4NEY | pdb_00004ney

Crystal Structure of an engineered protein with ferredoxin fold, Northeast Structural Genomics Consortium (NESG) Target OR277

PDB DOI: https://doi.org/10.2210/pdb4NEY/pdb

Classification: DE NOVO PROTEIN
Organism(s): synthetic construct
Mutation(s): No

Deposited: 2013-10-30 Released: 2014-01-15
Deposition Author(s): Guan, R., Lin, Y.-R., Koga, N., Koga, R., Castellanos, J., Seetharaman, J., Maglaqui, M., Sahdev, S., Mao, L., Xiao, R., Everett, J.K., Baker, D., Montelione, G.T., Northeast Structural Genomics Consortium (NESG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.32 Å
R-Value Free:
0.260 (Depositor), 0.260 (DCC)
R-Value Work:
0.216 (Depositor), 0.215 (DCC)
R-Value Observed:
0.220 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Northeast Structural Genomics Consortium Target OR277

Guan, R., Lin, Y.-R., Koga, N., Koga, R., Castellanos, J., Seetharaman, J., Maglaqui, M., Sahdev, S., Mao, L., Xiao, R., Everett, J.K., Baker, D., Montelione, G.T.

To be published.

Macromolecule Content

Total Structure Weight: 41.29 kDa
Atom Count: 2,948
Modeled Residue Count: 345
Deposited Residue Count: 346
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Engineered protein OR277	A, B	173	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
4NE Query on 4NE Download:Ideal Coordinates CCD File SDF format, chain D [auth B] MOL2 format, chain D [auth B] mmCIF format, chain D [auth B]	D [auth B]	tetrabutylphosphonium C₁₆ H₃₆ P BJQWBACJIAKDTJ-UHFFFAOYSA-N		Interactions Focus chain D [auth B] Interactions & Density Focus chain D [auth B]
TRS Query on TRS Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.32 Å
R-Value Free: 0.260 (Depositor), 0.260 (DCC)
R-Value Work: 0.216 (Depositor), 0.215 (DCC)
R-Value Observed: 0.220 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.282	α = 90
b = 79.289	β = 90
c = 97.759	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
MAR345dtb	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2014-01-15

Deposition Author(s):

Northeast Structural Genomics Consortium (NESG)

Revision History (Full details and data files)

Version 1.0: 2014-01-15
Type: Initial release
Version 1.1: 2024-11-06
Changes: Data collection, Database references, Derived calculations, Structure summary