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1bcm

BACTERIOPHAGE MU TRANSPOSASE CORE DOMAIN WITH 2 MONOMERS PER ASYMMETRIC UNIT

Method: X-RAY DIFFRACTION Dmax: 95.0 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

BACTERIOPHAGE MU 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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 248–574 Chain B； UniProt 248–574 Not recorded No other associated polymer X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 2.80 Å R-free 0.276

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 1BCM Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1BCO BACTERIOPHAGE MU TRANSPOSASE CORE DOMAIN Deposited 1995-05-26 Different construct Different mutation/modification Different oligomeric state 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 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 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
4FCY Crystal structure of the bacteriophage Mu transpososome Deposited 2012-05-25 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Homooligomer；Protein × 4 PDB declaration: decameric
Chain A 77–605（529 aa） Fragment：UNP residues 77-605
Chain B 77–605（529 aa） Fragment：UNP residues 77-605
Mutation：M521L, N525L Mutation：M521L, N525L No recorded non-water small molecule 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
4FCY Crystal structure of the bacteriophage Mu transpososome Deposited 2012-05-25 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Homooligomer；Protein × 8 PDB declaration: eicosameric
Chain A 77–605（529 aa） Fragment：UNP residues 77-605
Chain B 77–605（529 aa） Fragment：UNP residues 77-605
Mutation：M521L, N525L Mutation：M521L, N525L No recorded non-water small molecule 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

8 other PDB entries and 9 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 1–327； UniProt 248–574 Author chain B； PDBConstruct 1–327； UniProt 248–574

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 1bcm

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1bcm
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1bcm
Deposition date deposition_date1995-05-26
Structure title titleBACTERIOPHAGE MU TRANSPOSASE CORE DOMAIN WITH 2 MONOMERS PER ASYMMETRIC UNIT
Keywords keywordsPOLYNUCLEOTIDYL TRANSFERASE, DNA BINDING, ENDONUCLEASE, INTEGRASE, TRANSPOSASE; TRANSPOSASE
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_guinier28.35 Å
Radius of gyration Rg (electron density) rg_electron27.37 Å
Forward intensity I(0) i073844400.00
Molecular weight molecular_weight67466.0 kDa
Excluded volume excluded_volume84519 ų
Envelope volume envelope_volume104840 ų
Hydration-shell volume shell_volume32402 ų
Envelope diameter envelope_diameter98.0 Å
Shell Rg shell_rg34.04 Å
Envelope Rg envelope_rg27.40 Å
Shape Rg shape_rg27.37 Å
Total Rg total_rg28.05 Å
Total atoms total_atoms5815
Residues n_residues607
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 dmax95.0 Å
Rg (real space) rg_real28.34 Å
Rg uncertainty (real space) rg_real_error0.58 Å
I(0) (real space) i0_real7.3840e+07
I(0) uncertainty (real space) i0_real_error9.9980e+05
Rg (reciprocal space) rg_reciprocal28.35 Å
I(0) (reciprocal space) i0_reciprocal73840000.0000
Solution quality estimate total_estimate0.8835
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary33.9 Å
Skewness Skewness skewness0.354
Kurtosis Kurtosis kurtosis-0.235
Angular range angular_range— – 0.2800 Å−1
Current regularization parameter α current_alpha0.0001
Highest regularization parameter α highest_alpha17780000.0000
Real-space data points n_real_points57
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.853; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.982; Smooth: 0.941
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd1bcma1
Class classb — All beta proteins
Fold Fold foldb.48 — mu transposase, C-terminal domain
Superfamily Superfamily superfamilyb.48.1 — mu transposase, C-terminal domain
Family Family familyb.48.1.1 — mu transposase, C-terminal domain
Domain ID domain_idd1bcma2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamilyc.55.3 — Ribonuclease H-like
Family Family familyc.55.3.3 — mu transposase, core domain
Domain ID domain_idd1bcmb1
Class classb — All beta proteins
Fold Fold foldb.48 — mu transposase, C-terminal domain
Superfamily Superfamily superfamilyb.48.1 — mu transposase, C-terminal domain
Family Family familyb.48.1.1 — mu transposase, C-terminal domain
Domain ID domain_idd1bcmb2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamilyc.55.3 — Ribonuclease H-like
Family Family familyc.55.3.3 — mu transposase, core domain

CATH v4.4 (4 domains)

Domain ID domain_id1bcmA01
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_id1bcmA02
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology30 — SH3 type barrels.
Homologous superfamily homologous superfamily130 — Transposase, Mu, C-terminal
Domain ID domain_id1bcmB01
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_id1bcmB02
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology30 — SH3 type barrels.
Homologous superfamily homologous superfamily130 — Transposase, Mu, C-terminal
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8. Citations (1)

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9. Files and Curves (10)