 - 142
10X-RAY DIFFRACTION3FF19 - 14319 - 143
11X-RAY DIFFRACTION3EE149 - 226149 - 226
12X-RAY DIFFRACTION3FF149 - 226149 - 226

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