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- PDB-4ct8: Competence or damage-inducible protein CinA from Thermus thermophilus -

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Basic information

Entry
Database: PDB / ID: 4ct8
TitleCompetence or damage-inducible protein CinA from Thermus thermophilus
ComponentsCINA-LIKE PROTEIN
KeywordsBIOSYNTHETIC PROTEIN / COMPETENCE / DAMAGE / NAD RECYCLING
Function / homology
Function and homology information


ATP binding / metal ion binding
Similarity search - Function
Alpha-Beta Plaits - #2860 / Competence-induced protein CinA / CinA, KH domain / Damage-inducible protein CinA KH domain / : / CinA-like / CinA, C-terminal / CinA-like, C-terminal / Competence-damaged protein / Maf protein ...Alpha-Beta Plaits - #2860 / Competence-induced protein CinA / CinA, KH domain / Damage-inducible protein CinA KH domain / : / CinA-like / CinA, C-terminal / CinA-like, C-terminal / Competence-damaged protein / Maf protein / MoaB/Mog-like domain / Molybdenum Cofactor Biosythetic Enzyme; Chain A / MoaB/Mog domain / MoaB/Mog-like domain superfamily / Probable molybdopterin binding domain / Probable molybdopterin binding domain / Alpha-Beta Plaits / Alpha-Beta Complex / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesTHERMUS THERMOPHILUS HB8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.16 Å
AuthorsDerrick, J. / Karuppiah, V.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Structure and Mechanism of the Bifunctional Cina Enzyme from Thermus Thermophilus
Authors: Karuppiah, V. / Thistlethwaite, A. / Dajani, R. / Warwicker, J. / Derrick, J.P.
History
DepositionMar 12, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 15, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 22, 2014Group: Database references / Structure summary
Revision 1.2Oct 29, 2014Group: Database references
Revision 1.3Dec 17, 2014Group: Database references
Revision 1.4Jan 14, 2015Group: Database references
Revision 1.5Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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

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Assembly

Deposited unit
A: CINA-LIKE PROTEIN
B: CINA-LIKE PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,5788
Polymers86,0872
Non-polymers4916
Water5,729318
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7620 Å2
ΔGint-66.6 kcal/mol
Surface area30590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.970, 93.550, 132.690
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 CINA-LIKE PROTEIN / CINA


Mass: 43043.359 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMUS THERMOPHILUS HB8 (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q5SHB0
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 318 / 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: 2.61 Å3/Da / Density % sol: 53 % / Description: NONE
Crystal growDetails: 0.2 M SODIUM SULFATE 0.1 M BIS-TRIS PROPANE 20 % (W/V) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.16→54 Å / Num. obs: 49274 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 4.9 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 12.1
Reflection shellResolution: 2.16→2.22 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 2.2 / % possible all: 99.4

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2A9S

2a9s


Resolution: 2.16→76.46 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.915 / SU B: 5.165 / SU ML: 0.133 / Cross valid method: THROUGHOUT / ESU R: 0.225 / ESU R Free: 0.195 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES ON CHAIN B 193-203 INCLUSIVE ARE DISORDERED.
RfactorNum. reflection% reflectionSelection details
Rfree0.24073 2487 5.1 %RANDOM
Rwork0.18814 ---
obs0.19072 46653 99.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.804 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å20 Å20 Å2
2---0.22 Å20 Å2
3---0.28 Å2
Refinement stepCycle: LAST / Resolution: 2.16→76.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5962 0 29 318 6309
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0196100
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5181.9988273
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9695774
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.35121.56250
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.19151026
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9671580
X-RAY DIFFRACTIONr_chiral_restr0.1010.2934
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214601
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
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: 2.16→2.216 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.29 188 -
Rwork0.231 3149 -
obs--99.14 %

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