3N0B | pdb_00003n0b

TM0449 mutant crystals grown in loops/micromounts

PDB DOI: https://doi.org/10.2210/pdb3N0B/pdb

Classification: TRANSFERASE
Organism(s): Thermotoga maritima
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2010-05-13 Released: 2011-05-25
Deposition Author(s): Mathews, I.I.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.249 (Depositor), 0.243 (DCC)
R-Value Work:
0.198 (Depositor), 0.193 (DCC)
R-Value Observed:
0.200 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Diffraction study of protein crystals grown in cryoloops and micromounts.

Berger, M.A., Decker, J.H., Mathews, I.I.

(2010) J Appl Crystallogr 43: 1513-1518

PubMed: 22477781 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1107/S0021889810040409
Primary Citation Related Structures:
3MZQ, 3MZR, 3N02, 3N03, 3N0B, 3N0C

PubMed Abstract:
Protein crystals are usually grown in hanging or sitting drops and generally get transferred to a loop or micromount for cryocooling and data collection. This paper describes a method for growing crystals on cryoloops for easier manipulation of the crystals for data collection. This study also investigates the steps for the automation of this process and describes the design of a new tray for the method. The diffraction patterns and the structures of three proteins grown by both the new method and the conventional hanging-drop method are compared. The new setup is optimized for the automation of the crystal mounting process. Researchers could prepare nanolitre drops under ordinary laboratory conditions by growing the crystals directly in loops or micromounts. As has been pointed out before, higher levels of supersaturation can be obtained in very small volumes, and the new method may help in the exploration of additional crystallization conditions.

Organizational Affiliation

Stanford Synchrotron Radiation Lightsource, Stanford University, 2575 Sand Hill Road, SSRL MS 99, Menlo Park, CA 94025, USA.

Macromolecule Content

Total Structure Weight: 113.62 kDa
Atom Count: 7,464
Modeled Residue Count: 862
Deposited Residue Count: 928
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thymidylate synthase thyX	A, B, C, D	232	Thermotoga maritima	Mutation(s): 2 Gene Names: thy1, thyX, tm0449, TM_0449 EC: 2.1.1.148
UniProt
Find proteins for Q9WYT0 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9WYT0 Go to UniProtKB: Q9WYT0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9WYT0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD Query on FAD Download:Ideal Coordinates CCD File SDF format, chain K [auth D] SDF format, chain I [auth C] SDF format, chain H [auth B] SDF format, chain F [auth A] MOL2 format, chain K [auth D] MOL2 format, chain I [auth C] MOL2 format, chain H [auth B] MOL2 format, chain F [auth A] mmCIF format, chain K [auth D] mmCIF format, chain I [auth C] mmCIF format, chain H [auth B] mmCIF format, chain F [auth A]	F [auth A], H [auth B], I [auth C], K [auth D]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth C] Focus chain K [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth C] Focus chain K [auth D]
UMP Query on UMP Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth B] SDF format, chain J [auth C] SDF format, chain L [auth D] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain J [auth C] MOL2 format, chain L [auth D] mmCIF format, chain E [auth A] mmCIF format, chain G [auth B] mmCIF format, chain J [auth C] mmCIF format, chain L [auth D]	E [auth A], G [auth B], J [auth C], L [auth D]	2'-DEOXYURIDINE 5'-MONOPHOSPHATE C₉ H₁₃ N₂ O₈ P JSRLJPSBLDHEIO-SHYZEUOFSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain J [auth C] Focus chain L [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain J [auth C] Focus chain L [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.249 (Depositor), 0.243 (DCC)
R-Value Work: 0.198 (Depositor), 0.193 (DCC)
R-Value Observed: 0.200 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.523	α = 90
b = 116.754	β = 90
c = 141.053	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2011-05-25

Deposition Author(s):

Mathews, I.I.

Revision History (Full details and data files)

Version 1.0: 2011-05-25
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2012-04-25
Changes: Database references
Version 1.3: 2017-11-08
Changes: Refinement description
Version 1.4: 2023-09-06
Changes: Data collection, Database references, Derived calculations, Refinement description