4JBC | pdb_00004jbc

Crystal Structure of the computationally designed serine hydrolase 3mmj_2, Northeast Structural Genomics Consortium (NESG) Target OR318

PDB DOI: https://doi.org/10.2210/pdb4JBC/pdb

Classification: Structural Genomics, Unknown Function
Organism(s): synthetic construct
Mutation(s): No

Deposited: 2013-02-19 Released: 2013-03-20
Deposition Author(s): Kuzin, A., Lew, S., Rajagopalan, S., Seetharaman, J., Maglaqui, M., Xiao, R., Lee, D., Everett, J.K., Acton, T.B., Montelione, G.T., Tong, L., Baker, D., Hunt, J.F., Northeast Structural Genomics Consortium (NESG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.261 (Depositor), 0.259 (DCC)
R-Value Work:
0.202 (Depositor), 0.202 (DCC)
R-Value Observed:
0.204 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Crystal Structure of the computationally designed serine hydrolase 3mmj_2, Northeast Structural Genomics Consortium (NESG) Target OR318

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

To be published.

Macromolecule Content

Total Structure Weight: 75.38 kDa
Atom Count: 5,607
Modeled Residue Count: 627
Deposited Residue Count: 646
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
designed serine hydrolase 3mmj_2	A, B	323	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 B] SDF format, chain E [auth B] SDF format, chain F [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain E [auth B] MOL2 format, chain F [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain E [auth B] mmCIF format, chain F [auth B]	C [auth A], D [auth B], E [auth B], F [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain C [auth A] Focus chain D [auth B] Focus chain E [auth B] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B] Focus chain E [auth B] Focus chain F [auth B]

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: 2.00 Å
R-Value Free: 0.261 (Depositor), 0.259 (DCC)
R-Value Work: 0.202 (Depositor), 0.202 (DCC)
R-Value Observed: 0.204 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.243	α = 90
b = 194.552	β = 90
c = 46.09	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
HKL-2000	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: 2013-03-20

Deposition Author(s):

Northeast Structural Genomics Consortium (NESG)

Revision History (Full details and data files)

Version 1.0: 2013-03-20
Type: Initial release
Version 1.1: 2014-12-10
Changes: Structure summary
Version 1.2: 2018-01-24
Changes: Structure summary
Version 1.3: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.4: 2023-12-06
Changes: Data collection
Version 1.5: 2024-11-27
Changes: Structure summary