4GVW | pdb_00004gvw

Three-dimensional structure of the de novo designed serine hydrolase 2bfq_3, Northeast Structural Genomics Consortium (NESG) Target OR248

PDB DOI: https://doi.org/10.2210/pdb4GVW/pdb

Classification: DE NOVO PROTEIN, HYDROLASE
Mutation(s): No

Deposited: 2012-08-31 Released: 2012-09-12
Deposition Author(s): Kuzin, A., Lew, S., Seetharaman, J., Rajagopalan, S., Everett, J.K., Acton, T.B., Montelione, G.T., Tong, L., Hunt, J.F., Northeast Structural Genomics Consortium (NESG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.11 Å
R-Value Free:
0.239 (Depositor), 0.233 (DCC)
R-Value Work:
0.172 (Depositor), 0.171 (DCC)
R-Value Observed:
0.175 (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 OR248

Kuzin, A., Lew, S., Seetharaman, J., Rajagopalan, S., Everett, J.K., Acton, T.B., Montelione, G.T., Tong, L., Hunt, J.F.

To be published.

Macromolecule Content

Total Structure Weight: 22.08 kDa
Atom Count: 1,566
Modeled Residue Count: 192
Deposited Residue Count: 199
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
De novo designed serine hydrolase	A	199	N/A	Mutation(s): 0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MES Query on MES 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-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
ACY Query on ACY 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]	ACETIC ACID C₂ H₄ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.11 Å
R-Value Free: 0.239 (Depositor), 0.233 (DCC)
R-Value Work: 0.172 (Depositor), 0.171 (DCC)
R-Value Observed: 0.175 (Depositor)

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.644	α = 90
b = 62.052	β = 90
c = 107.067	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
msr165	data collection
HKL-2000	data reduction
HKL-2000	data scaling
BALBES	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2012-09-12

Deposition Author(s):

Northeast Structural Genomics Consortium (NESG)

Revision History (Full details and data files)

Version 1.0: 2012-09-12
Type: Initial release
Version 1.1: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description