2QSD | pdb_00002qsd

Crystal structure of a protein Il1583 from Idiomarina loihiensis

PDB DOI: https://doi.org/10.2210/pdb2QSD/pdb

Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
Organism(s): Idiomarina loihiensis
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2007-07-30 Released: 2007-08-14
Deposition Author(s): Patskovsky, Y., Bonanno, J., Sauder, J.M., Romero, R., Rutter, M., Koss, J., Mckenzie, C., Gheyi, T., Bain, K., Wasserman, S.R., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.253 (Depositor), 0.237 (DCC)
R-Value Work:
0.215 (Depositor), 0.205 (DCC)
R-Value Observed:
0.216 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Crystal Structure of a Protein Il1583 from Idiomarina loihiensis.

Patskovsky, Y., Bonanno, J., Sauder, J.M., Romero, R., Rutter, M., Koss, J., Mckenzie, C., Gheyi, T., Bain, K., Wasserman, S.R., Burley, S.K., Almo, S.C.

To be published.

Macromolecule Content

Total Structure Weight: 170.96 kDa
Atom Count: 9,688
Modeled Residue Count: 1,168
Deposited Residue Count: 1,496
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized conserved protein	A, B, C, D, E A, B, C, D, E, F, G, H	187	Idiomarina loihiensis	Mutation(s): 0 Gene Names: IL1583
UniProt
Find proteins for Q5QU98 (Idiomarina loihiensis (strain ATCC BAA-735 / DSM 15497 / L2-TR)) Explore Q5QU98 Go to UniProtKB: Q5QU98
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5QU98
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain I [auth E] MOL2 format, chain I [auth E] mmCIF format, chain I [auth E]	I [auth E]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain I [auth E] Interactions & Density Focus chain I [auth E]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.253 (Depositor), 0.237 (DCC)
R-Value Work: 0.215 (Depositor), 0.205 (DCC)
R-Value Observed: 0.216 (Depositor)

Space Group: P 2 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 185.401	α = 90
b = 185.401	β = 90
c = 185.401	γ = 90

Software Package:

Software Name	Purpose
SHELX	model building
REFMAC	refinement
MAR345	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SHELX	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2007-08-14

Deposition Author(s):

New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History (Full details and data files)

Version 1.0: 2007-08-14
Type: Initial release
Version 1.1: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 1.2: 2017-10-25
Changes: Refinement description
Version 1.3: 2018-11-14
Changes: Data collection, Structure summary
Version 1.4: 2021-02-03
Changes: Database references, Derived calculations, Structure summary
Version 1.5: 2024-11-13
Changes: Data collection, Database references, Refinement description, Structure summary