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- PDB-4f3q: Structure of a YebC family protein (CBU_1566) from Coxiella burnetii -

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Basic information

Entry
Database: PDB / ID: 4f3q
TitleStructure of a YebC family protein (CBU_1566) from Coxiella burnetii
ComponentsTranscriptional regulatory protein CBU_1566
KeywordsTRANSCRIPTION / YebC family
Function / homology
Function and homology information


regulation of DNA-templated transcription / DNA binding / cytosol
Similarity search - Function
YebC, transcriptional regulation domain / Transcriptional regulator TACO1-like / Transcriptional regulator TACO1-like, domain 3 / : / : / TACO1/YebC second and third domain / TACO1/YebC protein N-terminal domain / YebC-like / Integrase, N-terminal zinc-binding domain / Integrase-like, N-terminal ...YebC, transcriptional regulation domain / Transcriptional regulator TACO1-like / Transcriptional regulator TACO1-like, domain 3 / : / : / TACO1/YebC second and third domain / TACO1/YebC protein N-terminal domain / YebC-like / Integrase, N-terminal zinc-binding domain / Integrase-like, N-terminal / Arc Repressor Mutant, subunit A / Alpha-Beta Plaits / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Probable transcriptional regulatory protein CBU_1566
Similarity search - Component
Biological speciesCoxiella burnetii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.15 Å
AuthorsFranklin, M.C. / Cheung, J. / Rudolph, M. / Cassidy, M. / Gary, E. / Burshteyn, F. / Love, J.
CitationJournal: Proteins / Year: 2015
Title: Structural genomics for drug design against the pathogen Coxiella burnetii.
Authors: Franklin, M.C. / Cheung, J. / Rudolph, M.J. / Burshteyn, F. / Cassidy, M. / Gary, E. / Hillerich, B. / Yao, Z.K. / Carlier, P.R. / Totrov, M. / Love, J.D.
History
DepositionMay 9, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 27, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 24, 2015Group: Database references
Revision 1.2Oct 21, 2015Group: Database references
Revision 1.3Feb 10, 2016Group: Database references
Revision 1.4Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transcriptional regulatory protein CBU_1566
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,3022
Polymers27,2061
Non-polymers961
Water1,15364
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.062, 53.062, 167.538
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
DetailsAS PER THE AUTHORS THE BIOLOGICAL ASSEMBLY IS UNKNOWN

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Components

#1: Protein Transcriptional regulatory protein CBU_1566


Mass: 27206.361 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Coxiella burnetii (bacteria) / Strain: RSA 493 Nine Mile Phase I / Gene: CBU_1566 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q83BE4
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.17 Å3/Da / Density % sol: 43.25 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M Na HEPES, 2.4 M ammonium sulfate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 23, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.15→100 Å / Num. all: 13955 / Num. obs: 13933 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 26.5 % / Rsym value: 0.096 / Net I/σ(I): 48.4
Reflection shellResolution: 2.15→2.19 Å / Redundancy: 27.6 % / Mean I/σ(I) obs: 5.3 / Num. unique all: 666 / Rsym value: 0.681 / % possible all: 100

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Processing

Software
NameVersionClassification
CBASSdata collection
SOLVEphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.15→44.83 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.929 / SU B: 14.422 / SU ML: 0.163 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.276 / ESU R Free: 0.213
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25893 691 5 %RANDOM
Rwork0.21935 ---
obs0.22122 13165 99.79 %-
all-13193 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 50.555 Å2
Baniso -1Baniso -2Baniso -3
1-0.63 Å20 Å20 Å2
2--0.63 Å20 Å2
3----1.27 Å2
Refinement stepCycle: LAST / Resolution: 2.15→44.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1806 0 5 64 1875
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0221832
X-RAY DIFFRACTIONr_bond_other_d0.0010.021232
X-RAY DIFFRACTIONr_angle_refined_deg0.9461.9732477
X-RAY DIFFRACTIONr_angle_other_deg0.76433015
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6955232
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.67225.11488
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.13415328
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6151514
X-RAY DIFFRACTIONr_chiral_restr0.0510.2285
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.022052
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02341
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_it0.3151.51163
X-RAY DIFFRACTIONr_mcbond_other0.0571.5473
X-RAY DIFFRACTIONr_mcangle_it0.64321872
X-RAY DIFFRACTIONr_scbond_it1.1893669
X-RAY DIFFRACTIONr_scangle_it2.074.5605
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.15→2.202 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 46 -
Rwork0.249 959 -
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)
12.9652-0.1275-0.19566.5775-1.25627.1009-0.0107-0.0480.0744-0.01190.23610.7032-0.1006-0.1333-0.22530.12960.04530.00550.06960.04820.158515.60857.557464.1781
25.1337-0.94771.26213.0892-0.81554.49780.14590.1398-0.0858-0.126-0.0775-0.03560.26250.0067-0.06840.1552-0.0870.00810.11690.02520.026311.739818.802945.4252
37.79671.45390.95213.65021.50535.1373-0.3497-0.20980.44720.12650.16340.2242-0.3947-0.02680.18630.20720.0465-0.03620.0745-0.01130.0951-1.915233.72766.6191
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 74
2X-RAY DIFFRACTION2A80 - 136
3X-RAY DIFFRACTION2A200 - 244
4X-RAY DIFFRACTION3A137 - 199

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