4JXQ | pdb_00004jxq

Crystal structure of a GNAT superfamily phosphinothricin acetyltransferase (Pat) from Sinorhizobium meliloti 1021

PDB DOI: https://doi.org/10.2210/pdb4JXQ/pdb

Classification: TRANSFERASE
Organism(s): Sinorhizobium meliloti 1021
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2013-03-28 Released: 2013-05-08
Deposition Author(s): Majorek, K.A., Cooper, D.R., Osinski, T., Ahmed, M., Stead, M., Hillerich, B., Seidel, R., Bonanno, J.B., Almo, S.C., Minor, W., New York Structural Genomics Research Consortium (NYSGRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.15 Å
R-Value Free:
0.153 (Depositor), 0.152 (DCC)
R-Value Work:
0.120 (Depositor), 0.120 (DCC)
R-Value Observed:
0.122 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of a GNAT superfamily phosphinothricin acetyltransferase (Pat) from Sinorhizobium meliloti 1021

Majorek, K.A., Cooper, D.R., Ahmed, M., Stead, M., Hillerich, B., Seidel, R., Bonanno, J.B., Almo, S.C., Minor, W.

To be published.

Macromolecule Content

Total Structure Weight: 41.98 kDa
Atom Count: 3,895
Modeled Residue Count: 370
Deposited Residue Count: 372
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Acetyltransferase	A, B	186	Sinorhizobium meliloti 1021	Mutation(s): 0 Gene Names: R03223, SMc03840 EC: 2.3.1
UniProt
Find proteins for Q92L60 (Rhizobium meliloti (strain 1021)) Explore Q92L60 Go to UniProtKB: Q92L60
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q92L60
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
2PE Query on 2PE Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	NONAETHYLENE GLYCOL C₁₈ H₃₈ O₁₀ YZUUTMGDONTGTN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
FLC Query on FLC Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain H [auth B] MOL2 format, chain D [auth A] MOL2 format, chain H [auth B] mmCIF format, chain D [auth A] mmCIF format, chain H [auth B]	D [auth A], H [auth B]	CITRATE ANION C₆ H₅ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-K		Interactions Focus chain D [auth A] Focus chain H [auth B] Interactions & Density Focus chain D [auth A] Focus chain H [auth B]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain F [auth B] MOL2 format, chain F [auth B] mmCIF format, chain F [auth B]	F [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain F [auth B] Interactions & Density Focus chain F [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain G [auth B] MOL2 format, chain C [auth A] MOL2 format, chain G [auth B] mmCIF format, chain C [auth A] mmCIF format, chain G [auth B]	C [auth A], G [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain G [auth B] Interactions & Density Focus chain C [auth A] Focus chain G [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: 1.15 Å
R-Value Free: 0.153 (Depositor), 0.152 (DCC)
R-Value Work: 0.120 (Depositor), 0.120 (DCC)
R-Value Observed: 0.122 (Depositor)

Diffraction Data:

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.461	α = 90
b = 80.481	β = 90
c = 83.611	γ = 90

Software Package:

Software Name	Purpose
HKL-3000	data collection
HKL-3000	phasing
SHELXD	phasing
SHELXE	model building
MLPHARE	phasing
DM	model building
ARP/wARP	model building
REFMAC	refinement
Coot	model building
HKL-3000	data reduction
HKL-3000	data scaling
DM	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2013-05-08

Deposition Author(s):

New York Structural Genomics Research Consortium (NYSGRC)

Revision History (Full details and data files)

Version 1.0: 2013-05-08
Type: Initial release
Version 1.1: 2013-05-15
Changes: Structure summary
Version 1.2: 2022-04-13
Changes: Database references, Derived calculations, Structure summary
Version 1.3: 2024-10-16
Changes: Data collection, Structure summary