5NGW | pdb_00005ngw

Glycoside hydrolase-like protein

• PDB DOI: https://doi.org/10.2210/pdb5NGW/pdb

• Classification: HYDROLASE
• Organism(s): Ochrovirga pacifica
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2017-03-20 Released: 2018-01-31 
• Deposition Author(s): Robb, C.S., Hehemann, J.-H.
• Funding Organization(s): German Research Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.215 (Depositor), 0.221 (DCC) 
• R-Value Work: 
  0.164 (Depositor), 0.169 (DCC) 
• R-Value Observed: 
  0.166 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of a marine glycoside hydrolase family 99-related protein lacking catalytic machinery.

Robb, C.S., Mystkowska, A.A., Hehemann, J.H.

(2017) Protein Sci 26: 2445-2450

• PubMed: 28884852 
• DOI: https://doi.org/10.1002/pro.3291
• Primary Citation Related Structures: 
  5NGW


• PubMed Abstract: 
  

  Algal polysaccharides of diverse structures are one of the most abundant carbon resources for heterotrophic, marine bacteria with coevolved digestive enzymes. A putative sulfo-mannan polysaccharide utilization locus, which is conserved in marine flavobacteria, contains an unusual GH99-like protein that lacks the conserved catalytic residues of glycoside hydrolase family 99. Using X-ray crystallography, we structurally characterized this protein from the marine flavobacterium Ochrovirga pacifica to help elucidate its molecular function. The structure reveals the absence of potential catalytic residues for polysaccharide hydrolysis, which-together with additional structural features-suggests this protein may be noncatalytic and involved in carbohydrate binding.

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Organizational Affiliation: 
• Center for Marine Environmental Sciences, University of Bremen (MARUM), Bremen, 28359, Germany.
Max Planck-Institute for Marine Microbiology, Bremen, 28359, Germany.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 44.63 kDa 
• Atom Count: 3,005 
• Modeled Residue Count: 360 
• Deposited Residue Count: 389 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
OpGH99A	A	389	Ochrovirga pacifica	Mutation(s): 0  Gene Names: ZP09498382.1
UniProt
Find proteins for A0A2R2JFJ2 (Ochrovirga pacifica) Explore A0A2R2JFJ2  Go to UniProtKB:  A0A2R2JFJ2

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BR	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A]	BROMIDE ION Br CPELXLSAUQHCOX-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.215 (Depositor), 0.221 (DCC) 
• R-Value Work:  0.164 (Depositor), 0.169 (DCC) 
• R-Value Observed: 0.166 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.054	α = 90
b = 102.054	β = 90
c = 80.113	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-01-31 
Deposition Author(s): Robb, C.S., Hehemann, J.-H.

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Funding Organization	Location	Grant Number
German Research Foundation	Germany	--

Revision History  

• Version 1.0: 2018-01-31
  Type: Initial release
  
• Version 1.1: 2024-01-17
  Changes: Data collection, Database references, Refinement description