BMRB Entry 34304

Name: A computationally designed dRP lyase domain reconstructed from two heterologous fragments
Published: 2018-12-05

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PDB ID: 6h5h
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR34304
MolProbity Validation Chart

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Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title: A computationally designed dRP lyase domain reconstructed from two heterologous fragments PubMed: 30558718

Deposition date: 2018-07-24 Original release date: 2018-12-05

Authors: ElGamacy, M.; Coles, M.; Lupas, A.

Citation: ElGamacy, M.; Coles, M.; Lupas, A.. "Asymmetric protein design from conserved supersecondary structures" J. Struct. Biol. 204, 380-387 (2018).

Assembly members:
entity_1, polymer, 121 residues, 13443.259 Da.

Natural source: Common Name: not available Taxonomy ID: 32630 Superkingdom: not available Kingdom: not available Genus/species: not available not available

Experimental source: Production method: recombinant technology Host organism: Escherichia coli BL21(DE3)

Entity Sequences (FASTA):
entity_1: MKHHHHHHPMSDYDIPTTEN LYFQGAMGGQETLNGALVNM LKEEGNKALSVGNIDDALQY YAAAITLDKYPHKIKSGAEA KKLPGVGTKIAEKIDEFLAT GKLRKLEKIRQDDTSSSINF L

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	257
15N chemical shifts	61
1H chemical shifts	430

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	entity_1	1

Entities:

Entity 1, entity_1 121 residues - 13443.259 Da.

1

MET

LYS

HIS

PRO

MET

2

SER

ASP

TYR

ASP

ILE

PRO

THR

GLU

ASN

3

LEU

TYR

PHE

GLN

GLY

ALA

MET

GLY

GLN

4

GLU

THR

LEU

ASN

GLY

ALA

LEU

VAL

ASN

MET

5

LEU

LYS

GLU

GLY

ASN

LYS

ALA

LEU

SER

6

VAL

GLY

ASN

ILE

ASP

ALA

LEU

GLN

TYR

7

TYR

ALA

ILE

THR

LEU

ASP

LYS

TYR

8

PRO

HIS

LYS

ILE

LYS

SER

GLY

ALA

GLU

ALA

9

LYS

LEU

PRO

GLY

VAL

GLY

THR

LYS

ILE

10

ALA

GLU

LYS

ILE

ASP

GLU

PHE

LEU

ALA

THR

11

GLY

LYS

LEU

ARG

LYS

LEU

GLU

LYS

ILE

ARG

12

GLN

ASP

THR

SER

ILE

ASN

PHE

13

LEU

Samples:

sample_1: polb4, [U-15N], 500 uM; potassium phosphate 150 mM

sample_2: polb4, [U-13C; U-15N], 500 uM; potassium phosphate 150 mM

sample_conditions_1: ionic strength: 0.15 M; pH: 7.1; pressure: 1 atm; temperature: 313 K

Experiments:

Name	Sample	Sample state	Sample conditions
3D HNCO	sample_2	isotropic	sample_conditions_1
3D HNCA	sample_2	isotropic	sample_conditions_1
3D C(CO)NH	sample_2	isotropic	sample_conditions_1
3D H(CCO)NH	sample_2	isotropic	sample_conditions_1
3D 15N-HSQC NOESY	sample_1	isotropic	sample_conditions_1
3D 13C-HSQC NOESY	sample_2	isotropic	sample_conditions_1
3D CNH-NOESY	sample_2	isotropic	sample_conditions_1
3D NNH-NOESY	sample_1	isotropic	sample_conditions_1
3D CCH-TOCSY	sample_2	isotropic	sample_conditions_1
2D 15N-filtered NOESY	sample_1	isotropic	sample_conditions_1

Software:

TOPSPIN, Bruker Biospin - collection

SPARKY, Goddard - data analysis

X-PLOR, Brunger - structure calculation

Shine, Riss, M. and Coles, M. - refinement

NMR spectrometers:

Bruker AvanceIII 600 MHz
Bruker AvanceIII 800 MHz

Download simulated HSQC data in one of the following formats:
CSV: Backbone or all simulated shifts
SPARKY: Backbone or all simulated shifts