4AM8 | pdb_00004am8

Crystal structure of the R54G mutant of putrescine transcarbamylase from Enterococcus faecalis bound to a curing guanidinium ion

PDB DOI: https://doi.org/10.2210/pdb4AM8/pdb

Classification: TRANSFERASE
Organism(s): Enterococcus faecalis
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2012-03-08 Released: 2013-03-27
Deposition Author(s): Polo, L.M., Rubio, V.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.99 Å
R-Value Free:
0.206 (Depositor), 0.211 (DCC)
R-Value Work:
0.182 (Depositor), 0.186 (DCC)
R-Value Observed:
0.183 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Curing a Mutant Transcarbamylase with a Small Molecule: A Crystallographic View

Polo, L.M., Rubio, V.

To be published.

Macromolecule Content

Total Structure Weight: 243.36 kDa
Atom Count: 16,546
Modeled Residue Count: 2,015
Deposited Residue Count: 2,130
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 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	355	Enterococcus faecalis	Mutation(s): 1 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q837U7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PAO Query on PAO Download:Ideal Coordinates CCD File SDF format, chain AA [auth F] SDF format, chain H [auth A] SDF format, chain M [auth B] SDF format, chain Q [auth C] SDF format, chain T [auth D] SDF format, chain X [auth E] MOL2 format, chain AA [auth F] MOL2 format, chain H [auth A] MOL2 format, chain M [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain T [auth D] MOL2 format, chain X [auth E] mmCIF format, chain AA [auth F] mmCIF format, chain H [auth A] mmCIF format, chain M [auth B] mmCIF format, chain Q [auth C] mmCIF format, chain T [auth D] mmCIF format, chain X [auth E]	AA [auth F] H [auth A] M [auth B] Q [auth C] T [auth D] AA [auth F], H [auth A], M [auth B], Q [auth C], T [auth D], X [auth E]	N-(PHOSPHONOACETYL)-L-ORNITHINE C₇ H₁₅ N₂ O₆ P FCIHAQFHXJOLIF-YFKPBYRVSA-N		Interactions Focus chain AA [auth F] Focus chain H [auth A] Focus chain M [auth B] Focus chain Q [auth C] Focus chain T [auth D] Focus chain X [auth E] Interactions & Density Focus chain AA [auth F] Focus chain H [auth A] Focus chain M [auth B] Focus chain Q [auth C] Focus chain T [auth D] Focus chain X [auth E]
GLN Query on GLN Download:Ideal Coordinates CCD File SDF format, chain W [auth E] SDF format, chain P [auth C] SDF format, chain G [auth A] MOL2 format, chain W [auth E] MOL2 format, chain P [auth C] MOL2 format, chain G [auth A] mmCIF format, chain W [auth E] mmCIF format, chain P [auth C] mmCIF format, chain G [auth A]	G [auth A], P [auth C], W [auth E]	GLUTAMINE C₅ H₁₀ N₂ O₃ ZDXPYRJPNDTMRX-VKHMYHEASA-N		Interactions Focus chain G [auth A] Focus chain P [auth C] Focus chain W [auth E] Interactions & Density Focus chain G [auth A] Focus chain P [auth C] Focus chain W [auth E]
ILE Query on ILE Download:Ideal Coordinates CCD File SDF format, chain L [auth B] MOL2 format, chain L [auth B] mmCIF format, chain L [auth B]	L [auth B]	ISOLEUCINE C₆ H₁₃ N O₂ AGPKZVBTJJNPAG-WHFBIAKZSA-N		Interactions Focus chain L [auth B] Interactions & Density Focus chain L [auth B]
TRS Query on TRS Download:Ideal Coordinates CCD File SDF format, chain S [auth C] SDF format, chain O [auth B] SDF format, chain J [auth A] SDF format, chain CA [auth F] MOL2 format, chain S [auth C] MOL2 format, chain O [auth B] MOL2 format, chain J [auth A] MOL2 format, chain CA [auth F] mmCIF format, chain S [auth C] mmCIF format, chain O [auth B] mmCIF format, chain J [auth A] mmCIF format, chain CA [auth F]	CA [auth F], J [auth A], O [auth B], S [auth C]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain CA [auth F] Focus chain J [auth A] Focus chain O [auth B] Focus chain S [auth C] Interactions & Density Focus chain CA [auth F] Focus chain J [auth A] Focus chain O [auth B] Focus chain S [auth C]
GAI Query on GAI Download:Ideal Coordinates CCD File SDF format, chain Y [auth E] SDF format, chain V [auth D] SDF format, chain U [auth D] SDF format, chain R [auth C] SDF format, chain N [auth B] SDF format, chain I [auth A] SDF format, chain BA [auth F] MOL2 format, chain Y [auth E] MOL2 format, chain V [auth D] MOL2 format, chain U [auth D] MOL2 format, chain R [auth C] MOL2 format, chain N [auth B] MOL2 format, chain I [auth A] MOL2 format, chain BA [auth F] mmCIF format, chain Y [auth E] mmCIF format, chain V [auth D] mmCIF format, chain U [auth D] mmCIF format, chain R [auth C] mmCIF format, chain N [auth B] mmCIF format, chain I [auth A] mmCIF format, chain BA [auth F]	BA [auth F] I [auth A] N [auth B] R [auth C] U [auth D] BA [auth F], I [auth A], N [auth B], R [auth C], U [auth D], V [auth D], Y [auth E]	GUANIDINE C H₅ N₃ ZRALSGWEFCBTJO-UHFFFAOYSA-N		Interactions Focus chain BA [auth F] Focus chain I [auth A] Focus chain N [auth B] Focus chain R [auth C] Focus chain U [auth D] Focus chain V [auth D] Focus chain Y [auth E] Interactions & Density Focus chain BA [auth F] Focus chain I [auth A] Focus chain N [auth B] Focus chain R [auth C] Focus chain U [auth D] Focus chain V [auth D] Focus chain Y [auth E]
NI Query on NI Download:Ideal Coordinates CCD File SDF format, chain Z [auth F] SDF format, chain K [auth A] MOL2 format, chain Z [auth F] MOL2 format, chain K [auth A] mmCIF format, chain Z [auth F] mmCIF format, chain K [auth A]	K [auth A], Z [auth F]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain Z [auth F] Interactions & Density Focus chain K [auth A] Focus chain Z [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.99 Å
R-Value Free: 0.206 (Depositor), 0.211 (DCC)
R-Value Work: 0.182 (Depositor), 0.186 (DCC)
R-Value Observed: 0.183 (Depositor)

Space Group: I 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.69	α = 90
b = 130.6	β = 104.25
c = 164.157	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2013-03-27

Deposition Author(s):

Polo, L.M.

Rubio, V.

Revision History (Full details and data files)

Version 1.0: 2013-03-27
Type: Initial release
Version 1.1: 2017-07-12
Changes: Derived calculations
Version 1.2: 2023-12-20
Changes: Data collection, Database references, Derived calculations, Other, Refinement description