3TXX

Crystal structure of putrescine transcarbamylase from Enterococcus faecalis

PDB DOI: https://doi.org/10.2210/pdb3TXX/pdb

Classification: TRANSFERASE
Organism(s): Enterococcus faecalis
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2011-09-23 Released: 2012-02-01
Deposition Author(s): Shi, D., Yu, X., Zhao, G., Allewell, N.M., Tuchman, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.20 Å
R-Value Free: 0.234
R-Value Work: 0.190
R-Value Observed: 0.191

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Crystal structure of putrescine transcarbamylase from Enterococcus faecalis: Structural insights into the oligomeric assembly and the active site

Shi, D., Yu, X., Zhao, G., Ho, J., Lu, S., Allewell, N.M., Tuchman, M.

To be published.

Macromolecule Content

Total Structure Weight: 489.28 kDa
Atom Count: 32,142
Modelled Residue Count: 4,092
Deposited Residue Count: 4,308
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putrescine carbamoyltransferase	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	359	Enterococcus faecalis	Mutation(s): 0 Gene Names: agcB, argF-2, EF_0732, ptcA EC: 2.1.3.6
UniProt
Find proteins for Q837U7 (Enterococcus faecalis (strain ATCC 700802 / V583)) Explore Q837U7 Go to UniProtKB: Q837U7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q837U7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain AA [auth G] SDF format, chain BA [auth G] SDF format, chain CA [auth G] SDF format, chain DA [auth H] SDF format, chain EA [auth H] SDF format, chain FA [auth I] SDF format, chain GA [auth I] SDF format, chain HA [auth J] SDF format, chain IA [auth J] SDF format, chain JA [auth K] SDF format, chain KA [auth L] SDF format, chain LA [auth L] SDF format, chain M [auth A] SDF format, chain MA [auth L] SDF format, chain N [auth A] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain R [auth C] SDF format, chain S [auth C] SDF format, chain T [auth D] SDF format, chain U [auth D] SDF format, chain V [auth E] SDF format, chain W [auth E] SDF format, chain X [auth E] SDF format, chain Y [auth F] SDF format, chain Z [auth F] MOL2 format, chain AA [auth G] MOL2 format, chain BA [auth G] MOL2 format, chain CA [auth G] MOL2 format, chain DA [auth H] MOL2 format, chain EA [auth H] MOL2 format, chain FA [auth I] MOL2 format, chain GA [auth I] MOL2 format, chain HA [auth J] MOL2 format, chain IA [auth J] MOL2 format, chain JA [auth K] MOL2 format, chain KA [auth L] MOL2 format, chain LA [auth L] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth L] MOL2 format, chain N [auth A] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth C] MOL2 format, chain S [auth C] MOL2 format, chain T [auth D] MOL2 format, chain U [auth D] MOL2 format, chain V [auth E] MOL2 format, chain W [auth E] MOL2 format, chain X [auth E] MOL2 format, chain Y [auth F] MOL2 format, chain Z [auth F] mmCIF format, chain AA [auth G] mmCIF format, chain BA [auth G] mmCIF format, chain CA [auth G] mmCIF format, chain DA [auth H] mmCIF format, chain EA [auth H] mmCIF format, chain FA [auth I] mmCIF format, chain GA [auth I] mmCIF format, chain HA [auth J] mmCIF format, chain IA [auth J] mmCIF format, chain JA [auth K] mmCIF format, chain KA [auth L] mmCIF format, chain LA [auth L] mmCIF format, chain M [auth A] mmCIF format, chain MA [auth L] mmCIF format, chain N [auth A] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth C] mmCIF format, chain S [auth C] mmCIF format, chain T [auth D] mmCIF format, chain U [auth D] mmCIF format, chain V [auth E] mmCIF format, chain W [auth E] mmCIF format, chain X [auth E] mmCIF format, chain Y [auth F] mmCIF format, chain Z [auth F]	AA [auth G] BA [auth G] CA [auth G] DA [auth H] EA [auth H] AA [auth G], BA [auth G], CA [auth G], DA [auth H], EA [auth H], FA [auth I], GA [auth I], HA [auth J], IA [auth J], JA [auth K], KA [auth L], LA [auth L], M [auth A], MA [auth L], N [auth A], O [auth B], P [auth B], Q [auth B], R [auth C], S [auth C], T [auth D], U [auth D], V [auth E], W [auth E], X [auth E], Y [auth F], Z [auth F]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AA [auth G] Focus chain BA [auth G] Focus chain CA [auth G] Focus chain DA [auth H] Focus chain EA [auth H] Focus chain FA [auth I] Focus chain GA [auth I] Focus chain HA [auth J] Focus chain IA [auth J] Focus chain JA [auth K] Focus chain KA [auth L] Focus chain LA [auth L] Focus chain M [auth A] Focus chain MA [auth L] Focus chain N [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth D] Focus chain U [auth D] Focus chain V [auth E] Focus chain W [auth E] Focus chain X [auth E] Focus chain Y [auth F] Focus chain Z [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.20 Å
R-Value Free: 0.234
R-Value Work: 0.190
R-Value Observed: 0.191
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 273.856	α = 90
b = 87.791	β = 114.08
c = 241.299	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
DENZO	data reduction

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2012-02-01

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-02-01
Type: Initial release
Version 1.1: 2017-11-08
Changes: Refinement description
Version 1.2: 2024-02-28
Changes: Data collection, Database references, Derived calculations