6YPA | pdb_00006ypa

The C146A variant of an amidase from Pyrococcus horikoshii with bound glutaramide

PDB DOI: https://doi.org/10.2210/pdb6YPA/pdb

Classification: HYDROLASE
Organism(s): Pyrococcus horikoshii
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2020-04-15 Released: 2020-06-03
Deposition Author(s): Sewell, B.T., Su, S., Venter, P., Makumire, S.
Funding Organization(s): Global Challenges Research Fund

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.58 Å
R-Value Free:
0.240 (Depositor), 0.240 (DCC)
R-Value Work:
0.206 (Depositor), 0.207 (DCC)
R-Value Observed:
0.208 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6YPA

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Re-refinement Note

A newer entry is available that reflects an alternative modeling of the original data: 7OVG

Literature

The structure of the C146A variant of the amidase from Pyrococcus horikoshii bound to glutaramide suggests the basis of amide recognition.

Sewell, B.T., Su, S., Venter, P., Makumire, S.

To be published.

Macromolecule Content

Total Structure Weight: 128.55 kDa
Atom Count: 9,115
Modeled Residue Count: 1,059
Deposited Residue Count: 1,128
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CN hydrolase domain-containing protein	A, B, C, D	282	Pyrococcus horikoshii	Mutation(s): 1 Gene Names: PH0642
UniProt
Find proteins for O58376 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)) Explore O58376 Go to UniProtKB: O58376
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O58376
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
P6W (Subject of Investigation/LOI) Query on P6W Download:Ideal Coordinates CCD File SDF format, chain I [auth D] SDF format, chain H [auth C] SDF format, chain G [auth B] SDF format, chain E [auth A] MOL2 format, chain I [auth D] MOL2 format, chain H [auth C] MOL2 format, chain G [auth B] MOL2 format, chain E [auth A] mmCIF format, chain I [auth D] mmCIF format, chain H [auth C] mmCIF format, chain G [auth B] mmCIF format, chain E [auth A]	E [auth A], G [auth B], H [auth C], I [auth D]	pentanediamide C₅ H₁₀ N₂ O₂ RCCYSVYHULFYHE-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain H [auth C] Focus chain I [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain H [auth C] Focus chain I [auth D]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.58 Å
R-Value Free: 0.240 (Depositor), 0.240 (DCC)
R-Value Work: 0.206 (Depositor), 0.207 (DCC)
R-Value Observed: 0.208 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.684	α = 90
b = 100.639	β = 90
c = 134.096	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
xia2	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction
DIALS	data reduction

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2020-06-03

Deposition Author(s):

Funding Organization	Location	Grant Number
Global Challenges Research Fund	United Kingdom	ST/R002754/1

Revision History (Full details and data files)

Version 1.0: 2020-06-03
Type: Initial release
Version 1.1: 2024-01-24
Changes: Data collection, Database references, Refinement description

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.