BMRB Entry 18934

Name: Binary complex of African Swine Fever Virus Pol X with MgdGTP
Published: 2014-03-31

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PDB ID: 2m2u
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR18934
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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:

Binary complex of African Swine Fever Virus Pol X with MgdGTP

Deposition date:

2013-01-03

Original release date:

2014-03-31

Authors:

Wu, Wen-Jin; Su, Mei-I; Tsai, Ming-Daw

Citation:

Citation: Wu, Wen-Jin; Su, Mei-I; Wu, Jian-Li; Kumar, Sandeep; Lim, Liang-Hin; Wang, Chun-Wei Eric; Nelissen, Frank; Chen, Ming-Chuan Chad; Doreleijers, Jurgen; Wijmenga, Sybren; Tsai, Ming-Daw. "How a low-fidelity DNA polymerase chooses non-watson-crick from watson-crick incorporation." J. Am. Chem. Soc. 136, 4927-4937 (2014).
PubMed: 24617852

Assembly members:

Assembly members:
entity_1, polymer, 174 residues, 20351.670 Da.
entity_MG, non-polymer, 24.305 Da.
entity_DGT, non-polymer, 507.181 Da.

Natural source:

Natural source: Common Name: African Swine Fever Virus Taxonomy ID: 10497 Superkingdom: Viruses Kingdom: not available Genus/species: Asfivirus African Swine Fever Virus

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pET-17b

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: MLTLIQGKKIVNHLRSRLAF EYNGQLIKILSKNIVAVGSL RREEKMLNDVDLLIIVPEKK LLKHVLPNIRIKGLSFSVKV CGERKCVLFIEWEKKTYQLD LFTALAEEKPYAIFHFTGPV SYLIRIRAALKKKNYKLNQY GLFKNQTLVPLKITTEKELI KELGFTYRIPKKRL

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	796
15N chemical shifts	180
1H chemical shifts	1381

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
Hide all

Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	African Swine Fever Virus Pol X	1
2	2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE	3
3	MG2_1	2
4	MG2_2	2

Entities:

Entity 1, African Swine Fever Virus Pol X 174 residues - 20351.670 Da.

1

MET

LEU

THR

LEU

ILE

GLN

GLY

LYS

ILE

2

VAL

ASN

HIS

LEU

ARG

SER

ARG

LEU

ALA

PHE

3

GLU

TYR

ASN

GLY

GLN

LEU

ILE

LYS

ILE

LEU

4

SER

LYS

ASN

ILE

VAL

ALA

VAL

GLY

SER

LEU

5

ARG

GLU

LYS

MET

LEU

ASN

ASP

VAL

6

ASP

LEU

ILE

VAL

PRO

GLU

LYS

7

LEU

LYS

HIS

VAL

LEU

PRO

ASN

ILE

ARG

8

ILE

LYS

GLY

LEU

SER

PHE

SER

VAL

LYS

VAL

9

CYS

GLY

GLU

ARG

LYS

CYS

VAL

LEU

PHE

ILE

10

GLU

TRP

GLU

LYS

THR

TYR

GLN

LEU

ASP

11

LEU

PHE

THR

ALA

LEU

ALA

GLU

LYS

PRO

12

TYR

ALA

ILE

PHE

HIS

PHE

THR

GLY

PRO

VAL

13

SER

TYR

LEU

ILE

ARG

ILE

ARG

ALA

LEU

14

LYS

ASN

TYR

LYS

LEU

ASN

GLN

TYR

15

GLY

LEU

PHE

LYS

ASN

GLN

THR

LEU

VAL

PRO

16

LEU

LYS

ILE

THR

GLU

LYS

GLU

LEU

ILE

17

LYS

GLU

LEU

GLY

PHE

THR

TYR

ARG

ILE

PRO

18

LYS

ARG

LEU

Entity 3, 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE - C10 H16 N5 O13 P3 - 507.181 Da.

1

DGT

Entity 2, MG2_1 - Mg - 24.305 Da.

1

MG

Samples:

sample_1: African Swine Fever Virus Pol X, [U-100% 13C; U-100% 15N], 0.5 mM; 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE, [U-100% 13C; U-100% 15N], 5 mM; MG2 10 mM; DTT, [U-100% 2H], 10 mM; Borate 50 mM; potassium chloride 50 mM

sample_2: African Swine Fever Virus Pol X, [U-13C; U-15N; U-2H], 0.5 mM; 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE 5 mM; MG2 10 mM; DTT, [U-100% 2H], 10 mM; Borate 50 mM; potassium chloride 50 mM

sample_conditions_1: ionic strength: 100 mM; pH: 6.5; pressure: 1 atm; temperature: 293 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_1	isotropic	sample_conditions_1
3D HNCO	sample_2	isotropic	sample_conditions_1
3D HNCA	sample_2	isotropic	sample_conditions_1
3D HNCACB	sample_2	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_1	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY aliphatic	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC aromatic	sample_1	isotropic	sample_conditions_1

Software:

CYANA, Guntert, Mumenthaler and Wuthrich - structure solution

HADDOCK, Dr. Alexandre Bonvin - refinement

NMR spectrometers:

Bruker Avance 800 MHz
Bruker Avance 850 MHz
Bruker Avance 600 MHz

BMRB	18933 18935
PDB	1JAJ 1JQR 2M2T 2M2U 2M2V 2M2W
EMBL	CAN10196 CAN10446 CBH29197
GB	AAA65326 AIY22288 AIY22446 AKO62778
PRF	2113434DC
REF	NP_042790
SP	P0C984 P42494
AlphaFold	P0C984 P42494