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Found 1 Document (1.032 seconds)

BMRB: 27151

6NUI

Human Guanylate Kinase

Authors

Sabo, M., Khan, N., Ban, D., Trigo-Mourino, P., Carneiro, M., Konrad, M., Lee, D.

Assembly

hGMPK

Entity

1. hGMPK (polymer, Thiol state: all free), 198 monomers, 21862.46 Da Detail

HMSGPRPVVL SGPSGAGKST LLKRLLQEHS GIFGFSVSHT TRNPRPGEEN GKDYYFVTRE VMQRDIAAGD FIEHAEFSGN LYGTSKVAVQ AVQAMNRICV LDVDLQGVRN IKATDLRPIY ISVQPPSLHV LEQRLRQRNT ETEESLVKRL AAAQADMESS KEPGLFDVVI INDSLDQAYA ELKEALSEEI KKAQRTGA

Formula weight

21862.46 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

molecular dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 92.6 %, Completeness (bb): 94.8 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	92.6 % (2095 of 2263)	92.9 % (1096 of 1180)	91.6 % (802 of 876)	95.2 % (197 of 207)
Backbone	94.8 % (1109 of 1170)	93.5 % (375 of 401)	95.5 % (554 of 580)	95.2 % (180 of 189)
Sidechain	91.4 % (1167 of 1277)	92.6 % (721 of 779)	89.4 % (429 of 480)	94.4 % (17 of 18)
Aromatic	60.0 % (72 of 120)	86.7 % (52 of 60)	33.3 % (20 of 60)
Methyl	99.6 % (227 of 228)	99.1 % (113 of 114)	100.0 % (114 of 114)

1. hGMPK

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2

#	Name	Isotope labeling	Concentration
1	hGMPK	[U-100% 13C; U-100% 15N]	1 mM
2	sodium chloride	natural abundance	100 mM
3	sodium phosphate	natural abundance	20 mM
4	TCEP	natural abundance	1 mM
5	sodium azide	natural abundance	3 mM
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %
8	DSS	natural abundance	5 uM

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2

#	Name	Isotope labeling	Concentration
9	hGMPK	[U-100% 13C; U-100% 15N]	1 mM
10	sodium chloride	natural abundance	100 mM
11	sodium phosphate	natural abundance	20 mM
12	TCEP	natural abundance	1 mM
13	sodium azide	natural abundance	3 mM
14	D2O	natural abundance	100 %

LACS Plot; CA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: 0.16 ppm, Outliers: 1 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: 0.16 ppm, Outliers: 1 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: -0.02 ppm, Outliers: 2 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: -0.23 ppm, Outliers: 3 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 6NUI, Strand ID: A Detail

Release date

2017-06-20

Citation

¹H, ¹³C and ¹⁵N resonance assignment of human guanylate kinase
Khan, N., Ban, D., Trigo-Mourino, P., Carneiro, M., Konrad, M., Lee, D., Sabo, M.
Biomol. NMR Assign. (2017), 12, 11-14, PubMed 28861857 , DOI 10.1007/s12104-017-9771-6 , Abstract

Related entities 1. hGMPK, : 1 : 2 : 248 entities Detail

Interaction partners 1. hGMPK, : 4 interactors Detail

More details for 4 interactors identified by 4 citations

Experiments performed 10 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2

#	Name	Isotope labeling	Concentration
1	hGMPK	[U-100% 13C; U-100% 15N]	1 mM
2	sodium chloride	natural abundance	100 mM
3	sodium phosphate	natural abundance	20 mM
4	TCEP	natural abundance	1 mM
5	sodium azide	natural abundance	3 mM
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %
8	DSS	natural abundance	5 uM

2 2D 1H-13C HSQC aliphatic

Instrument

Bruker Avance - 950 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2

#	Name	Isotope labeling	Concentration
9	hGMPK	[U-100% 13C; U-100% 15N]	1 mM
10	sodium chloride	natural abundance	100 mM
11	sodium phosphate	natural abundance	20 mM
12	TCEP	natural abundance	1 mM
13	sodium azide	natural abundance	3 mM
14	D2O	natural abundance	100 %

3 2D 1H-13C HSQC aromatic

Instrument

Bruker Avance - 950 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2

#	Name	Isotope labeling	Concentration
9	hGMPK	[U-100% 13C; U-100% 15N]	1 mM
10	sodium chloride	natural abundance	100 mM
11	sodium phosphate	natural abundance	20 mM
12	TCEP	natural abundance	1 mM
13	sodium azide	natural abundance	3 mM
14	D2O	natural abundance	100 %

