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- PDB-3gdw: Crystal structure of sigma-54 interaction domain protein from Ent... -

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Basic information

Entry
Database: PDB / ID: 3gdw
TitleCrystal structure of sigma-54 interaction domain protein from Enterococcus faecalis
ComponentsSigma-54 interaction domain protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Enterococcus faecalis / sigma-54 interaction domain protein / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG / ATP-binding / Nucleotide-binding
Function / homology
Function and homology information


phosphoenolpyruvate-dependent sugar phosphotransferase system / transcription factor binding / kinase activity / membrane => GO:0016020 / regulation of DNA-templated transcription / ATP binding
Similarity search - Function
PRD domain / PRD domain / PRD domain superfamily / PRD domain profile. / PTS system mannose/sorbose specific IIA subunit / Phosphotransferase system, mannose-type IIA component / Phosphotransferase system, mannose-type IIA component / Phosphotransferase system, mannose-type IIA component superfamily / PTS system fructose IIA component / PTS_EIIA type-4 domain profile. ...PRD domain / PRD domain / PRD domain superfamily / PRD domain profile. / PTS system mannose/sorbose specific IIA subunit / Phosphotransferase system, mannose-type IIA component / Phosphotransferase system, mannose-type IIA component / Phosphotransferase system, mannose-type IIA component superfamily / PTS system fructose IIA component / PTS_EIIA type-4 domain profile. / Sigma-54 interaction domain, ATP-binding site 2 / Sigma-54 interaction domain ATP-binding region B signature. / Sigma-54 interaction domain profile. / Sigma-54 interaction domain / RNA polymerase sigma factor 54 interaction domain / ArsR-like helix-turn-helix domain / Winged helix DNA-binding domain superfamily / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Sigma-54 interaction domain protein
Similarity search - Component
Biological speciesEnterococcus faecalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsChang, C. / Sather, A. / Buck, K. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of sigma-54 interaction domain protein from Enterococcus faecalis
Authors: Chang, C. / Sather, A. / Buck, K. / Joachimiak, A.
History
DepositionFeb 24, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / 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: Sigma-54 interaction domain protein
B: Sigma-54 interaction domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8693
Polymers31,8072
Non-polymers621
Water3,603200
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2910 Å2
ΔGint-25.7 kcal/mol
Surface area12120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.127, 71.418, 94.502
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Sigma-54 interaction domain protein


Mass: 15903.516 Da / Num. of mol.: 2 / Fragment: UNP residues 544-679
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecalis (bacteria) / Strain: V583 / Gene: EF_1010 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: Q836U6
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 200 / 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: 2.29 Å3/Da / Density % sol: 46.24 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M Sodium malonate, 20% PEG 3350, pH 7.0, 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: 0.97931 Å
DetectorType: ADSC QUANTUM Q315r / Detector: CCD / Date: Jan 31, 2009
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 20362 / Num. obs: 20315 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 13.7 % / Biso Wilson estimate: 34.8 Å2 / Rmerge(I) obs: 0.109 / Net I/σ(I): 65.7
Reflection shellResolution: 2→2.02 Å / Redundancy: 13.8 % / Rmerge(I) obs: 0.606 / Mean I/σ(I) obs: 6.35 / Num. unique all: 483 / % possible all: 99.8

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000phasing
MLPHAREphasing
DMmodel building
SHELXDphasing
RESOLVEmodel building
ARP/wARPmodel building
Cootmodel building
REFMAC5.5.0054refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2→50 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.958 / SU B: 8.777 / SU ML: 0.111 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.187 / ESU R Free: 0.155 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21431 1041 5.1 %RANDOM
Rwork0.18349 ---
all0.18503 20261 --
obs0.18503 20261 99.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.495 Å2
Baniso -1Baniso -2Baniso -3
1-1.97 Å20 Å20 Å2
2---0.75 Å20 Å2
3----1.23 Å2
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2088 0 4 200 2292
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0222230
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3291.9653018
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9735296
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.41225.62596
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.23915433
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4051513
X-RAY DIFFRACTIONr_chiral_restr0.0890.2363
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021639
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.7241.51424
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.35722316
X-RAY DIFFRACTIONr_scbond_it2.7013806
X-RAY DIFFRACTIONr_scangle_it4.3154.5702
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.266 68 -
Rwork0.203 1363 -
obs-1431 97.21 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.5928-0.7552-0.32713.12070.48521.1298-0.0812-0.0838-0.0347-0.10350.00340.08010.0145-0.06020.07780.0295-0.01180.00040.0779-0.02040.011122.031623.045619.4271
23.3677-1.9299-0.55877.9540.44892.8780.19610.2230.1639-0.7998-0.0689-0.1295-0.0889-0.0635-0.12710.0918-0.01060.01130.09430.01010.013725.855227.51129.947
30.35360.1201-0.09223.61672.17233.0853-0.0917-0.14640.07-0.20810.2758-0.7365-0.01020.4364-0.18410.0972-0.02530.05530.2275-0.0480.257539.525319.648813.4933
41.4556-0.9941-0.19261.3283-0.38632.15-0.0597-0.1558-0.2061-0.08130.06970.02810.2330.0894-0.010.0566-0.00530.00440.06060.0550.099128.0231-3.15316.0898
51.8501-2.09630.14258.15110.74924.32810.0158-0.1504-0.0364-0.21140.0252-0.43580.25220.4713-0.04110.04030.04740.05460.14750.01660.141837.8898-3.432411.5663
60.17890.3155-0.23511.705-1.33341.1575-0.00370.1199-0.0787-0.40320.14240.05490.1567-0.0633-0.13870.3656-0.02830.08160.1422-0.080.152831.88957.85320.7237
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A541 - 602
2X-RAY DIFFRACTION2A603 - 636
3X-RAY DIFFRACTION3A637 - 675
4X-RAY DIFFRACTION4B541 - 602
5X-RAY DIFFRACTION5B603 - 636
6X-RAY DIFFRACTION6B637 - 675

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