5GKV | pdb_00005gkv

Crystal Structure of a Novel Penicillin-Binding Protein (PBP) Homolog from Caulobacter crescentus

• PDB DOI: https://doi.org/10.2210/pdb5GKV/pdb

• Classification: HYDROLASE
• Organism(s): Caulobacter vibrioides CB15
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-07-07 Released: 2017-07-12 
• Deposition Author(s): Ngo, T.D., Ryu, B.H., Kim, B.Y., Yoo, W.K., Lee, E.J., Lee, S.J., Kim, T.D., Kim, K.K.
• Funding Organization(s): National Research Foundation of Korea

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.201 (Depositor), 0.201 (DCC) 
• R-Value Work: 
  0.170 (Depositor), 0.171 (DCC) 
• R-Value Observed: 
  0.173 (Depositor) 

Starting Model: experimental

Literature

Biochemical and Structural Analysis of a Novel Penicillin-Binding Protein (PBP) Homolog from Caulobacter crescentus

Ryu, B.H., Ngo, T.D., Kim, B.Y., Yoo, W.K., Lee, E.J., Lee, S.J., Kim, K.K., Kim, T.D.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 41.35 kDa 
• Atom Count: 3,120 
• Modeled Residue Count: 371 
• Deposited Residue Count: 386 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Esterase A	A	386	Caulobacter vibrioides CB15	Mutation(s): 0  Gene Names: CC_0255
UniProt
Find proteins for Q9ABH2 (Caulobacter vibrioides (strain ATCC 19089 / CIP 103742 / CB 15)) Explore Q9ABH2  Go to UniProtKB:  Q9ABH2

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.201 (Depositor), 0.201 (DCC) 
• R-Value Work:  0.170 (Depositor), 0.171 (DCC) 
• R-Value Observed: 0.173 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.277	α = 90
b = 67.308	β = 90
c = 92.093	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
HKL-2000	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2017-07-12 
Deposition Author(s): Ngo, T.D., Ryu, B.H., Kim, B.Y., Yoo, W.K., Lee, E.J., Lee, S.J., Kim, T.D., Kim, K.K.

---

Funding Organization	Location	Grant Number
National Research Foundation of Korea	Korea, Republic Of	NRF-2013K2A1A2053659

Revision History  

• Version 1.0: 2017-07-12
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Refinement description