8DGD | pdb_00008dgd

Crystal Structure of GAF domain-containing protein, from Klebsiella pneumoniae

PDB DOI: https://doi.org/10.2210/pdb8DGD/pdb

Classification: UNKNOWN FUNCTION
Organism(s): Klebsiella pneumoniae subsp. pneumoniae HS11286
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2022-06-23 Released: 2023-03-01
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease, Delker, S.L., Weiss, M.J., Lorimer, D.D., Edwards, T.E., Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.220 (Depositor), 0.219 (DCC)
R-Value Work:
0.172 (Depositor), 0.173 (DCC)
R-Value Observed:
0.176 (Depositor)

Starting Model: experimental
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This is version 1.2 of the entry. See complete history.

Literature

Crystal Structure of GAF domain-containing protein, from Klebsiella pneumoniae

Seattle Structural Genomics Center for Infectious Disease, Delker, S.L., Weiss, M.J., Lorimer, D.D., Edwards, T.E.

To be published.

Macromolecule Content

Total Structure Weight: 39.83 kDa
Atom Count: 2,830
Modeled Residue Count: 328
Deposited Residue Count: 356
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GAF domain-containing protein	A, B	178	Klebsiella pneumoniae subsp. pneumoniae HS11286	Mutation(s): 0 Gene Names: KPHS_33640
UniProt
Find proteins for A0A0H3GUR8 (Klebsiella pneumoniae subsp. pneumoniae (strain HS11286)) Explore A0A0H3GUR8 Go to UniProtKB: A0A0H3GUR8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0H3GUR8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MES Query on MES Download:Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain C [auth A] MOL2 format, chain F [auth B] MOL2 format, chain C [auth A] mmCIF format, chain F [auth B] mmCIF format, chain C [auth A]	C [auth A], F [auth B]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain F [auth B]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A], E [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.220 (Depositor), 0.219 (DCC)
R-Value Work: 0.172 (Depositor), 0.173 (DCC)
R-Value Observed: 0.176 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.68	α = 90
b = 114.38	β = 90
c = 73.89	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
SCALEPACK	data scaling
MOLREP	phasing
PDB_EXTRACT	data extraction

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2023-03-01

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	--

Revision History (Full details and data files)

Version 1.0: 2023-03-01
Type: Initial release
Version 1.1: 2024-03-13
Changes: Data collection, Source and taxonomy
Version 1.2: 2024-11-20
Changes: Structure summary

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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.