4 3D HNCO

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2

#	Name	Isotope labeling	Concentration
1	hGMPK	[U-100% 13C; U-100% 15N]	1 mM
2	sodium chloride	natural abundance	100 mM
3	sodium phosphate	natural abundance	20 mM
4	TCEP	natural abundance	1 mM
5	sodium azide	natural abundance	3 mM
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %
8	DSS	natural abundance	5 uM

5 3D HNCA

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2

#	Name	Isotope labeling	Concentration
1	hGMPK	[U-100% 13C; U-100% 15N]	1 mM
2	sodium chloride	natural abundance	100 mM
3	sodium phosphate	natural abundance	20 mM
4	TCEP	natural abundance	1 mM
5	sodium azide	natural abundance	3 mM
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %
8	DSS	natural abundance	5 uM

6 3D HNCACB

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2

#	Name	Isotope labeling	Concentration
1	hGMPK	[U-100% 13C; U-100% 15N]	1 mM
2	sodium chloride	natural abundance	100 mM
3	sodium phosphate	natural abundance	20 mM
4	TCEP	natural abundance	1 mM
5	sodium azide	natural abundance	3 mM
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %
8	DSS	natural abundance	5 uM

7 3D HCCH-TOCSY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2

#	Name	Isotope labeling	Concentration
9	hGMPK	[U-100% 13C; U-100% 15N]	1 mM
10	sodium chloride	natural abundance	100 mM
11	sodium phosphate	natural abundance	20 mM
12	TCEP	natural abundance	1 mM
13	sodium azide	natural abundance	3 mM
14	D2O	natural abundance	100 %

8 3D 1H-15N NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2

#	Name	Isotope labeling	Concentration
1	hGMPK	[U-100% 13C; U-100% 15N]	1 mM
2	sodium chloride	natural abundance	100 mM
3	sodium phosphate	natural abundance	20 mM
4	TCEP	natural abundance	1 mM
5	sodium azide	natural abundance	3 mM
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %
8	DSS	natural abundance	5 uM

9 3D 1H-13C NOESY aliphatic

Instrument

Bruker Avance - 950 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2

#	Name	Isotope labeling	Concentration
9	hGMPK	[U-100% 13C; U-100% 15N]	1 mM
10	sodium chloride	natural abundance	100 mM
11	sodium phosphate	natural abundance	20 mM
12	TCEP	natural abundance	1 mM
13	sodium azide	natural abundance	3 mM
14	D2O	natural abundance	100 %

10 3D 1H-13C NOESY aromatic

Instrument

Bruker Avance - 950 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2

#	Name	Isotope labeling	Concentration
9	hGMPK	[U-100% 13C; U-100% 15N]	1 mM
10	sodium chloride	natural abundance	100 mM
11	sodium phosphate	natural abundance	20 mM
12	TCEP	natural abundance	1 mM
13	sodium azide	natural abundance	3 mM
14	D2O	natural abundance	100 %

NMR combined restraints 6 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, RDC restraints	combined_27151_6nui.nef
Input source #2: Coordindates	6nui.cif
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	None
Whether the assembly has a other bond	None
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Error

Disulfide bonds

None

Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)

None

Non-standard residues

None

Sequence alignments

Entity_assembly_ID (NMR): A vs Auth_asym_ID (model): A

0--------10--------20--------30--------40--------50--------60--------70--------80--------90-------10
HMSGPRPVVLSGPSGAGKSTLLKRLLQEHSGIFGFSVSHTTRNPRPGEENGKDYYFVTREVMQRDIAAGDFIEHAEFSGNLYGTSKVAVQAVQAMNRICV
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
HMSGPRPVVLSGPSGAGKSTLLKRLLQEHSGIFGFSVSHTTRNPRPGEENGKDYYFVTREVMQRDIAAGDFIEHAEFSGNLYGTSKVAVQAVQAMNRICV
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

0-------110-------120-------130-------140-------150-------160-------170-------180-------190-------
LDVDLQGVRNIKATDLRPIYISVQPPSLHVLEQRLRQRNTETEESLVKRLAAAQADMESSKEPGLFDVVIINDSLDQAYAELKEALSEEIKKAQRTGA
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LDVDLQGVRNIKATDLRPIYISVQPPSLHVLEQRLRQRNTETEESLVKRLAAAQADMESSKEPGLFDVVIINDSLDQAYAELKEALSEEIKKAQRTGA
-------110-------120-------130-------140-------150-------160-------170-------180-------190--------

