4KYB | pdb_00004kyb

Crystal Structure of de novo designed serine hydrolase OSH55.14_E3, Northeast Structural Genomics Consortium Target OR342

PDB DOI: https://doi.org/10.2210/pdb4KYB/pdb

Classification: DE NOVO PROTEIN
Organism(s): synthetic construct
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2013-05-28 Released: 2013-06-19
Deposition Author(s): Kuzin, A., Lew, S., Rajagopalan, S., Seetharaman, J., Mao, L., Xiao, R., Lee, D., Raja, S., Everett, J.K., Acton, T.B., Baker, D., Montelione, G.T., Tong, L., Hunt, J.F., Northeast Structural Genomics Consortium (NESG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.91 Å
R-Value Free:
0.301 (Depositor), 0.314 (DCC)
R-Value Work:
0.201 (Depositor), 0.213 (DCC)
R-Value Observed:
0.206 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Northeast Structural Genomics Consortium Target OR342

Kuzin, A., Lew, S., Rajagopalan, S., Seetharaman, J., Mao, L., Xiao, R., Lee, D., Raja, S., Everett, J.K., Acton, T.B., Baker, D., Montelione, G.T., Tong, L., Hunt, J.F.

To be published.

Macromolecule Content

Total Structure Weight: 35.85 kDa
Atom Count: 2,372
Modeled Residue Count: 318
Deposited Residue Count: 334
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Designed Protein OR342	A, B	167	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth B] SDF format, chain F [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth B] MOL2 format, chain F [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth B] mmCIF format, chain F [auth B]	C [auth A], D [auth A], E [auth B], F [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.91 Å
R-Value Free: 0.301 (Depositor), 0.314 (DCC)
R-Value Work: 0.201 (Depositor), 0.213 (DCC)
R-Value Observed: 0.206 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 30.054	α = 90
b = 76.401	β = 90
c = 132.584	γ = 90

Software Package:

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

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2013-06-19

Deposition Author(s):

Northeast Structural Genomics Consortium (NESG)

Revision History (Full details and data files)

Version 1.0: 2013-06-19
Type: Initial release
Version 1.1: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description