6UN9 | pdb_00006un9

Crystal Structure of the Q7VLF5_HAEDU protein from Haemophilus ducreyi. Northeast Structural Genomics Consortium Target Hdr25

PDB DOI: https://doi.org/10.2210/pdb6UN9/pdb

Classification: UNKNOWN FUNCTION
Organism(s): [Haemophilus] ducreyi
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2019-10-11 Released: 2020-12-09
Deposition Author(s): Vorobiev, S.M., Seetharaman, J., Kolev, M., Xiao, R., Everett, J.K., Acton, T.B., Montelione, G.T., Tong, L., Hunt, J.F., Northeast Structural Genomics Consortium (NESG)
Funding Organization(s): National Institutes of Health/National Institute of Dental and Craniofacial Research (NIH/NIDCR)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free:
0.373 (Depositor), 0.370 (DCC)
R-Value Work:
0.296 (Depositor), 0.299 (DCC)
R-Value Observed:
0.303 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 6UN9

This is version 1.1 of the entry. See complete history.

Literature

Crystal Structure of the Q7VLF5_HAEDU protein from Haemophilus ducreyi. Northeast Structural Genomics Consortium Target Hdr25

Vorobiev, S.M., Seetharaman, J., Kolev, M., Xiao, R., Everett, J.K., Acton, T.B., Montelione, G.T., Tong, L., Hunt, J.F., Northeast Structural Genomics Consortium (NESG)

To be published.

Macromolecule Content

Total Structure Weight: 51.67 kDa
Atom Count: 2,253
Modeled Residue Count: 269
Deposited Residue Count: 436
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein	A, B, C, D	109	[Haemophilus] ducreyi	Mutation(s): 2 Gene Names: HD_1495
UniProt
Find proteins for Q7VLF5 (Haemophilus ducreyi (strain 35000HP / ATCC 700724)) Explore Q7VLF5 Go to UniProtKB: Q7VLF5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q7VLF5
Sequence Annotations Expand
Reference Sequence

Small Molecules

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.373 (Depositor), 0.370 (DCC)
R-Value Work: 0.296 (Depositor), 0.299 (DCC)
R-Value Observed: 0.303 (Depositor)

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.609	α = 90
b = 70.609	β = 90
c = 504.039	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
SHELXDE	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2020-12-09

Deposition Author(s):

Seetharaman, J.

Montelione, G.T.

Northeast Structural Genomics Consortium (NESG)

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Dental and Craniofacial Research (NIH/NIDCR)	United States	--

Revision History (Full details and data files)

Version 1.0: 2020-12-09
Type: Initial release
Version 1.1: 2024-10-16
Changes: Data collection, Database references, 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.