2PYQ | pdb_00002pyq

Crystal structure of a duf2853 member protein (jann_4075) from jannaschia sp. ccs1 at 1.500 A resolution

PDB DOI: https://doi.org/10.2210/pdb2PYQ/pdb

Classification: UNKNOWN FUNCTION
Organism(s): Jannaschia sp. CCS1
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2007-05-16 Released: 2007-05-29
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free:
0.195 (Depositor), 0.200 (DCC)
R-Value Work:
0.176 (Depositor), 0.180 (DCC)
R-Value Observed:
0.176 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.5 of the entry. See complete history.

Literature

Crystal structure of uncharacterized protein (YP_512017.1) from Jannaschia sp. CCS1 at 1.500 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 52.09 kDa
Atom Count: 3,810
Modeled Residue Count: 456
Deposited Residue Count: 456
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein	A, B, C, D	114	Jannaschia sp. CCS1	Mutation(s): 6 Gene Names: YP_512017.1, Jann_4075
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PG4 Query on PG4 Download Ideal Coordinates CCD File SDF format, chain F [auth D] SDF format, chain E [auth D] MOL2 format, chain F [auth D] MOL2 format, chain E [auth D] mmCIF format, chain F [auth D] mmCIF format, chain E [auth D]	E [auth D], F [auth D]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain E [auth D] Focus chain F [auth D] Interactions & Density Focus chain E [auth D] Focus chain F [auth D]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.195 (Depositor), 0.200 (DCC)
R-Value Work: 0.176 (Depositor), 0.180 (DCC)
R-Value Observed: 0.176 (Depositor)

Diffraction Data: https://doi.org/10.18430/M32PYQ

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 32.92	α = 90
b = 98.71	β = 90.39
c = 58.56	γ = 90

Software Package:

Software Name	Purpose
MolProbity	model building
PHENIX	refinement
SHELX	phasing
XSCALE	data scaling
PDB_EXTRACT	data extraction
MAR345	data collection
XDS	data reduction
autoSHARP	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2007-05-29

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2007-05-29
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2017-10-18
Changes: Refinement description
Version 1.4: 2023-01-25
Changes: Database references, Derived calculations
Version 1.5: 2024-10-30
Changes: Data collection, Structure summary

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.