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- PDB-3rpj: Structure of a curlin genes transcriptional regulator protein fro... -

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Basic information

Entry
Database: PDB / ID: 3rpj
TitleStructure of a curlin genes transcriptional regulator protein from Proteus mirabilis HI4320.
ComponentsCurlin genes transcriptional regulator
Keywordstranscription regulator / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / transcriptional regulator
Function / homology
Function and homology information


positive regulation of DNA-templated transcription / cytoplasm
Similarity search - Function
Sigma factor-binding protein Crl monomer / Sigma factor-binding transcriptional regulator Crl / Sigma factor-binding protein Crl superfamily / Sigma factor-binding transcriptional regulator Crl / TATA-Binding Protein / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Sigma factor-binding protein Crl
Similarity search - Component
Biological speciesProteus mirabilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsCuff, M.E. / Wu, R. / Feldmann, B. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: TO BE PUBLISHED
Title: Structure of a curlin genes transcriptional regulator protein from Proteus mirabilis HI4320.
Authors: Cuff, M.E. / Wu, R. / Feldmann, B. / Joachimiak, A.
History
DepositionApr 26, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Curlin genes transcriptional regulator
B: Curlin genes transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,03416
Polymers31,9952
Non-polymers1,03914
Water2,162120
1
A: Curlin genes transcriptional regulator
hetero molecules

B: Curlin genes transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,03416
Polymers31,9952
Non-polymers1,03914
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_755-x+2,y+1/2,-z+1/21
Buried area3420 Å2
ΔGint-43 kcal/mol
Surface area14330 Å2
MethodPISA
2
A: Curlin genes transcriptional regulator
hetero molecules

B: Curlin genes transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,03416
Polymers31,9952
Non-polymers1,03914
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_455x-1/2,-y+1/2,-z1
Buried area3850 Å2
ΔGint-38 kcal/mol
Surface area13900 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.380, 77.952, 86.163
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
DetailsLikely dimer in AU

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Components

#1: Protein Curlin genes transcriptional regulator


Mass: 15997.664 Da / Num. of mol.: 2 / Fragment: targeted domain 2-131
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Proteus mirabilis (bacteria) / Strain: HI4320 / Gene: crl, PMI0368 / Plasmid: pMCSG19b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B4EUU9
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 120 / 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: 2.64 Å3/Da / Density % sol: 53.48 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1M Bis-Tris propane, 2.0M Ammonium Sulfate, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97904 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 21, 2009
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97904 Å / Relative weight: 1
ReflectionRedundancy: 9.1 % / Av σ(I) over netI: 41.02 / Number: 247920 / Rmerge(I) obs: 0.084 / Χ2: 1.95 / D res high: 1.9 Å / D res low: 50 Å / Num. obs: 27263 / % possible obs: 99.8
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
5.165097.710.087.7248.1
4.095.1610010.0594.3168.7
3.584.0910010.0663.9178.8
3.253.5810010.0753.438.9
3.023.2599.910.0892.9279.1
2.843.0210010.0952.3839.2
2.72.8410010.0981.829.2
2.582.710010.1171.6279.3
2.482.5810010.1181.3399.3
2.392.4810010.1341.2029.3
2.322.3910010.1541.1039.3
2.252.3210010.1761.0239.3
2.192.2510010.1870.9489.3
2.142.1910010.2040.8619.3
2.092.1410010.2380.8419.4
2.052.0910010.2590.8179.3
2.012.0599.910.3120.7989.3
1.972.0110010.3860.7699.2
1.931.9710010.4790.7949.1
1.91.9399.510.5790.8068.8
ReflectionResolution: 1.9→50 Å / Num. all: 27263 / Num. obs: 27263 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 9.1 % / Biso Wilson estimate: 30.1 Å2 / Rmerge(I) obs: 0.084 / Χ2: 1.954 / Net I/σ(I): 8.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.9-1.938.80.57913480.80699.5
1.93-1.979.10.47913370.794100
1.97-2.019.20.38613430.769100
2.01-2.059.30.31213330.79899.9
2.05-2.099.30.25913370.817100
2.09-2.149.40.23813390.841100
2.14-2.199.30.20413620.861100
2.19-2.259.30.18713320.948100
2.25-2.329.30.17613601.023100
2.32-2.399.30.15413491.103100
2.39-2.489.30.13413371.202100
2.48-2.589.30.11813701.339100
2.58-2.79.30.11713601.627100
2.7-2.849.20.09813491.82100
2.84-3.029.20.09513822.383100
3.02-3.259.10.08913582.92799.9
3.25-3.588.90.07513893.43100
3.58-4.098.80.06613923.917100
4.09-5.168.70.05914124.316100
5.16-508.10.0814747.72497.7

