3RHT | pdb_00003rht

Crystal structure of type 1 glutamine amidotransferase (GATase1)-like protein from Planctomyces limnophilus

PDB DOI: https://doi.org/10.2210/pdb3RHT/pdb

Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
Organism(s): Planctopirus limnophila DSM 3776
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2011-04-12 Released: 2011-04-27
Deposition Author(s): Michalska, K., Li, H., Bearden, J., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.83 Å
R-Value Free:
0.192 (Depositor), 0.178 (DCC)
R-Value Work:
0.158 (Depositor)
R-Value Observed:
0.158 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of type 1 glutamine amidotransferase (GATase1)-like protein from Planctomyces limnophilus

Michalska, K., Li, H., Bearden, J., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

To be published.

Macromolecule Content

Total Structure Weight: 115.62 kDa
Atom Count: 8,501
Modeled Residue Count: 1,008
Deposited Residue Count: 1,036
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
(GATase1)-like protein	A, B, C, D	259	Planctopirus limnophila DSM 3776	Mutation(s): 0 Gene Names: Plim_2614
UniProt
Find proteins for D5SQH6 (Planctopirus limnophila (strain ATCC 43296 / DSM 3776 / IFAM 1008 / Mu 290)) Explore D5SQH6 Go to UniProtKB: D5SQH6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	D5SQH6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain R [auth C] SDF format, chain S [auth C] SDF format, chain W [auth D] SDF format, chain X [auth D] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain R [auth C] MOL2 format, chain S [auth C] MOL2 format, chain W [auth D] MOL2 format, chain X [auth D] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain R [auth C] mmCIF format, chain S [auth C] mmCIF format, chain W [auth D] mmCIF format, chain X [auth D]	G [auth A] H [auth A] L [auth B] M [auth B] R [auth C] G [auth A], H [auth A], L [auth B], M [auth B], R [auth C], S [auth C], W [auth D], X [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain W [auth D] Focus chain X [auth D] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain W [auth D] Focus chain X [auth D]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain N [auth B] SDF format, chain T [auth C] SDF format, chain Y [auth D] MOL2 format, chain I [auth A] MOL2 format, chain N [auth B] MOL2 format, chain T [auth C] MOL2 format, chain Y [auth D] mmCIF format, chain I [auth A] mmCIF format, chain N [auth B] mmCIF format, chain T [auth C] mmCIF format, chain Y [auth D]	I [auth A], N [auth B], T [auth C], Y [auth D]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain I [auth A] Focus chain N [auth B] Focus chain T [auth C] Focus chain Y [auth D] Interactions & Density Focus chain I [auth A] Focus chain N [auth B] Focus chain T [auth C] Focus chain Y [auth D]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain J [auth B] SDF format, chain O [auth C] SDF format, chain U [auth D] MOL2 format, chain E [auth A] MOL2 format, chain J [auth B] MOL2 format, chain O [auth C] MOL2 format, chain U [auth D] mmCIF format, chain E [auth A] mmCIF format, chain J [auth B] mmCIF format, chain O [auth C] mmCIF format, chain U [auth D]	E [auth A], J [auth B], O [auth C], U [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain J [auth B] Focus chain O [auth C] Focus chain U [auth D] Interactions & Density Focus chain E [auth A] Focus chain J [auth B] Focus chain O [auth C] Focus chain U [auth D]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain V [auth D] MOL2 format, chain K [auth B] MOL2 format, chain V [auth D] mmCIF format, chain K [auth B] mmCIF format, chain V [auth D]	K [auth B], V [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain K [auth B] Focus chain V [auth D] Interactions & Density Focus chain K [auth B] Focus chain V [auth D]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain P [auth C] SDF format, chain Q [auth C] MOL2 format, chain F [auth A] MOL2 format, chain P [auth C] MOL2 format, chain Q [auth C] mmCIF format, chain F [auth A] mmCIF format, chain P [auth C] mmCIF format, chain Q [auth C]	F [auth A], P [auth C], Q [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain P [auth C] Focus chain Q [auth C] Interactions & Density Focus chain F [auth A] Focus chain P [auth C] Focus chain Q [auth C]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.83 Å
R-Value Free: 0.192 (Depositor), 0.178 (DCC)
R-Value Work: 0.158 (Depositor)
R-Value Observed: 0.158 (Depositor)

Diffraction Data:

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.287	α = 90
b = 126.827	β = 96.6
c = 101.964	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
SHELX	model building
MLPHARE	phasing
DM	model building
ARP/wARP	model building
Coot	model building
PHENIX	model building
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
SHELX	phasing
DM	phasing
PHENIX	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2011-04-27

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2011-04-27
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2024-10-09
Changes: Data collection, Database references, Derived calculations, Structure summary