3SOO | pdb_00003soo

Crystal structure of a LINE-1 type transposase domain-containing protein 1 (L1TD1) from HOMO SAPIENS at 2.73 A resolution

PDB DOI: https://doi.org/10.2210/pdb3SOO/pdb

Classification: RNA BINDING PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2011-06-30 Released: 2011-07-20
Deposition Author(s): Joint Center for Structural Genomics (JCSG), Partnership for Stem Cell Biology (STEMCELL)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.73 Å
R-Value Free:
0.259 (Depositor), 0.290 (DCC)
R-Value Work:
0.226 (Depositor), 0.250 (DCC)
R-Value Observed:
0.228 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Crystal structure of a LINE-1 type transposase domain-containing protein 1 (L1TD1) from HOMO SAPIENS at 2.73 A resolution

Joint Center for Structural Genomics (JCSG), Partnership for Stem Cell Biology (STEMCELL)

To be published.

Macromolecule Content

Total Structure Weight: 31.63 kDa
Atom Count: 2,018
Modeled Residue Count: 260
Deposited Residue Count: 264
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LINE-1 type transposase domain-containing protein 1	A, B, C	88	Homo sapiens	Mutation(s): 2 Gene Names: BC111559, ECAT11, L1TD1
UniProt & NIH Common Fund Data Resources
Find proteins for Q5T7N2 (Homo sapiens) Explore Q5T7N2 Go to UniProtKB: Q5T7N2
PHAROS: Q5T7N2 GTEx: ENSG00000240563
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5T7N2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain K [auth C] SDF format, chain J [auth B] SDF format, chain I [auth B] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain K [auth C] MOL2 format, chain J [auth B] MOL2 format, chain I [auth B] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain K [auth C] mmCIF format, chain J [auth B] mmCIF format, chain I [auth B] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A] E [auth A] F [auth A] G [auth A] H [auth A] D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth B], J [auth B], K [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth C] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth C]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain L [auth C] MOL2 format, chain L [auth C] mmCIF format, chain L [auth C]	L [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain L [auth C] Interactions & Density Focus chain L [auth C]

Modified Residues 2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MLY Query on MLY	A, B, C	L-PEPTIDE LINKING	C₈ H₁₈ N₂ O₂		LYS
MSE Query on MSE	A, B, C	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.73 Å
R-Value Free: 0.259 (Depositor), 0.290 (DCC)
R-Value Work: 0.226 (Depositor), 0.250 (DCC)
R-Value Observed: 0.228 (Depositor)

Diffraction Data: https://doi.org/10.18430/M33SOO

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.14	α = 90
b = 69.14	β = 90
c = 292.27	γ = 120

Software Package:

Software Name	Purpose
MolProbity	model building
PDB_EXTRACT	data extraction
SHELX	phasing
SHARP	phasing
XSCALE	data scaling
BUSTER-TNT	refinement
XDS	data reduction
SHELXD	phasing
BUSTER	refinement