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Phasing

PhasingMethod: SAD
Phasing MADD res high: 1.9 Å / D res low: 50 Å / FOM : 0.269 / FOM acentric: 0.305 / FOM centric: 0 / Reflection: 27297 / Reflection acentric: 24146 / Reflection centric: 3151
Phasing MAD setR cullis acentric: 1.45 / R cullis centric: 1 / Highest resolution: 1.9 Å / Lowest resolution: 50 Å / Loc acentric: 0.1 / Loc centric: 0.1 / Power acentric: 0 / Power centric: 0 / Reflection acentric: 24146 / Reflection centric: 3151
Phasing MAD set shell

ID: 1 / R cullis centric: 1 / Power acentric: 0 / Power centric: 0

Resolution (Å)R cullis acentricLoc acentricLoc centricReflection acentricReflection centric
12.01-501.150.50.36247
6.82-12.011.230.50.3374158
4.76-6.821.510.40.3943258
3.66-4.761.050.30.31801351
2.97-3.661.260.20.12896442
2.5-2.971.690.10.14298545
2.16-2.52.170.105939632
1.9-2.162.56007833718
Phasing MAD set site

Atom type symbol: Se / Occupancy iso: 0

IDB isoFract xFract yFract zOccupancy
156.73910.8110.4190.025.907
268.54320.7240.212-0.2345.581
362.0990.9510.4290.0664.999
464.22730.9620.4660.2144.208
576.80960.6650.245-0.3163.785
6102.24230.5120.152-0.4054.713
Phasing MAD shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
12.01-500.2050.36101096247
6.82-12.010.3470.4940532374158
4.76-6.820.4650.59201201943258
3.66-4.760.4470.534021521801351
2.97-3.660.440.507033382896442
2.5-2.970.3610.407048434298545
2.16-2.50.2220.245065715939632
1.9-2.160.1120.122085517833718
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 27297
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
7.39-10073.10.315502
5.86-7.3965.80.839503
5.09-5.8660.70.908501
4.57-5.0961.40.925575
4.17-4.5761.30.918633
3.87-4.1759.60.919670
3.62-3.8760.80.916732
3.42-3.6258.20.892755
3.24-3.4258.50.893819
3.09-3.2461.60.883834
2.96-3.09580.885889
2.85-2.9657.40.882921
2.74-2.8562.70.863953
2.65-2.7460.40.875964
2.57-2.6563.40.8551032
2.49-2.5763.80.8481041
2.42-2.49680.8621079
2.36-2.4269.50.8471100
2.3-2.3669.60.8561126
2.24-2.370.50.8341168
2.19-2.2473.30.8541164
2.14-2.1975.10.8561226
2.1-2.1474.20.8651210
2.06-2.174.80.8831289
2.02-2.0676.30.8641257
1.98-2.0279.90.8531317
1.94-1.9881.60.8131327
1.9-1.9483.90.7451710

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
DM6phasing
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
SHELXDphasing
SHELXEmodel building
SOLVEphasing
RESOLVEphasing
ARP/wARPmodel building
CCP4phasing
Omodel building
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.9→38.98 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.948 / Occupancy max: 1 / Occupancy min: 0.8 / SU B: 6.203 / SU ML: 0.081 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.122
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2112 1364 5 %RANDOM
Rwork0.1825 ---
all0.184 27125 --
obs0.184 27125 99.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 108.01 Å2 / Biso mean: 46.1636 Å2 / Biso min: 25.67 Å2
Baniso -1Baniso -2Baniso -3
1-2.52 Å20 Å20 Å2
2--1.07 Å20 Å2
3----3.59 Å2
Refinement stepCycle: LAST / Resolution: 1.9→38.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2089 0 61 120 2270
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0222193
X-RAY DIFFRACTIONr_bond_other_d0.0010.021520
X-RAY DIFFRACTIONr_angle_refined_deg1.3391.9592955
X-RAY DIFFRACTIONr_angle_other_deg0.85933674
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5595249
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.45924.286112
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.27615368
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.2821512
X-RAY DIFFRACTIONr_chiral_restr0.0890.2305
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212369
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02459
X-RAY DIFFRACTIONr_mcbond_it0.8881.51259
X-RAY DIFFRACTIONr_mcbond_other0.2281.5502
X-RAY DIFFRACTIONr_mcangle_it1.70322036
X-RAY DIFFRACTIONr_scbond_it2.5333934
X-RAY DIFFRACTIONr_scangle_it4.1884.5919
LS refinement shellResolution: 1.904→1.953 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.279 93 -
Rwork0.267 1863 -
all-1956 -
obs--98.19 %
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)
11.46440.09611.35071.62091.1646.0739-0.07080.08730.11220.15460.0766-0.1607-0.17450.5316-0.00580.05010.0038-0.00950.07480.00590.065850.206930.45172.9199
21.5699-0.9919-0.55353.36760.09272.7669-0.2455-0.2907-0.00970.57710.22120.0493-0.1752-0.12970.02440.13070.0531-0.00040.12110.01180.007258.754914.563225.7297
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 131
2X-RAY DIFFRACTION2B5 - 131

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