7A66 | pdb_00007a66

structure of Pcc2 from Pyrococcus abyssi

PDB DOI: https://doi.org/10.2210/pdb7A66/pdb

Classification: STRUCTURAL PROTEIN
Organism(s): Pyrococcus abyssi GE5
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2020-08-25 Released: 2022-03-23
Deposition Author(s): Missoury, S., Tilbeurgh, V.H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free:
0.229 (Depositor), 0.233 (DCC)
R-Value Work:
0.204 (Depositor), 0.203 (DCC)
R-Value Observed:
0.205 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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Literature

Structure of Pcc2 at 1.84 Angstroms resolution

Missoury, S., Tilbeurgh, V.H.

To be published.

Macromolecule Content

Total Structure Weight: 29.84 kDa
Atom Count: 2,091
Modeled Residue Count: 255
Deposited Residue Count: 258
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pcc2	A, B, C	86	Pyrococcus abyssi GE5	Mutation(s): 0
UniProt
Find proteins for A0A915Q983 (Pyrococcus abyssi (strain GE5 / Orsay)) Explore A0A915Q983 Go to UniProtKB: A0A915Q983
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A915Q983
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL (Subject of Investigation/LOI) Query on GOL Download:Ideal Coordinates CCD File SDF format, chain H [auth C] SDF format, chain G [auth C] SDF format, chain F [auth B] SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain H [auth C] MOL2 format, chain G [auth C] MOL2 format, chain F [auth B] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain H [auth C] mmCIF format, chain G [auth C] mmCIF format, chain F [auth B] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A], E [auth A], F [auth B], G [auth C], H [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth C] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth C]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SEP Query on SEP	A, B, C	L-PEPTIDE LINKING	C₃ H₈ N O₆ P		SER

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free: 0.229 (Depositor), 0.233 (DCC)
R-Value Work: 0.204 (Depositor), 0.203 (DCC)
R-Value Observed: 0.205 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.8	α = 90
b = 81.31	β = 121.59
c = 66.48	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
BUSTER	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2022-03-23

Deposition Author(s):

Tilbeurgh, V.H.

Revision History (Full details and data files)

Version 1.0: 2022-03-23
Type: Initial release
Version 1.1: 2024-01-31
Changes: Data collection, Refinement description
Version 1.2: 2024-11-13
Changes: Structure summary

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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.