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- PDB-3kor: Crystal structure of a putative Trp repressor from Staphylococcus... -

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Basic information

Entry
Database: PDB / ID: 3kor
TitleCrystal structure of a putative Trp repressor from Staphylococcus aureus
ComponentsPossible Trp repressor
KeywordsTRANSCRIPTION / Putative DNA-binding Trp repressor / TrpR like protein / structural genomics
Function / homologyTrpR-like / Trp Operon Repressor; Chain A / Orthogonal Bundle / Mainly Alpha / :
Function and homology information
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å
AuthorsLam, R. / Vodsedalek, J. / Lam, K. / Romanov, V. / Battaile, K.P. / Beletskaya, I. / Pai, E.F. / Chirgadze, N.Y.
CitationJournal: To be Published
Title: Crystal structure of a putative Trp repressor from Staphylococcus aureus
Authors: Lam, R. / Vodsedalek, J. / Lam, K. / Romanov, V. / Battaile, K.P. / Beletskaya, I. / Pai, E.F. / Chirgadze, N.Y.
History
DepositionNov 13, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 17, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Possible Trp repressor
B: Possible Trp repressor
C: Possible Trp repressor
D: Possible Trp repressor


Theoretical massNumber of molelcules
Total (without water)55,1874
Polymers55,1874
Non-polymers00
Water5,675315
1
A: Possible Trp repressor
D: Possible Trp repressor


Theoretical massNumber of molelcules
Total (without water)27,5932
Polymers27,5932
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5590 Å2
ΔGint-42 kcal/mol
Surface area10220 Å2
MethodPISA
2
B: Possible Trp repressor
C: Possible Trp repressor


Theoretical massNumber of molelcules
Total (without water)27,5932
Polymers27,5932
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5610 Å2
ΔGint-41 kcal/mol
Surface area10380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.973, 68.461, 73.170
Angle α, β, γ (deg.)90.000, 96.860, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Possible Trp repressor


Mass: 13796.653 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: USA300 / TCH1516 / Gene: USA300HOU_1908 / Plasmid: PET15B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)CodonPlus RIPL / References: UniProt: A8Z2S1
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 315 / 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: 1.94 Å3/Da / Density % sol: 36.48 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 25% PEG3350, 0.2M sodium chloride, 0.1M HEPES pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-BM / Wavelength: 0.9796 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 11, 2009 / Details: Si(111) double-crystal monochromator
RadiationMonochromator: Si(111) double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 55538 / % possible obs: 99.7 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.098 / Χ2: 1.726 / Net I/σ(I): 9.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.6-1.6450.35735570.61996.3
1.64-1.686.10.31836770.64299.3
1.68-1.7270.29836850.677100
1.72-1.777.50.26436620.74100
1.77-1.837.50.23237320.782100
1.83-1.97.50.19636900.883100
1.9-1.977.60.16537231.107100
1.97-2.067.60.13436921.249100
2.06-2.177.60.11237011.575100
2.17-2.317.60.10736971.994100
2.31-2.497.60.09837282.31100
2.49-2.747.60.09537102.617100
2.74-3.137.60.08537542.784100
3.13-3.957.60.07537282.595100
3.95-507.30.07938024.48699.6

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Phasing

PhasingMethod: SAD
Phasing MAD set
IDR cullis acentricR cullis centricHighest resolution (Å)Lowest resolution (Å)Reflection acentricReflection centric
ISO_1001.626.7535071905
ANO_10.55301.626.7530880
Phasing MAD set shell
IDResolution (Å)R cullis acentricR cullis centricReflection acentricReflection centric
ISO_16.92-26.70061894
ISO_14.98-6.9200109194
ISO_14.09-4.9800141195
ISO_13.55-4.0900166797
ISO_13.18-3.5500189794
ISO_12.91-3.1800211996
ISO_12.7-2.9100226793
ISO_12.52-2.700244796
ISO_12.38-2.5200263495
ISO_12.26-2.3800278097
ISO_12.15-2.2600290992
ISO_12.06-2.1500305996
ISO_11.98-2.0600321498
ISO_11.91-1.98003283101
ISO_11.85-1.9100342395
ISO_11.79-1.8500351488
ISO_11.73-1.7900370699
ISO_11.69-1.7300377698
ISO_11.64-1.6900383594
ISO_11.6-1.6400385793
ANO_16.92-26.70.31506120
ANO_14.98-6.920.273010880
ANO_14.09-4.980.376014100
ANO_13.55-4.090.409016660
ANO_13.18-3.550.381018960
ANO_12.91-3.180.382021190
ANO_12.7-2.910.383022670
ANO_12.52-2.70.41024470
ANO_12.38-2.520.421026340
ANO_12.26-2.380.486027790
ANO_12.15-2.260.539029090
ANO_12.06-2.150.596030580
ANO_11.98-2.060.657032140
ANO_11.91-1.980.713032830
ANO_11.85-1.910.778034230
ANO_11.79-1.850.845035140
ANO_11.73-1.790.871037060
ANO_11.69-1.730.93037740
ANO_11.64-1.690.954037520
ANO_11.6-1.640.989035370
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 55412
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
7.71-10059.30.859517
5.76-7.7160.30.842703
4.8-5.76540.9885
4.2-4.855.50.9161043
3.78-4.254.50.9161160
3.47-3.7855.30.9151263
3.22-3.47550.9091356
3.02-3.2255.80.8941487
2.85-3.0255.20.9021551
2.71-2.8555.60.8881624
2.58-2.7156.30.8921740
2.48-2.58570.8951808
2.38-2.4853.20.9021831
2.3-2.3855.70.891945
2.22-2.354.60.92028
2.15-2.2255.90.9012050
2.09-2.1558.20.892167
2.03-2.0957.70.8892188
1.98-2.0358.70.8742273
1.93-1.9861.20.872291
1.88-1.9362.10.862388
1.84-1.8861.50.8542458
1.8-1.8464.30.8442467
1.76-1.864.70.8572567
1.73-1.7668.50.8452570
1.69-1.73690.8352671
1.66-1.6968.80.8272662
1.63-1.6674.50.7942744
1.6-1.6375.10.7382975

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
DM5phasing
REFMACrefmac_5.5.0102refinement
PDB_EXTRACT3.005data extraction
JDirectordata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.6→26.7 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.937 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 1.64 / SU ML: 0.059 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.094 / ESU R Free: 0.094 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.221 2813 5.1 %RANDOM
Rwork0.191 ---
obs0.192 55412 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 54.46 Å2 / Biso mean: 22.046 Å2 / Biso min: 10.99 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.6→26.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3204 0 0 315 3519
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0223265
X-RAY DIFFRACTIONr_angle_refined_deg1.2091.9574402
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9785407
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.72425.294170
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.40715627
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.1981524
X-RAY DIFFRACTIONr_chiral_restr0.0820.2504
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022436
X-RAY DIFFRACTIONr_mcbond_it0.7541.51998
X-RAY DIFFRACTIONr_mcangle_it1.40623216
X-RAY DIFFRACTIONr_scbond_it2.3731267
X-RAY DIFFRACTIONr_scangle_it3.8884.51181
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.262 206 -
Rwork0.217 3744 -
all-3950 -
obs--96.74 %

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