5Y8X | pdb_00005y8x

Crystal structure of Bacillus licheniformis Gamma glutamyl transpeptidase with Azaserine

PDB DOI: https://doi.org/10.2210/pdb5Y8X/pdb

Classification: TRANSFERASE
Organism(s): Bacillus licheniformis
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2017-08-21 Released: 2018-10-17
Deposition Author(s): Kumari, S., Goel, M., Pal, R., Gupta, R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.97 Å
R-Value Free:
0.194 (Depositor), 0.201 (DCC)
R-Value Work:
0.143 (Depositor), 0.154 (DCC)
R-Value Observed:
0.146 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of Bacillus licheniformis Gamma glutamyl transpeptidase with Azaserine

Goel, M., Kumari, S., Gupta, R.

To be published.

Macromolecule Content

Total Structure Weight: 64.63 kDa
Atom Count: 4,635
Modeled Residue Count: 543
Deposited Residue Count: 585
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Gamma glutamyl transpeptidase	A	398	Bacillus licheniformis	Mutation(s): 0 EC: 2.3.2.2

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Gamma glutamyl transpeptidase	B	187	Bacillus licheniformis	Mutation(s): 0 EC: 2.3.2.2

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AZS Query on AZS Download:Ideal Coordinates CCD File SDF format, chain I [auth B] MOL2 format, chain I [auth B] mmCIF format, chain I [auth B]	I [auth B]	O-DIAZOACETYL-L-SERINE C₅ H₇ N₃ O₄ MZZGOOYMKKIOOX-VKHMYHEASA-N		Interactions Focus chain I [auth B] Interactions & Density Focus chain I [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A]	D [auth A], E [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain H [auth B] MOL2 format, chain H [auth B] mmCIF format, chain H [auth B]	H [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain H [auth B] Interactions & Density Focus chain H [auth B]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain G [auth B] SDF format, chain F [auth B] MOL2 format, chain C [auth A] MOL2 format, chain G [auth B] MOL2 format, chain F [auth B] mmCIF format, chain C [auth A] mmCIF format, chain G [auth B] mmCIF format, chain F [auth B]	C [auth A], F [auth B], G [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain F [auth B] Focus chain G [auth B] Interactions & Density Focus chain C [auth A] Focus chain F [auth B] Focus chain G [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.97 Å
R-Value Free: 0.194 (Depositor), 0.201 (DCC)
R-Value Work: 0.143 (Depositor), 0.154 (DCC)
R-Value Observed: 0.146 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.164	α = 90
b = 60.016	β = 100.42
c = 74.781	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing
Coot	model building

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2018-10-17

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2018-10-17
Type: Initial release
Version 1.1: 2023-11-22
Changes: Data collection, Database references, Derived calculations, Refinement description