7YC6 | pdb_00007yc6

Crystal structure of D110P mutant of GATase subunit of Methanocaldococcus jannaschii GMP synthetase

PDB DOI: https://doi.org/10.2210/pdb7YC6/pdb

Classification: TRANSFERASE
Organism(s): Methanocaldococcus jannaschii
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2022-06-30 Released: 2023-06-14
Deposition Author(s): Chandrashekarmath, A., Bellur, A.
Funding Organization(s): Department of Biotechnology (DBT, India), Science and Engineering Research Board (SERB)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.221 (Depositor), 0.220 (DCC)
R-Value Work:
0.199 (Depositor), 0.203 (DCC)
R-Value Observed:
0.200 (Depositor)

Starting Model: experimental
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This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of D110P mutant of GATase subunit of Methanocaldococcus jannaschii GMP synthetase

Chandrashekarmath, A., Bellur, A., Balaram, H.

To be published.

Macromolecule Content

Total Structure Weight: 21.43 kDa
Atom Count: 1,468
Modeled Residue Count: 183
Deposited Residue Count: 188
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GMP synthase [glutamine-hydrolyzing] subunit A	A	188	Methanocaldococcus jannaschii	Mutation(s): 1 EC: 6.3.5.2
UniProt
Find proteins for Q58970 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)) Explore Q58970 Go to UniProtKB: Q58970
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q58970
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] SDF format, chain B [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain B [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A] mmCIF format, chain B [auth A]	B [auth A] C [auth A] D [auth A] E [auth A] F [auth A] B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.221 (Depositor), 0.220 (DCC)
R-Value Work: 0.199 (Depositor), 0.203 (DCC)
R-Value Observed: 0.200 (Depositor)

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.08	α = 90
b = 63.08	β = 90
c = 101.94	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2023-06-14

Deposition Author(s):

Chandrashekarmath, A.

Funding Organization	Location	Grant Number
Department of Biotechnology (DBT, India)	India	--
Science and Engineering Research Board (SERB)	India	--

Revision History (Full details and data files)

Version 1.0: 2023-06-14
Type: Initial release
Version 1.1: 2023-11-29
Changes: Data collection, Refinement description

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