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- PDB-2bw3: Three-dimensional structure of the Hermes DNA transposase -

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Basic information

Entry
Database: PDB / ID: 2bw3
TitleThree-dimensional structure of the Hermes DNA transposase
Components(TRANSPOSASE) x 2
KeywordsDNA RECOMBINATION / TRANSPOSITION
Function / homology
Function and homology information


nucleic acid metabolic process / protein dimerization activity / regulation of transcription by RNA polymerase II / DNA binding / identical protein binding / nucleus / metal ion binding
Similarity search - Function
Zinc finger, BED domain-containing / Hermes trasposase, DNA-binding domain / Hermes transposase DNA-binding domain / HAT, C-terminal dimerisation domain / hAT family C-terminal dimerisation region / BED zinc finger / Zinc finger, BED-type / Zinc finger BED-type profile. / Arc Repressor Mutant, subunit A / Ribonuclease H-like superfamily ...Zinc finger, BED domain-containing / Hermes trasposase, DNA-binding domain / Hermes transposase DNA-binding domain / HAT, C-terminal dimerisation domain / hAT family C-terminal dimerisation region / BED zinc finger / Zinc finger, BED-type / Zinc finger BED-type profile. / Arc Repressor Mutant, subunit A / Ribonuclease H-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Hermes transposase / Transposase
Similarity search - Component
Biological speciesMUSCA DOMESTICA (house fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsHickman, A.B. / Perez, Z.N. / Zhou, L. / Musingarimi, P. / Ghirlando, R. / Hinshaw, J.E. / Craig, N.L. / Dyda, F.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2005
Title: Molecular Architecture of a Eukaryotic DNA Transposase
Authors: Hickman, A.B. / Perez, Z.N. / Zhou, L. / Musingarimi, P. / Ghirlando, R. / Hinshaw, J.E. / Craig, N.L. / Dyda, F.
History
DepositionJul 11, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 28, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TRANSPOSASE
B: TRANSPOSASE


Theoretical massNumber of molelcules
Total (without water)71,0112
Polymers71,0112
Non-polymers00
Water7,494416
1
A: TRANSPOSASE
B: TRANSPOSASE

A: TRANSPOSASE
B: TRANSPOSASE


Theoretical massNumber of molelcules
Total (without water)142,0214
Polymers142,0214
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
MethodPQS
Unit cell
Length a, b, c (Å)116.353, 84.974, 73.856
Angle α, β, γ (deg.)90.00, 93.71, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein TRANSPOSASE


Mass: 61555.984 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUSCA DOMESTICA (house fly) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q25442, UniProt: Q25438*PLUS
#2: Protein TRANSPOSASE


Mass: 9454.559 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUSCA DOMESTICA (house fly) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q25442
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 416 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, SER 163 TO GLY ENGINEERED RESIDUE IN CHAIN A, LEU 233 TO SER ...ENGINEERED RESIDUE IN CHAIN A, SER 163 TO GLY ENGINEERED RESIDUE IN CHAIN A, LEU 233 TO SER ENGINEERED RESIDUE IN CHAIN A, VAL 286 TO MET

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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: 2.57 Å3/Da / Density % sol: 49.2 %
Crystal growpH: 6.6 / Details: pH 6.60

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.9686
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 23, 2004
RadiationMonochromator: SI 220 / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 48443 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 3.85 % / Biso Wilson estimate: 24.4 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 14.5
Reflection shellResolution: 2→2.05 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.17 / Mean I/σ(I) obs: 7.5 / % possible all: 99.9

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Processing

Software
NameVersionClassification
CNX2002refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASESphasing
RefinementMethod to determine structure: MAD / Resolution: 2→29.03 Å / Rfactor Rfree error: 0.006 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.211 1427 3 %RANDOM
Rwork0.185 ---
obs-47745 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 25.6589 Å2 / ksol: 0.304281 e/Å3
Displacement parametersBiso mean: 30 Å2
Baniso -1Baniso -2Baniso -3
1-1.28 Å20 Å2-0.52 Å2
2--3.23 Å20 Å2
3----4.52 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.15 Å0.1 Å
Refinement stepCycle: LAST / Resolution: 2→29.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4817 0 0 416 5233
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.012
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_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.5
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6 /
Rfactor% reflection
Rfree0.251 3.1 %
Rwork0.2 -
obs-95.4 %
Xplor fileSerial no: 1 / Param file: PARHCSDX.PRO / Topol file: TOPH19_MOD.SOL

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