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- PDB-4yba: The structure of the C.Kpn2I controller protein -

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Basic information

Entry
Database: PDB / ID: 4yba
TitleThe structure of the C.Kpn2I controller protein
ComponentsRegulatory protein C
KeywordsGENE REGULATION / DNA-protein interactions / helix-turn-helix / restriction-modification / controller protein
Function / homology
Function and homology information


Helix-turn-helix / lambda repressor-like DNA-binding domains / Cro/C1-type HTH domain profile. / Cro/C1-type helix-turn-helix domain / 434 Repressor (Amino-terminal Domain) / Lambda repressor-like, DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Regulatory protein C
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsShevtsov, M.B. / Martin, R.N. / Swiderska, A. / McGeehan, G.E. / Kneale, G.G.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/H00680X/1 United Kingdom
CitationJournal: To Be Published
Title: The structure of the C.kpn2I controller protein
Authors: Shevtsov, M.B. / Swiderska, A. / Martin, R.N. / McGeehan, G.E. / Kneale, G.
History
DepositionFeb 18, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 2, 2016Provider: repository / Type: Initial release
Revision 2.0Aug 30, 2017Group: Atomic model / Author supporting evidence / Derived calculations
Category: atom_site / pdbx_audit_support / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_audit_support.funding_organization / _struct_site_gen.auth_seq_id
Revision 2.1Jan 10, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Regulatory protein C
B: Regulatory protein C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,9693
Polymers21,8772
Non-polymers921
Water1,78399
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1350 Å2
ΔGint-10 kcal/mol
Surface area8180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.890, 44.730, 109.700
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 Regulatory protein C / C.kpn2I controller protein


Mass: 10938.591 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Plasmid: pET-28 / Details (production host): Novagen / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q93K36
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.07 Å3/Da / Density % sol: 40.7 % / Description: long slim needles
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2 LiSO4, 0.1 M Bis Tris methane pH5.5, 25% PEG3350; cryoprotection: 30% PEG3350, 10% glycerol

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 31, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.7→28.46 Å / Num. obs: 17568 / % possible obs: 86.7 % / Redundancy: 3.4 % / Biso Wilson estimate: 13.8 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 7.8
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.611 / Mean I/σ(I) obs: 2.3 / % possible all: 89

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
MOSFLM7.0.9data reduction
SCALA3.3.21data scaling
PHASER2.5.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4IR6

4ir6


Resolution: 1.7→22.37 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.933 / SU B: 5.178 / SU ML: 0.081 / Cross valid method: THROUGHOUT / ESU R: 0.119 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.22604 902 5.1 %RANDOM
Rwork0.19021 ---
obs0.19209 16616 84.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.585 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20 Å2
2---0.03 Å20 Å2
3---0.05 Å2
Refinement stepCycle: LAST / Resolution: 1.7→22.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1194 0 6 99 1299
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0191249
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5621.9671684
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9755163
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.20424.13858
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.48815235
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6731511
X-RAY DIFFRACTIONr_chiral_restr0.1060.2193
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021931
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1930.978628
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.8051.452784
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.7311.389621
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined5.70310.4245199
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 85 -
Rwork0.298 1196 -
obs--86.15 %
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)
12.6045-0.46561.09262.8384-0.42312.72530.0013-0.32080.19920.15990.02280.0438-0.1077-0.0466-0.02420.0169-0.00490.01550.0434-0.02770.0339-17.545817.6354-17.0571
23.4246-0.3393-0.96612.46950.42372.14150.0288-0.2519-0.08140.1256-0.00030.01630.114-0.022-0.02850.0187-0.0095-0.01380.02330.01010.023-1.38853.5094-15.6573
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 81
2X-RAY DIFFRACTION2B4 - 82

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