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	198	0	0	100.0

Content subtype: combined_27151_6nui.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	2145		100.0 (chain: A, length: 198)
1	Distance restraints	DYANA/DIANA_distance_constraints_3	OK	3566 (1)	noe	97.0 (chain: A, length: 198)
2	Distance restraints	DYANA/DIANA_distance_constraints_5	Warning	57 (1)	hbond	20.7 (chain: A, length: 198)
1	RDC restraints	DYANA/DIANA_dipolar_coupling_2	OK	89 (89)	.	44.9 (chain: A, length: 198)
2	RDC restraints	DYANA/DIANA_dipolar_coupling_4	Error	85 (85)	.	64.6 (chain: A, length: 198)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 198, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 1137
  - ¹³C chemical shifts: 812
  - ¹⁵N chemical shifts: 196
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- Peptide bond of PRO
- Tautomeric state of HIS
- Rotameric state of ILE , LEU, and VAL
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: A

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
95	ASN	CG	178.112
109	ASN	CG	176.29
138	ASN	CG	177.71

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	1180	1137	96.4
¹³C chemical shifts	876	809	92.4
¹⁵N chemical shifts	221	196	88.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	401	391	97.5
¹³C chemical shifts	396	376	94.9
¹⁵N chemical shifts	189	179	94.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	779	746	95.8
¹³C chemical shifts	480	433	90.2
¹⁵N chemical shifts	32	17	53.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	118	117	99.2
¹³C chemical shifts	118	117	99.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	60	52	86.7
¹³C chemical shifts	60	20	33.3

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_3
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 198, Sequence coverage: 97.0%
- Total number of restraints: 3543
- Weight of restraints: 1.0 (3543)
- Potential type of restraints: upper-bound-parabolic (3543)
- Range of distance target values: 2.36, 6.01 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
- Distance restraints on contact map
- Saveframe: DYANA/DIANA_distance_constraints_5
  - Status: Warning
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 198, Sequence coverage: 20.7%
  - Total number of restraints: 57
  - Weight of restraints: 1.0 (57)
  - Potential type of restraints: upper-bound-parabolic (57)
  - Range of distance target values: 2.0, 3.0 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
  - Distance restraints on contact map

RDC restraints

Saveframe: DYANA/DIANA_dipolar_coupling_2

Status: OK
Experiment type: .
Sequence coverage of experimental data
- Entity_assembly_ID: A, Chain length: 198, Sequence coverage: 44.9%
Total number of restraints: 89
Potential type of restraints: undefined (89)
Range of observed RDC values: 100.0, -100.0 (Hz)
RDC restraints per residue

Saveframe: DYANA/DIANA_dipolar_coupling_4

Status: Error
Experiment type: .

Sequence coverage of experimental data

Entity_assembly_ID: A, Chain length: 198, Sequence coverage: 64.6%

0--------10--------20--------30--------40--------50--------60--------70--------80--------90-------10
HMSGPRPVVLSGPSGAGKSTLLKRLLQEHSGIFGFSVSHTTRNPRPGEENGKDYYFVTREVMQRDIAAGDFIEHAEFSGNLYGTSKVAVQAVQAMNRICV
       ||||     ||| |||| |||  ||||||||||||    |||||||||||||||||||||||||  ||  ||  ||   || |||||||||||
.......VVLS.....GKS.LLKR.LQE..GIFGFSVSHTTR....GEENGKDYYFVTREVMQRDIAAGDF..HA..SG..YG...VA.QAVQAMNRICV
0--------10--------20--------30--------40--------50--------60--------70--------80--------90-------10

0-------110-------120-------130-------140-------150-------160-------170-------180-------190-------
LDVDLQGVRNIKATDLRPIYISVQPPSLHVLEQRLRQRNTETEESLVKRLAAAQADMESSKEPGLFDVVIINDSLDQAYAELKEALSEEIKKAQRTGA
||| |||||||   ||  ||||||     |||            || ||||  ||   |||  ||| ||||||  ||||||| |||||| ||||    
LDV.LQGVRNI...DL..IYISVQ.....VLE............SL.KRLA..QA...SSK..GLF.VVIIND..DQAYAEL.EALSEE.KKAQ    
0-------110-------120-------130-------140-------150-------160-------170-------180-------190---

Total number of restraints: 85
Potential type of restraints: undefined (85)
Range of observed RDC values: 100.0, -100.0 (Hz)
RDC restraints per residue
- Chain_ID: A
  None

Keywords NMR assignment, enzyme, guanylate kinase (GMPK), nucleotide kinase

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Found 1 Document (1.032 seconds)

BMRB: 27151

Sample #1

Sample #2

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. hGMPK, : 1 : 2 : 248 entities Detail

Interaction partners 1. hGMPK, : 4 interactors Detail

Experiments performed 10 experiments Detail

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NMR combined restraints 6 contents Detail