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- PDB-2duy: Crystal structure of competence protein ComEA-related protein fro... -

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Basic information

Entry
Database: PDB / ID: 2duy
TitleCrystal structure of competence protein ComEA-related protein from Thermus thermophilus HB8
ComponentsCompetence protein ComEA-related protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / HELIX-HAIRPIN-HELIX / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homologyPhotosystem II 12 kDa extrinsic protein / Helix-hairpin-helix DNA-binding motif, class 1 / Helix-hairpin-helix DNA-binding motif class 1 / DNA polymerase; domain 1 / DNA repair / DNA binding / Orthogonal Bundle / Mainly Alpha / Competence protein ComEA-related protein
Function and homology information
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.75 Å
AuthorsNiwa, H. / Shimada, A. / Chen, L. / Liu, Z.-J. / Wang, B.-C. / Ebihara, A. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of competence protein ComEA-related protein from Thermus thermophilus HB8
Authors: Niwa, H. / Shimada, A. / Chen, L. / Liu, Z.-J. / Wang, B.-C. / Ebihara, A. / Yokoyama, S.
History
DepositionJul 27, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 14, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Competence protein ComEA-related protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,3232
Polymers8,2871
Non-polymers351
Water66737
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Competence protein ComEA-related protein
hetero molecules

A: Competence protein ComEA-related protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,6464
Polymers16,5752
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area960 Å2
ΔGint-19 kcal/mol
Surface area7130 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)42.635, 42.635, 53.756
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-100-

CL

21A-136-

HOH

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Components

#1: Protein Competence protein ComEA-related protein


Mass: 8287.488 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta834(DE3) / References: UniProt: Q5SGW3
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
11.472216.451578
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2931vapor diffusion, sitting drop6.41.5M Ammonium citrate, 0.1M Bis-tris propane, pH 6.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K
2932vapor diffusion, sitting drop6.61.5M Ammonium citrate, 0.1M Bis-tris propane, pH 6.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 22-ID10.9724
SYNCHROTRONSPring-8 BL26B220.9789, 0.9793, 0.9000
Detector
TypeIDDetectorDate
MARMOSAIC 300 mm CCD1CCDFeb 12, 2006
RIGAKU JUPITER 2102CCDDec 16, 2005
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SI DOUBLE CRYSTALSINGLE WAVELENGTHMx-ray1
2SI DOUBLE CRYSTALMADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.97241
20.97891
30.97931
40.91
ReflectionResolution: 1.75→50 Å / Num. all: 5420 / Num. obs: 5420 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 26 % / Biso Wilson estimate: 18 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 69.2
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 19.6 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 10.2 / Num. unique all: 522 / % possible all: 99.6

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 1.75→50 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 861188.7 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.218 809 15.1 %RANDOM
Rwork0.188 ---
all0.193 5383 --
obs0.193 5352 99.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 40.246 Å2 / ksol: 0.354968 e/Å3
Displacement parametersBiso mean: 23.7 Å2
Baniso -1Baniso -2Baniso -3
1-2.02 Å20 Å20 Å2
2--2.02 Å20 Å2
3----4.04 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.12 Å0.11 Å
Refinement stepCycle: LAST / Resolution: 1.75→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms500 0 1 37 538
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.15
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.361.5
X-RAY DIFFRACTIONc_mcangle_it2.062
X-RAY DIFFRACTIONc_scbond_it2.432
X-RAY DIFFRACTIONc_scangle_it3.662.5
LS refinement shellResolution: 1.75→1.86 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.289 123 14.4 %
Rwork0.242 734 -
obs-857 98.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

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