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- PDB-5fhp: SeMet regulator of nicotine degradation -

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Basic information

Entry
Database: PDB / ID: 5fhp
TitleSeMet regulator of nicotine degradation
ComponentsNicR
KeywordsAPOPTOSIS / co-crystal derepression / Nicotine regulator 2
Function / homology
Function and homology information


transcription cis-regulatory region binding / DNA-binding transcription factor activity
Similarity search - Function
PsrA, tetracyclin repressor-like, C-terminal domain / Tetracyclin repressor-like, C-terminal domain / : / Tetracycline Repressor, domain 2 / Tetracyclin repressor-like, C-terminal domain superfamily / Tetracycline Repressor; domain 2 / Bacterial regulatory proteins, tetR family / DNA-binding HTH domain, TetR-type / TetR-type HTH domain profile. / Homeobox-like domain superfamily ...PsrA, tetracyclin repressor-like, C-terminal domain / Tetracyclin repressor-like, C-terminal domain / : / Tetracycline Repressor, domain 2 / Tetracyclin repressor-like, C-terminal domain superfamily / Tetracycline Repressor; domain 2 / Bacterial regulatory proteins, tetR family / DNA-binding HTH domain, TetR-type / TetR-type HTH domain profile. / Homeobox-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsZhang, K. / Tang, H. / Wu, G. / Wang, W. / Hu, H. / Xu, P.
Funding support China, 3items
OrganizationGrant numberCountry
Chinese National Natural Science Foundation31230002 China
Chinese National Natural Science Foundation31270154 China
Chinese National Science Foundation for Excellent Young Scholars31422004 China
CitationJournal: To Be Published
Title: Co-crystal Structure of NicR2_Hsp
Authors: Zhang, K. / Tang, H. / Wu, G. / Wang, W. / Hu, H. / Xu, P.
History
DepositionDec 22, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 21, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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: NicR
B: NicR
C: NicR
D: NicR
E: NicR
F: NicR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,10712
Polymers147,5316
Non-polymers5766
Water3,315184
1
A: NicR
D: NicR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,3614
Polymers49,1772
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5190 Å2
ΔGint-38 kcal/mol
Surface area18700 Å2
MethodPISA
2
B: NicR
F: NicR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,3734
Polymers49,1772
Non-polymers1962
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5170 Å2
ΔGint-41 kcal/mol
Surface area18610 Å2
MethodPISA
3
C: NicR
E: NicR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,3734
Polymers49,1772
Non-polymers1962
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5030 Å2
ΔGint-43 kcal/mol
Surface area19420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)150.011, 150.011, 156.689
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein
NicR


Mass: 24588.500 Da / Num. of mol.: 6 / Fragment: UNP residues 31-238
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (strain S16) (bacteria)
Strain: S16 / Gene: nicR / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A0B4KIF6
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-MLA / MALONIC ACID / DICARBOXYLIC ACID C3 / PROPANEDIOLIC ACID / METHANEDICARBOXYLIC ACID


Mass: 104.061 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H4O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 184 / 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

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Sample preparation

CrystalDensity Matthews: 2.99 Å3/Da / Density % sol: 63.82 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop
Details: 1M Sodium malonate pH5.0, 0.1M Sodium acetate trihydrate pH4.5, 2%(w/v) polyethylene 20000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.987 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.65→50 Å / Num. obs: 52428 / % possible obs: 100 % / Redundancy: 12.1 % / Net I/σ(I): 36.96
Reflection shellResolution: 2.65→2.74 Å / Redundancy: 12.1 % / Mean I/σ(I) obs: 8.41 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.65→41.61 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.893 / SU B: 10.158 / SU ML: 0.213 / Cross valid method: THROUGHOUT / ESU R: 0.564 / ESU R Free: 0.306 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25055 2672 5.1 %RANDOM
Rwork0.19677 ---
obs0.1995 49682 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.615 Å2
Baniso -1Baniso -2Baniso -3
1--0.32 Å20 Å20 Å2
2---0.32 Å20 Å2
3---0.64 Å2
Refinement stepCycle: LAST / Resolution: 2.65→41.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9940 0 38 184 10162
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.01910165
X-RAY DIFFRACTIONr_bond_other_d0.0020.029642
X-RAY DIFFRACTIONr_angle_refined_deg1.8181.97113691
X-RAY DIFFRACTIONr_angle_other_deg1.093322118
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.22451222
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.22723.981525
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.834151671
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5571577
X-RAY DIFFRACTIONr_chiral_restr0.1060.21485
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211507
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022422
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_it11.2673.7954912
X-RAY DIFFRACTIONr_mcbond_other11.2663.7944911
X-RAY DIFFRACTIONr_mcangle_it13.9085.6566126
X-RAY DIFFRACTIONr_mcangle_other13.9075.6576127
X-RAY DIFFRACTIONr_scbond_it12.6254.2575253
X-RAY DIFFRACTIONr_scbond_other12.6254.2575253
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other15.5036.1587566
X-RAY DIFFRACTIONr_long_range_B_refined18.74829.97511733
X-RAY DIFFRACTIONr_long_range_B_other18.75529.98111722
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.65→2.719 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 218 -
Rwork0.241 3529 -
obs--98.45 %

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