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- PDB-1bcm: BACTERIOPHAGE MU TRANSPOSASE CORE DOMAIN WITH 2 MONOMERS PER ASYM... -

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Basic information

Entry
Database: PDB / ID: 1bcm
TitleBACTERIOPHAGE MU TRANSPOSASE CORE DOMAIN WITH 2 MONOMERS PER ASYMMETRIC UNIT
ComponentsBACTERIOPHAGE MU TRANSPOSASE
KeywordsTRANSPOSASE / POLYNUCLEOTIDYL TRANSFERASE / DNA BINDING / ENDONUCLEASE / INTEGRASE
Function / homology
Function and homology information


Ligases; Forming phosphoric-ester bonds / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 3'-phosphomonoesters / latency-replication decision / transposase activity / DNA transposition / double-stranded DNA endonuclease activity / viral DNA genome replication / ligase activity / DNA integration / DNA replication ...Ligases; Forming phosphoric-ester bonds / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 3'-phosphomonoesters / latency-replication decision / transposase activity / DNA transposition / double-stranded DNA endonuclease activity / viral DNA genome replication / ligase activity / DNA integration / DNA replication / host cell cytoplasm / DNA repair / DNA binding / metal ion binding
Similarity search - Function
Transposase, Mu, C-terminal / Bacteriophage Mu, transposase / Transposase, Mu, C-terminal / Mu DNA binding, I gamma subdomain / Transposase-like, Mu, C-terminal / Bacteriophage Mu transposase / Mu DNA binding, I gamma subdomain / Mu transposase, C-terminal / Mu-type HTH domain / Mu DNA-binding domain ...Transposase, Mu, C-terminal / Bacteriophage Mu, transposase / Transposase, Mu, C-terminal / Mu DNA binding, I gamma subdomain / Transposase-like, Mu, C-terminal / Bacteriophage Mu transposase / Mu DNA binding, I gamma subdomain / Mu transposase, C-terminal / Mu-type HTH domain / Mu DNA-binding domain / Mu-type HTH domain profile. / Putative DNA-binding domain superfamily / Ribonuclease H-like superfamily/Ribonuclease H / Homeobox-like domain superfamily / SH3 type barrels. / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Roll / Winged helix-like DNA-binding domain superfamily / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesEnterobacteria phage Mu (virus)
MethodX-RAY DIFFRACTION / Resolution: 2.8 Å
AuthorsRice, P.A. / Mizuuchi, K.
CitationJournal: Cell(Cambridge,Mass.) / Year: 1995
Title: Structure of the bacteriophage Mu transposase core: a common structural motif for DNA transposition and retroviral integration.
Authors: Rice, P. / Mizuuchi, K.
History
DepositionMay 26, 1995Processing site: BNL
Revision 1.0Oct 15, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BACTERIOPHAGE MU TRANSPOSASE
B: BACTERIOPHAGE MU TRANSPOSASE


Theoretical massNumber of molelcules
Total (without water)73,7762
Polymers73,7762
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)172.200, 52.200, 101.600
Angle α, β, γ (deg.)90.00, 115.50, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.6177, -0.0594, -0.7841), (-0.0103, -0.9964, 0.0836), (-0.7863, 0.0598, 0.6149)
Vector: 66.5149, 18.365, 31.8693)
DetailsMTRIX THE TRANSFORMATIONS PRESENTED ON MTRIX RECORDS BELOW DESCRIBE NON-CRYSTALLOGRAPHIC RELATIONSHIPS AMONG THE VARIOUS DOMAINS IN THIS ENTRY. APPLYING THE APPROPRIATE MTRIX TRANSFORMATION TO THE RESIDUES LISTED FIRST WILL YIELD APPROXIMATE COORDINATES FOR THE RESIDUES LISTED SECOND. APPLIED TO TRANSFORMED TO MTRIX RESIDUES RESIDUES RMSD M1 B 258 .. B 560 A 258 .. A 560 0.593 THIS REPRESENTS A NON-CRYSTALLOGRAPHIC TWO-FOLD AXIS.

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Components

#1: Protein BACTERIOPHAGE MU TRANSPOSASE / MUA DOMAIN II


Mass: 36888.078 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage Mu (virus) / Genus: Mu-like viruses / Strain: WILD TYPE / Gene: MUA (AMINO ACIDS 248 - 574) / Plasmid: PMK602 / Gene (production host): MUA (AMINO ACIDS 248 - 574) / Production host: Escherichia coli (E. coli) / Strain (production host): T7 / References: UniProt: P07636

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.79 Å3/Da / Density % sol: 55.95 %
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
113-16 %(w/v)PEG40001reservoir
20.2 M1reservoirLi2SO4
375 mMNa3 citrate1reservoir
42-15 mMDTT1reservoir
516 mg/mlprotain1drop

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Data collection

Diffraction sourceWavelength: 1.54
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Aug 27, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.7→20 Å / Num. obs: 21089 / % possible obs: 92.5 % / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Rmerge(I) obs: 0.095
Reflection
*PLUS
Highest resolution: 2.7 Å / Rmerge(I) obs: 0.095

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1phasing
RefinementResolution: 2.8→8 Å / σ(F): 1
Details: RESIDUES ARG A 355 AND ARG B 355 LIE IN A DISALLOWED REGION OF A RAMACHANDRAN PLOT. THIS WAS CONFIRMED IN THE C 2 2 21 STRUCTURE BY SIMULATED ANNEALING OMIT MAP.
RfactorNum. reflection% reflection
Rfree0.276 -5 %
Rwork0.214 --
obs0.214 18179 93 %
Displacement parametersBiso mean: 20.7 Å2
Refinement stepCycle: LAST / Resolution: 2.8→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5815 0 0 0 5815
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.321
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scbond_it2
X-RAY DIFFRACTIONx_scangle_it2.5
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.32
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shell
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 2.92 Å

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