3FKY | pdb_00003fky

Crystal structure of the glutamine synthetase Gln1deltaN18 from the yeast Saccharomyces cerevisiae

PDB DOI: https://doi.org/10.2210/pdb3FKY/pdb

Classification: LIGASE
Organism(s): Saccharomyces cerevisiae
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2008-12-18 Released: 2009-10-06
Deposition Author(s): He, Y.X., Gui, L., Liu, Y.Z., Du, Y., Zhou, Y.Y., Li, P., Zhou, C.Z.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.95 Å
R-Value Free:
0.258 (Depositor), 0.245 (DCC)
R-Value Work:
0.225 (Depositor), 0.213 (DCC)
R-Value Observed:
0.226 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Crystal structure of Saccharomyces cerevisiae glutamine synthetase Gln1 suggests a nanotube-like supramolecular assembly

He, Y.X., Gui, L., Liu, Y.Z., Du, Y., Zhou, Y., Li, P., Zhou, C.Z.

(2009) Proteins 76: 249-254

PubMed: 19322816 Search on PubMed
DOI: https://doi.org/10.1002/prot.22403
Primary Citation Related Structures:
3FKY

Organizational Affiliation

Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, People's Republic of China.

Macromolecule Content

Total Structure Weight: 838.98 kDa
Atom Count: 53,518
Modeled Residue Count: 6,726
Deposited Residue Count: 7,400
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamine synthetase	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T	370	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: GLN1 EC: 6.3.1.2
UniProt
Find proteins for P32288 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P32288 Go to UniProtKB: P32288
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P32288
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FLC Query on FLC Download:Ideal Coordinates CCD File SDF format, chain Z [auth F] SDF format, chain Y [auth E] SDF format, chain X [auth D] SDF format, chain W [auth C] SDF format, chain V [auth B] SDF format, chain U [auth A] SDF format, chain NA [auth T] SDF format, chain MA [auth S] SDF format, chain LA [auth R] SDF format, chain KA [auth Q] SDF format, chain JA [auth P] SDF format, chain IA [auth O] SDF format, chain HA [auth N] SDF format, chain GA [auth M] SDF format, chain FA [auth L] SDF format, chain EA [auth K] SDF format, chain DA [auth J] SDF format, chain CA [auth I] SDF format, chain BA [auth H] SDF format, chain AA [auth G] MOL2 format, chain Z [auth F] MOL2 format, chain Y [auth E] MOL2 format, chain X [auth D] MOL2 format, chain W [auth C] MOL2 format, chain V [auth B] MOL2 format, chain U [auth A] MOL2 format, chain NA [auth T] MOL2 format, chain MA [auth S] MOL2 format, chain LA [auth R] MOL2 format, chain KA [auth Q] MOL2 format, chain JA [auth P] MOL2 format, chain IA [auth O] MOL2 format, chain HA [auth N] MOL2 format, chain GA [auth M] MOL2 format, chain FA [auth L] MOL2 format, chain EA [auth K] MOL2 format, chain DA [auth J] MOL2 format, chain CA [auth I] MOL2 format, chain BA [auth H] MOL2 format, chain AA [auth G] mmCIF format, chain Z [auth F] mmCIF format, chain Y [auth E] mmCIF format, chain X [auth D] mmCIF format, chain W [auth C] mmCIF format, chain V [auth B] mmCIF format, chain U [auth A] mmCIF format, chain NA [auth T] mmCIF format, chain MA [auth S] mmCIF format, chain LA [auth R] mmCIF format, chain KA [auth Q] mmCIF format, chain JA [auth P] mmCIF format, chain IA [auth O] mmCIF format, chain HA [auth N] mmCIF format, chain GA [auth M] mmCIF format, chain FA [auth L] mmCIF format, chain EA [auth K] mmCIF format, chain DA [auth J] mmCIF format, chain CA [auth I] mmCIF format, chain BA [auth H] mmCIF format, chain AA [auth G]	AA [auth G] BA [auth H] CA [auth I] DA [auth J] EA [auth K] AA [auth G], BA [auth H], CA [auth I], DA [auth J], EA [auth K], FA [auth L], GA [auth M], HA [auth N], IA [auth O], JA [auth P], KA [auth Q], LA [auth R], MA [auth S], NA [auth T], U [auth A], V [auth B], W [auth C], X [auth D], Y [auth E], Z [auth F]	CITRATE ANION C₆ H₅ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-K		Interactions Focus chain AA [auth G] Focus chain BA [auth H] Focus chain CA [auth I] Focus chain DA [auth J] Focus chain EA [auth K] Focus chain FA [auth L] Focus chain GA [auth M] Focus chain HA [auth N] Focus chain IA [auth O] Focus chain JA [auth P] Focus chain KA [auth Q] Focus chain LA [auth R] Focus chain MA [auth S] Focus chain NA [auth T] Focus chain U [auth A] Focus chain V [auth B] Focus chain W [auth C] Focus chain X [auth D] Focus chain Y [auth E] Focus chain Z [auth F] Interactions & Density Focus chain AA [auth G] Focus chain BA [auth H] Focus chain CA [auth I] Focus chain DA [auth J] Focus chain EA [auth K] Focus chain FA [auth L] Focus chain GA [auth M] Focus chain HA [auth N] Focus chain IA [auth O] Focus chain JA [auth P] Focus chain KA [auth Q] Focus chain LA [auth R] Focus chain MA [auth S] Focus chain NA [auth T] Focus chain U [auth A] Focus chain V [auth B] Focus chain W [auth C] Focus chain X [auth D] Focus chain Y [auth E] Focus chain Z [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.95 Å
R-Value Free: 0.258 (Depositor), 0.245 (DCC)
R-Value Work: 0.225 (Depositor), 0.213 (DCC)
R-Value Observed: 0.226 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 128.65	α = 93.46
b = 129.94	β = 104.61
c = 135.61	γ = 104.01

Software Package:

Software Name	Purpose
MAR345dtb	data collection
MOLREP	phasing
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2009-10-06

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2009-10-06
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2023-11-01
Changes: Data collection, Database references, Derived calculations, Refinement description