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4fcy

Crystal structure of the bacteriophage Mu transpososome

Method: X-RAY DIFFRACTION Dmax: 193.8 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Transposase

Enterobacteria phage Mu

UniProt P07636

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–DNA Homooligomer Protein × 4 DNA 6 PDB declaration: decameric（10） Consistent with all polymer counts Chain A； UniProt 77–605 Chain B； UniProt 77–605 Fragment：UNP residues 77-605 Mutation：M521L, N525L DNA (68-MER) × 2 DNA (13-MER) × 2 DNA (49-MER) × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；292 K；24-28% PEG400, 0.2 M magnesium chloride, 0.1 M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K Resolution 3.71 Å R-free 0.437
2 Protein–DNA Homooligomer Protein × 8 DNA 12 PDB declaration: eicosameric（20） Consistent with all polymer counts Chain A； UniProt 77–605 Chain B； UniProt 77–605 Fragment：UNP residues 77-605 Mutation：M521L, N525L DNA (68-MER) × 4 DNA (13-MER) × 4 DNA (49-MER) × 4 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；292 K；24-28% PEG400, 0.2 M magnesium chloride, 0.1 M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K Resolution 3.71 Å R-free 0.437

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 4FCY Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1BCM BACTERIOPHAGE MU TRANSPOSASE CORE DOMAIN WITH 2 MONOMERS PER ASYMMETRIC UNIT Deposited 1995-05-26 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 248–574（327 aa）
Chain B 248–574（327 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.80 Å R-free 0.276
1BCO BACTERIOPHAGE MU TRANSPOSASE CORE DOMAIN Deposited 1995-05-26 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 248–574（327 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.40 Å R-free 0.260
1TNS A NOVEL CLASS OF WINGED HELIX-TURN-HELIX PROTEIN: THE DNA-BINDING DOMAIN OF MU TRANSPOSASE Deposited 1994-10-10 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–76（76 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR mmCIF provides none of the parsed conditions Resolution not provided
1TNT A NOVEL CLASS OF WINGED HELIX-TURN-HELIX PROTEIN: THE DNA-BINDING DOMAIN OF MU TRANSPOSASE Deposited 1994-10-10 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–76（76 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR mmCIF provides none of the parsed conditions Resolution not provided
2EZH SOLUTION NMR STRUCTURE OF THE IGAMMA SUBDOMAIN OF THE MU END DNA BINDING DOMAIN OF MU PHAGE TRANSPOSASE, MINIMIZED AVERAGE STRUCTURE Deposited 1997-07-25 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 174–247（74 aa） Fragment：IGAMMA SUBDOMAIN, RESIDUES 174 - 247
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.3；303 K
Resolution not provided
2EZI SOLUTION NMR STRUCTURE OF THE IGAMMA SUBDOMAIN OF THE MU END DNA BINDING DOMAIN OF MU PHAGE TRANSPOSASE, 30 STRUCTURES Deposited 1997-07-25 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 174–247（74 aa） Fragment：IGAMMA SUBDOMAIN, RESIDUES 174 - 247
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.3；303 K
Resolution not provided
2EZK SOLUTION NMR STRUCTURE OF THE IBETA SUBDOMAIN OF THE MU END DNA BINDING DOMAIN OF PHAGE MU TRANSPOSASE, REGULARIZED MEAN STRUCTURE Deposited 1997-10-04 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 77–174（98 aa） Fragment：IBETA SUBDOMAIN, RESIDUES 77 - 174
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.3；303 K
Resolution not provided
2EZL SOLUTION NMR STRUCTURE OF THE IBETA SUBDOMAIN OF THE MU END DNA BINDING DOMAIN OF PHAGE MU TRANSPOSASE, 29 STRUCTURES Deposited 1997-10-04 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 77–174（98 aa） Fragment：IBETA SUBDOMAIN, RESIDUES 77 - 174
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.3；303 K
Resolution not provided

8 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TRA_BPMU
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–529； UniProt 77–605 Author chain B； PDBConstruct 1–529； UniProt 77–605

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 4fcy

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4fcy
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4fcy
Deposition date deposition_date2012-05-25
Structure title titleCrystal structure of the bacteriophage Mu transpososome
Keywords keywordsRNaseH, DDE transposase, DNA BINDING PROTEIN-DNA complex; DNA BINDING PROTEIN/DNA
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier54.99 Å
Radius of gyration Rg (electron density) rg_electron54.58 Å
Forward intensity I(0) i0439745000.00
Molecular weight molecular_weight145080.0 kDa
Excluded volume excluded_volume170040 ų
Envelope volume envelope_volume307350 ų
Hydration-shell volume shell_volume53601 ų
Envelope diameter envelope_diameter204.7 Å
Shell Rg shell_rg48.00 Å
Envelope Rg envelope_rg53.97 Å
Shape Rg shape_rg54.46 Å
Total Rg total_rg54.66 Å
Total atoms total_atoms10056
Residues n_residues1049
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax193.8 Å
Rg (real space) rg_real55.87 Å
Rg uncertainty (real space) rg_real_error2.47 Å
I(0) (real space) i0_real4.3970e+08
I(0) uncertainty (real space) i0_real_error8.7840e+06
Rg (reciprocal space) rg_reciprocal54.28 Å
I(0) (reciprocal space) i0_reciprocal438700000.0000
Solution quality estimate total_estimate0.7741
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary53.5 Å
Skewness Skewness skewness0.714
Kurtosis Kurtosis kurtosis0.040
Angular range angular_range— – 0.1450 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha15880000.0000
Real-space data points n_real_points30
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.706; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.750; Smooth: 0.191
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

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7. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

Domain ID domain_id4fcyA01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily60 — Homeodomain-like
Domain ID domain_id4fcyA02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily60 — Homeodomain-like
Domain ID domain_id4fcyA03
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily10 — Ribonuclease H-like superfamily/Ribonuclease H
Domain ID domain_id4fcyB01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily60 — Homeodomain-like
Domain ID domain_id4fcyB02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily60 — Homeodomain-like
Domain ID domain_id4fcyB03
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily10 — Ribonuclease H-like superfamily/Ribonuclease H
Domain ID domain_id4fcyB04
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology30 — SH3 type barrels.
Homologous superfamily homologous superfamily130 — Transposase, Mu, C-terminal
Domain ID domain_id4fcyB05
Class class6 — Special
Architecture architecture10 — Helix non-globular
Topology topology250 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily2550 —
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8. Citations (1)

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9. Files and Curves (10)