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- PDB-6ko9: Crystal structure of the Gefitinib Intermediate 1 bound RamR dete... -

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Basic information

Entry
Database: PDB / ID: 6ko9
TitleCrystal structure of the Gefitinib Intermediate 1 bound RamR determined with XtaLAB Synergy
ComponentsPutative regulatory protein
KeywordsDNA BINDING PROTEIN / multisite binding pocket / HTH-MOTIF
Function / homology
Function and homology information


DNA binding / RNA binding
Similarity search - Function
DNA-binding HTH domain, TetR-type, conserved site / TetR-type HTH domain signature. / : / Tetracycline Repressor, domain 2 / 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
Chem-XZ1 / Putative regulatory protein / Transcriptional regulator RamR
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium str. 14028S (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
Model detailsframework as crystalline sponge method
AuthorsMatsumoto, T. / Nakashima, R. / Yamano, A. / Nishino, K.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2019
Title: Development of a structure determination method using a multidrug-resistance regulator protein as a framework.
Authors: Matsumoto, T. / Nakashima, R. / Yamano, A. / Nishino, K.
History
DepositionAug 8, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 9, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: 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

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Assembly

Deposited unit
A: Putative regulatory protein
B: Putative regulatory protein
C: Putative regulatory protein
D: Putative regulatory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,93613
Polymers88,1774
Non-polymers1,7599
Water11,926662
1
A: Putative regulatory protein
B: Putative regulatory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9206
Polymers44,0892
Non-polymers8324
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2940 Å2
ΔGint-50 kcal/mol
Surface area17280 Å2
MethodPISA
2
C: Putative regulatory protein
D: Putative regulatory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0167
Polymers44,0892
Non-polymers9285
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2990 Å2
ΔGint-62 kcal/mol
Surface area17680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.513, 54.792, 92.224
Angle α, β, γ (deg.)74.640, 81.940, 89.980
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Putative regulatory protein


Mass: 22044.262 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S (bacteria)
Strain: 14028s / SGSC 2262 / Gene: STM14_0676 / Plasmid: PET DUET / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: A0A0F6AY66, UniProt: Q8ZR43*PLUS
#2: Chemical
ChemComp-XZ1 / 4-[(3-chloranyl-4-fluoranyl-phenyl)amino]-7-methoxy-quinazolin-6-ol


Mass: 319.718 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H11ClFN3O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 662 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.51 Å3/Da / Density % sol: 51.01 % / Mosaicity: 0.99 °
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.6 / Details: PEG3350, ammonium sulfate, sodium Citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-X / Wavelength: 1.5406 Å
DetectorType: RIGAKU HyPic-6000HE / Detector: PIXEL / Date: Nov 25, 2016
RadiationMonochromator: multi-layer mirror optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5406 Å / Relative weight: 1
ReflectionResolution: 2.2→18.44 Å / Num. obs: 40974 / % possible obs: 99.3 % / Redundancy: 3.4 % / CC1/2: 0.992 / Rmerge(I) obs: 0.106 / Rpim(I) all: 0.062 / Rrim(I) all: 0.123 / Net I/σ(I): 6.2 / Num. measured all: 138507 / Scaling rejects: 554
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.2-2.272.30.587868437790.5650.4760.761.998.9
8.8-18.4430.07815655250.9890.0470.09212.881.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
MOLREPphasing
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
CrysalisProdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VVY

3vvy


Resolution: 2.2→18.44 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.914 / SU B: 11.223 / SU ML: 0.265 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.364 / ESU R Free: 0.278 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2992 2033 5 %RANDOM
Rwork0.2196 ---
obs0.2236 38659 98.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 327.2 Å2 / Biso mean: 57.627 Å2 / Biso min: 27.47 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20.16 Å2-0.64 Å2
2---1.78 Å2-1.17 Å2
3---0.72 Å2
Refinement stepCycle: final / Resolution: 2.2→18.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5848 0 113 662 6623
Biso mean--67.5 72.52 -
Num. residues----736
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0136068
X-RAY DIFFRACTIONr_bond_other_d0.0020.0175636
X-RAY DIFFRACTIONr_angle_refined_deg1.5661.6628190
X-RAY DIFFRACTIONr_angle_other_deg1.3211.58512948
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.585732
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.4320.69348
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.509151060
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.5841560
X-RAY DIFFRACTIONr_chiral_restr0.0680.2792
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.026800
X-RAY DIFFRACTIONr_gen_planes_other0.0080.021420
LS refinement shellResolution: 2.2→2.257 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.467 181 -
Rwork0.461 2796 -
all-2977 -
obs--97.83 %

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