1YDL | pdb_00001ydl

Crystal Structure of the Human TFIIH, Northeast Structural Genomics Target HR2045.

PDB DOI: https://doi.org/10.2210/pdb1YDL/pdb

Classification: TRANSCRIPTION
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2004-12-24 Released: 2005-02-08
Deposition Author(s): Forouhar, F., Edstrom, W., Xiao, R., Acton, T.B., Montelione, G.T., Tong, L., Hunt, J.F., Northeast Structural Genomics Consortium (NESG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.297 (Depositor), 0.306 (DCC)
R-Value Work:
0.236 (Depositor), 0.246 (DCC)
R-Value Observed:
0.236 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 1YDL

This is version 1.5 of the entry. See complete history.

Literature

Crystal Structure of the Human TFIIH, Northeast Structural Genomics Target HR2045.

Forouhar, F., Edstrom, W., Xiao, R., Acton, T.B., Montelione, G.T., Tong, L., Hunt, J.F.

To be published.

Macromolecule Content

Total Structure Weight: 9.23 kDa
Atom Count: 600
Modeled Residue Count: 71
Deposited Residue Count: 79
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
general transcription factor IIH, polypeptide 5	A	79	Homo sapiens	Mutation(s): 3 Gene Names: C6orf175
UniProt & NIH Common Fund Data Resources
Find proteins for Q6ZYL4 (Homo sapiens) Explore Q6ZYL4 Go to UniProtKB: Q6ZYL4
PHAROS: Q6ZYL4 GTEx: ENSG00000272047
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6ZYL4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.297 (Depositor), 0.306 (DCC)
R-Value Work: 0.236 (Depositor), 0.246 (DCC)
R-Value Observed: 0.236 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.412	α = 90
b = 53.922	β = 90
c = 34.818	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
SnB	phasing
SOLVE	phasing
RESOLVE	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2005-02-08

Deposition Author(s):

Montelione, G.T.

Northeast Structural Genomics Consortium (NESG)

Revision History (Full details and data files)

Version 1.0: 2005-02-08
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2017-10-11
Changes: Refinement description
Version 1.4: 2021-10-20
Changes: Database references, Derived calculations
Version 1.5: 2024-10-30
Changes: Data collection, Structure summary

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.