2OTM | pdb_00002otm

Crystal structure of a putative endoribonuclease (so_1960) from shewanella oneidensis mr-1 at 1.85 A resolution

PDB DOI: https://doi.org/10.2210/pdb2OTM/pdb

Classification: UNKNOWN FUNCTION
Organism(s): Shewanella oneidensis MR-1
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2007-02-08 Released: 2007-02-20
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free:
0.177 (Depositor), 0.186 (DCC)
R-Value Work:
0.151 (Depositor), 0.159 (DCC)
R-Value Observed:
0.152 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of hypothetical protein (NP_717567.1) from Shewanella oneidensis at 1.85 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 51.63 kDa
Atom Count: 3,968
Modeled Residue Count: 456
Deposited Residue Count: 462
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical protein	A, B, C	154	Shewanella oneidensis MR-1	Mutation(s): 5 Gene Names: NP_717567.1, SO_1960
UniProt
Find proteins for Q8EFL1 (Shewanella oneidensis (strain ATCC 700550 / JCM 31522 / CIP 106686 / LMG 19005 / NCIMB 14063 / MR-1)) Explore Q8EFL1 Go to UniProtKB: Q8EFL1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8EFL1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain K [auth B] MOL2 format, chain K [auth B] mmCIF format, chain K [auth B]	K [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain K [auth B] Interactions & Density Focus chain K [auth B]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain N [auth C] SDF format, chain M [auth C] SDF format, chain J [auth B] SDF format, chain I [auth B] SDF format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain N [auth C] MOL2 format, chain M [auth C] MOL2 format, chain J [auth B] MOL2 format, chain I [auth B] MOL2 format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain N [auth C] mmCIF format, chain M [auth C] mmCIF format, chain J [auth B] mmCIF format, chain I [auth B] mmCIF format, chain F [auth A]	F [auth A] G [auth A] I [auth B] J [auth B] M [auth C] F [auth A], G [auth A], I [auth B], J [auth B], M [auth C], N [auth C]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain M [auth C] Focus chain N [auth C] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain M [auth C] Focus chain N [auth C]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain L [auth C] SDF format, chain H [auth B] MOL2 format, chain E [auth A] MOL2 format, chain L [auth C] MOL2 format, chain H [auth B] mmCIF format, chain E [auth A] mmCIF format, chain L [auth C] mmCIF format, chain H [auth B]	E [auth A], H [auth B], L [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain L [auth C] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain L [auth C]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free: 0.177 (Depositor), 0.186 (DCC)
R-Value Work: 0.151 (Depositor), 0.159 (DCC)
R-Value Observed: 0.152 (Depositor)

Diffraction Data:

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 112.083	α = 90
b = 62.908	β = 93.24
c = 78.689	γ = 90

Software Package:

Software Name	Purpose
MolProbity	model building
SHELX	phasing
REFMAC	refinement
SCALA	data scaling
PDB_EXTRACT	data extraction
MAR345	data collection
MOSFLM	data reduction
CCP4	data scaling
SHELXD	phasing
autoSHARP	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2007-02-20

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2007-02-20
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Advisory, Source and taxonomy, 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, Refinement description, Structure summary

2OTM | pdb_00002otm

Crystal structure of a putative endoribonuclease (so_1960) from shewanella oneidensis mr-1 at 1.85 A resolution

Literature

Crystal structure of hypothetical protein (NP_717567.1) from Shewanella oneidensis at 1.85 A resolution

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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