4U12 | pdb_00004u12

Crystal structure of protein HP0242 from Helicobacter pylori at 1.94 A resolution: a knotted homodimer

PDB DOI: https://doi.org/10.2210/pdb4U12/pdb
Entry: 4U12 supersedes: 2OUF

Classification: Structural Genomics, Unknown Function
Organism(s): Helicobacter pylori 26695
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2014-07-14 Released: 2014-07-23
Deposition Author(s): Grabowski, M., Shabalin, I.G., Chruszcz, M., Skarina, T., Onopriyenko, O., Guthrie, J., Savchenko, A., Edwards, A., Joachimiak, A., Minor, W., Midwest Center for Structural Genomics (MCSG)
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.94 Å
R-Value Free:
0.253 (Depositor), 0.260 (DCC)
R-Value Work:
0.221 (Depositor), 0.225 (DCC)
R-Value Observed:
0.222 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.6 of the entry. See complete history.

Literature

Crystal structure of protein HP0242 from Helicobacter pylori at 1.94 A resolution: a knotted homodimer

Grabowski, M., Shabalin, I.G., Chruszcz, M., Skarina, T., Onopriyenko, O., Guthrie, J., Savchenko, A., Edwards, A., Joachimiak, A., Minor, W.

To be published.

Macromolecule Content

Total Structure Weight: 11.2 kDa
Atom Count: 698
Modeled Residue Count: 80
Deposited Residue Count: 94
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein HP0242	A	94	Helicobacter pylori 26695	Mutation(s): 0 Gene Names: C694_01225, HP_0242
UniProt
Find proteins for O25025 (Helicobacter pylori (strain ATCC 700392 / 26695)) Explore O25025 Go to UniProtKB: O25025
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O25025
Sequence Annotations Expand
Reference Sequence

Small Molecules

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.94 Å
R-Value Free: 0.253 (Depositor), 0.260 (DCC)
R-Value Work: 0.221 (Depositor), 0.225 (DCC)
R-Value Observed: 0.222 (Depositor)

Space Group: P 4₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.944	α = 90
b = 44.944	β = 90
c = 117.883	γ = 90

Software Package:

Software Name	Purpose
HKL-3000	data collection
HKL-3000	data reduction
HKL-3000	data scaling
SCALEPACK	data scaling
HKL-3000	phasing
SHELXDE	phasing
DM	phasing
RESOLVE	phasing
ARP	model building
Coot	model building
PDB_EXTRACT	data extraction
REFMAC	refinement

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2014-07-23

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

This entry supersedes: 2OUF

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01-GM053163
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	U54-GM094585-04

Revision History (Full details and data files)

Version 1.0: 2014-07-23
Type: Initial release
Version 1.1: 2014-08-06
Changes: Structure summary
Version 1.2: 2017-09-20
Changes: Author supporting evidence, Database references, Derived calculations, Other, Source and taxonomy
Version 1.3: 2019-12-25
Changes: Author supporting evidence
Version 1.4: 2022-04-13
Changes: Database references, Refinement description, Structure summary
Version 1.5: 2023-12-27
Changes: Data collection
Version 1.6: 2024-11-13
Changes: Structure summary