3LLC | pdb_00003llc

Crystal structure of Putative hydrolase (YP_002548124.1) from Agrobacterium vitis S4 at 1.80 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3LLC/pdb

• Classification: HYDROLASE
• Organism(s): Allorhizobium ampelinum S4
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-01-28 Released: 2010-03-23 
• 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: 
  0.185 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.160 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.161 (Depositor) 

Literature

Crystal structure of Putative hydrolase (YP_002548124.1) from Agrobacterium vitis S4 at 1.80 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 30.64 kDa 
• Atom Count: 2,410 
• Modeled Residue Count: 261 
• Deposited Residue Count: 270 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative hydrolase	A	270	Allorhizobium ampelinum S4	Mutation(s): 0  Gene Names: Avi_0199 EC: 3.1.2.22 (UniProt), 3.1.1.93 (UniProt)
UniProt
Find proteins for B9JYM4 (Allorhizobium ampelinum (strain ATCC BAA-846 / DSM 112012 / S4)) Explore B9JYM4  Go to UniProtKB:  B9JYM4

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PG4	I [auth A]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
PEG	H [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
EDO	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL	B [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	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:  0.185 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.160 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.161 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33LLC

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 112.652	α = 90
b = 112.652	β = 90
c = 59.497	γ = 90

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: 2010-03-23 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2010-03-23
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2019-07-17
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.4: 2023-02-01
  Changes: Database references, Derived calculations
• Version 1.5: 2024-11-20
  Changes: Data collection, Structure summary