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- PDB-3dmn: The crystal structure of the C-terminal domain of a possilbe DNA ... -

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Basic information

Entry
Database: PDB / ID: 3dmn
TitleThe crystal structure of the C-terminal domain of a possilbe DNA helicase from Lactobacillus plantarun WCFS1
ComponentsPutative DNA helicase
Keywordsstructural genomics / unknown function / APC89291.2 / DNA helicase / Lactobacillus plantarum WCFS1 / PSI-2 / midwest center for structural genomics / MCSG / Protein Structure Initiative / Helicase
Function / homology
Function and homology information


recombinational repair / 3'-5' DNA helicase activity / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / hydrolase activity / DNA binding / ATP binding / cytosol
Similarity search - Function
: / UvrD-like helicase C-terminal domain / UvrD-like helicase C-terminal domain / UvrD/REP helicase N-terminal domain / UvrD-like helicase, ATP-binding domain / UvrD-like DNA helicase ATP-binding domain profile. / DNA helicase, UvrD/REP type / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase ...: / UvrD-like helicase C-terminal domain / UvrD-like helicase C-terminal domain / UvrD/REP helicase N-terminal domain / UvrD-like helicase, ATP-binding domain / UvrD-like DNA helicase ATP-binding domain profile. / DNA helicase, UvrD/REP type / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / FORMIC ACID / DNA helicase / :
Similarity search - Component
Biological speciesLactobacillus plantarum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.66 Å
AuthorsTan, K. / Zhou, M. / Gu, M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of the C-terminal domain of a possilbe DNA helicase from Lactobacillus plantarun WCFS1
Authors: Tan, K. / Zhou, M. / Gu, M. / Joachimiak, A.
History
DepositionJul 1, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative DNA helicase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,12616
Polymers19,2601
Non-polymers86615
Water3,387188
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)99.292, 99.292, 72.365
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Detailsauthors state that the biological unit is experimentally unknown. The domain seems to be monomeric in solution.

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Components

#1: Protein Putative DNA helicase


Mass: 19260.322 Da / Num. of mol.: 1 / Fragment: C-terminal residues 597-767
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus plantarum (bacteria) / Strain: WCFS1 / Gene: lp_0910 / Plasmid: pMCSG19 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q88Y78, UniProt: F9UMB1*PLUS
#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 188 / 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: 2.67 Å3/Da / Density % sol: 53.99 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1M HEPES, 30% (w/v) Jeffamine ED-2001@Reagent pH70, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 20, 2007 / Details: mirror
RadiationMonochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.65→23.85 Å / Num. all: 25526 / Num. obs: 25526 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.8 % / Rmerge(I) obs: 0.101 / Net I/σ(I): 52.4
Reflection shellResolution: 1.65→1.69 Å / Redundancy: 15.2 % / Rmerge(I) obs: 0.709 / Mean I/σ(I) obs: 4.2 / Num. unique all: 1641 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
SHELXDphasing
MLPHAREphasing
DMphasing
RESOLVEphasing
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.66→23.8 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.943 / SU B: 2.922 / SU ML: 0.053 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.093 / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22538 1294 5.1 %RANDOM
Rwork0.19126 ---
all0.19291 24182 --
obs0.19291 24182 99.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.302 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å2-0.03 Å20 Å2
2---0.05 Å20 Å2
3---0.08 Å2
Refinement stepCycle: LAST / Resolution: 1.66→23.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1246 0 58 188 1492
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221320
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.661.9861778
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6095164
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.42225.57461
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.39715223
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.311158
X-RAY DIFFRACTIONr_chiral_restr0.1520.2212
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02998
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2350.2721
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3120.2898
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1360.2150
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2950.281
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1470.222
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1941.5866
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.73821332
X-RAY DIFFRACTIONr_scbond_it2.6213500
X-RAY DIFFRACTIONr_scangle_it4.1224.5443
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.656→1.699 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 96 -
Rwork0.237 1692 -
obs-1788 98.03 %
Refinement TLS params.Method: refined / Origin x: 39.094 Å / Origin y: 56.143 Å / Origin z: 2.76 Å
111213212223313233
T-0.1605 Å20.0021 Å2-0.0116 Å2--0.169 Å2-0.007 Å2---0.2062 Å2
L1.0429 °20.2768 °2-0.3478 °2-0.7971 °2-0.2996 °2--0.9455 °2
S0.031 Å °0.109 Å °0.0055 Å °-0.0907 Å °-0.004 Å °0.0252 Å °0.0719 Å °-0.0156 Å °-0.027 Å °

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