3H8U | pdb_00003h8u

Crystal structure of uncharacterized conserved protein with double-stranded beta-helix domain (YP_001338853.1) from Klebsiella pneumoniae subsp. pneumoniae MGH 78578 at 1.80 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3H8U/pdb

• Classification: structural genomics, unknown function
• Organism(s): Klebsiella pneumoniae subsp. pneumoniae MGH 78578
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-04-29 Released: 2009-05-12 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.196 (Depositor), 0.202 (DCC) 
• R-Value Work: 
  0.152 (Depositor), 0.163 (DCC) 
• R-Value Observed: 
  0.154 (Depositor) 

Literature

Crystal structure of uncharacterized conserved protein with double-stranded beta-helix domain (YP_001338853.1) from Klebsiella pneumoniae subsp. pneumoniae MGH 78578 at 1.80 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 27.62 kDa 
• Atom Count: 2,075 
• Modeled Residue Count: 237 
• Deposited Residue Count: 250 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
uncharacterized conserved protein with double-stranded beta-helix domain	A, B	125	Klebsiella pneumoniae subsp. pneumoniae MGH 78578	Mutation(s): 0  Gene Names: KPN78578_51600, KPN_pKPN5p08243, YP_001338853.1
UniProt
Find proteins for A6TJ50 (Klebsiella pneumoniae subsp. pneumoniae (strain ATCC 700721 / MGH 78578)) Explore A6TJ50  Go to UniProtKB:  A6TJ50

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
2PE	F [auth B]	NONAETHYLENE GLYCOL C18 H38 O10 YZUUTMGDONTGTN-UHFFFAOYSA-N
SO4	C [auth A], D [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	E [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.196 (Depositor), 0.202 (DCC) 
• R-Value Work:  0.152 (Depositor), 0.163 (DCC) 
• R-Value Observed: 0.154 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33H8U

Space Group: P 3₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.85	α = 90
b = 46.85	β = 90
c = 94.94	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
SHELXD	phasing
autoSHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-05-12 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2009-05-12
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Author supporting evidence, Refinement description
• Version 1.3: 2019-07-24
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.4: 2023-02-01
  Changes: Database references, Derived calculations
• Version 1.5: 2024-11-06
  Changes: Data collection, Structure summary