4LOA | pdb_00004loa

X-ray structure of the de-novo design amidase at the resolution 1.8A, Northeast Structural Genomics Consortium (NESG) Target OR398

PDB DOI: https://doi.org/10.2210/pdb4LOA/pdb

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

Deposited: 2013-07-12 Released: 2013-08-07
Deposition Author(s): Kuzin, A., Lew, S., Vorobiev, S.M., Seetharaman, J., Sahdev, S., Xiao, R., Maglaqui, M., Kogan, S., Khersonsky, O., Everett, J.K., Acton, T.B., Montelione, G.T., Hunt, J.F., Tong, L., Northeast Structural Genomics Consortium (NESG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.82 Å
R-Value Free:
0.242 (Depositor), 0.236 (DCC)
R-Value Work:
0.203 (Depositor), 0.199 (DCC)
R-Value Observed:
0.205 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Northeast Structural Genomics Consortium Target OR398

Kuzin, A., Lew, S., Vorobiev, S.M., Seetharaman, J., Sahdev, S., Xiao, R., Maglaqui, M., Kogan, S., Khersonsky, O., Everett, J.K., Acton, T.B., Montelione, G.T., Hunt, J.F., Tong, L.

To be published.

Macromolecule Content

Total Structure Weight: 40.65 kDa
Atom Count: 2,677
Modeled Residue Count: 312
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
De-novo design amidase	A, B	173	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEG Query on PEG 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]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain D [auth B] Interactions & Density Focus chain D [auth B]
CL Query on CL 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]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		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: 1.82 Å
R-Value Free: 0.242 (Depositor), 0.236 (DCC)
R-Value Work: 0.203 (Depositor), 0.199 (DCC)
R-Value Observed: 0.205 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 34.485	α = 71.07
b = 44.335	β = 75.97
c = 57.515	γ = 86.86

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
HKL-2000	data reduction
SCALA	data scaling
BALBES	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2013-08-07

Deposition Author(s):

Northeast Structural Genomics Consortium (NESG)

Revision History (Full details and data files)

Version 1.0: 2013-08-07
Type: Initial release
Version 1.1: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.2: 2023-12-06
Changes: Data collection
Version 1.3: 2024-10-30
Changes: Structure summary