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- PDB-2ppx: Crystal structure of a HTH XRE-family like protein from Agrobacte... -

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Basic information

Entry
Database: PDB / ID: 2ppx
TitleCrystal structure of a HTH XRE-family like protein from Agrobacterium tumefaciens
ComponentsUncharacterized protein Atu1735
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Agrobacterium tumefaciens / HTH-motif / XRE-family / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


Helix-turn-helix / Helix-turn-helix XRE-family like proteins / Cro/C1-type HTH domain profile. / lambda repressor-like DNA-binding domains / Cro/C1-type helix-turn-helix domain / 434 Repressor (Amino-terminal Domain) / Lambda repressor-like, DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
HTH cro/C1-type domain-containing protein / :
Similarity search - Component
Biological speciesAgrobacterium tumefaciens str. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsCuff, M.E. / Skarina, T. / Onopriyenko, O. / Edwards, A. / Savchenko, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: TO BE PUBLISHED
Title: Structure of a HTH XRE-family like protein from Agrobacterium tumefaciens.
Authors: Cuff, M.E. / Skarina, T. / Onopriyenko, O. / Edwards, A. / Savchenko, A. / Joachimiak, A.
History
DepositionApr 30, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations ...Advisory / Derived calculations / Source and taxonomy / Version format compliance
Remark 300 BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 ... BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). AUTHORS STATE THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS UNKNOWN. THE POTENTIAL TETRAMERIC ASSEMBLY SHOWN IN REMARK 350 IS PREDICTED BY THE ANALYSIS OF PROTEIN INTERFACES BASED ON THIS CRYSTAL STRUCTURE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein Atu1735
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,6889
Polymers10,9281
Non-polymers7618
Water1,22568
1
A: Uncharacterized protein Atu1735
hetero molecules

A: Uncharacterized protein Atu1735
hetero molecules

A: Uncharacterized protein Atu1735
hetero molecules

A: Uncharacterized protein Atu1735
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,75436
Polymers43,7124
Non-polymers3,04232
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_655-x+1,-y,z1
crystal symmetry operation8_555x-y,-y,-z1
crystal symmetry operation11_655-x+y+1,y,-z1
Buried area10260 Å2
ΔGint-285 kcal/mol
Surface area12930 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)70.696, 70.696, 103.736
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422
Components on special symmetry positions
IDModelComponents
11A-223-

HOH

21A-225-

HOH

31A-269-

HOH

Detailspotential tetramer

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Components

#1: Protein Uncharacterized protein Atu1735 / AGR_C_3184p


Mass: 10927.922 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium tumefaciens str. (bacteria)
Species: Agrobacterium tumefaciens / Strain: C58 / Gene: Atu1735, AGR_C_3184 / Plasmid: modified p11 / Production host: Escherichia coli (E. coli) / Strain (production host): modified BL21(DE3) / References: UniProt: Q8UEM2, UniProt: A9CIQ1*PLUS
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 68 / 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: 3.42 Å3/Da / Density % sol: 64.05 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 2M Ammonium sulfate, 0.2M K/Na tartrate, 0.1M Na citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97948, 0.97935
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 5, 2006
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979481
20.979351
ReflectionResolution: 1.95→35.35 Å / Num. all: 10649 / Num. obs: 10649 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 38.6 Å2 / Rsym value: 0.049 / Net I/σ(I): 11.9
Reflection shellResolution: 1.95→2.05 Å / Redundancy: 5.9 % / Mean I/σ(I) obs: 2 / Rsym value: 0.347 / % possible all: 81.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
SHELXDphasing
SHELXEmodel building
MLPHAREphasing
DMphasing
SOLVEphasing
RESOLVEphasing
ARP/wARPmodel building
CCP4phasing
Omodel building
Cootmodel building
RefinementMethod to determine structure: MAD / Resolution: 2→35.35 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.93 / SU B: 5.095 / SU ML: 0.075 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3 / ESU R: 0.118 / ESU R Free: 0.126
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24382 509 4.8 %RANDOM
Rwork0.19607 ---
all0.19831 10139 --
obs0.19831 10139 97.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 65.677 Å2
Baniso -1Baniso -2Baniso -3
1-0.9 Å20.45 Å20 Å2
2--0.9 Å20 Å2
3----1.35 Å2
Refinement stepCycle: LAST / Resolution: 2→35.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms501 0 42 68 611
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.022586
X-RAY DIFFRACTIONr_angle_refined_deg1.452.045798
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.268571
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.97421.48127
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.76915105
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.649159
X-RAY DIFFRACTIONr_chiral_restr0.1120.281
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02428
X-RAY DIFFRACTIONr_nbd_refined0.2070.2271
X-RAY DIFFRACTIONr_nbtor_refined0.3070.2382
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1230.254
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1840.225
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1240.29
X-RAY DIFFRACTIONr_mcbond_it0.8341.5347
X-RAY DIFFRACTIONr_mcangle_it1.3122542
X-RAY DIFFRACTIONr_scbond_it2.3563268
X-RAY DIFFRACTIONr_scangle_it3.8564.5253
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.396 34 -
Rwork0.31 616 -
obs--83.12 %
Refinement TLS params.Method: refined / Origin x: 44.6426 Å / Origin y: 3.0189 Å / Origin z: 11.9951 Å
111213212223313233
T-0.2037 Å2-0.0742 Å2-0.0435 Å2--0.4355 Å2-0.0405 Å2---0.47 Å2
L4.0654 °21.6966 °20.7968 °2-4.0375 °20.2281 °2--5.0941 °2
S0.3751 Å °-0.3671 Å °-0.1045 Å °0.3664 Å °-0.0809 Å °-0.2228 Å °0.1751 Å °0.1834 Å °-0.2942 Å °

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