BMRBj - BMREntryMaster

Found 1 Document (1.097 seconds)

BMRB: 25760

2N6D

NMR structure of the 140-315 fragment of the N-acetylglucosamine-1-phosphate transferase, alpha and beta subunits

Authors

Serrano, P., Geralt, M., Wuthrich, K.

Assembly

GNPTAB

Entity

1. GNPTAB (polymer, Thiol state: all free), 172 monomers, 19132.88 Da Detail

MKVPMLVLDP ALPANITLKD LPSLYPSFHS ASDIFNVAKP KNPSTNVSVV VFDSTKDVED AHSGLLKGNS RQTVWRGYLT TDKEVPGLVL MQDLAFLSGF PPTFKETNQL KTKLPENLSS KVKLLQLYSE ASVALLKLNN PKDFQELNKQ TKKNMTIDGK ELTISPAYLL WD

Formula weight

19132.88 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

Torsion Angle Dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 97.7 %, Completeness: 91.4 %, Completeness (bb): 91.7 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	91.4 % (1881 of 2058)	93.1 % (998 of 1072)	87.5 % (707 of 808)	98.9 % (176 of 178)
Backbone	91.7 % (922 of 1006)	97.9 % (330 of 337)	85.3 % (435 of 510)	98.7 % (157 of 159)
Sidechain	92.0 % (1121 of 1218)	90.9 % (668 of 735)	93.5 % (434 of 464)	100.0 % (19 of 19)
Aromatic	95.5 % (128 of 134)	97.0 % (65 of 67)	93.8 % (61 of 65)	100.0 % (2 of 2)
Methyl	95.3 % (204 of 214)	95.3 % (102 of 107)	95.3 % (102 of 107)

1. entity

MKVPMLVLDP ALPANITLKD LPSLYPSFHS ASDIFNVAKP KNPSTNVSVV VFDSTKDVED AHSGLLKGNS RQTVWRGYLT TDKEVPGLVL MQDLAFLSGF PPTFKETNQL KTKLPENLSS KVKLLQLYSE ASVALLKLNN PKDFQELNKQ TKKNMTIDGK ELTISPAYLL WD

Show sample condition

Sample

Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0, Details [U-98% 13C; U-98% 15N], 1.2 mM;20 mM phosphate buffer; 50 mM NaCl; 5 mM Sodium Azide; pH 6.0; 90% H2O; 10% D2O

#	Name	Isotope labeling	Concentration
1	entity	[U-98% 13C; U-98% 15N]	1.2 mM
2	sodium chloride	natural abundance	50 mM
3	sodium phosphate	natural abundance	20 mM
4	sodium azide	natural abundance	5 mM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

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: 2.49 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: 2.49 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: 0.0 ppm, Outliers: 1 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: 2.98 ppm, Outliers: 2 Detail

Protein Blocks Logo

Calculated from 19 models in PDB: 2N6D, Strand ID: A Detail

Release date

2015-10-11

Related entities 1. GNPTAB, : 2 : 6 entities Detail

Interaction partners 1. GNPTAB, : 16 interactors Detail

More details for 16 interactors identified by 5 citations

Experiments performed 7 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 6.0, Details [U-98% 13C; U-98% 15N], 1.2 mM;20 mM phosphate buffer; 50 mM NaCl; 5 mM Sodium Azide; pH 6.0; 90% H2O; 10% D2O

#	Name	Isotope labeling	Concentration
1	entity	[U-98% 13C; U-98% 15N]	1.2 mM
2	sodium chloride	natural abundance	50 mM
3	sodium phosphate	natural abundance	20 mM
4	sodium azide	natural abundance	5 mM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

2 3D 1H-13C NOESY aliphatic

Instrument

Bruker Avance - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	entity	[U-98% 13C; U-98% 15N]	1.2 mM
2	sodium chloride	natural abundance	50 mM
3	sodium phosphate	natural abundance	20 mM
4	sodium azide	natural abundance	5 mM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

3 3D 1H-13C NOESY aromatic

Instrument

Bruker Avance - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	entity	[U-98% 13C; U-98% 15N]	1.2 mM
2	sodium chloride	natural abundance	50 mM
3	sodium phosphate	natural abundance	20 mM
4	sodium azide	natural abundance	5 mM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

4 3D 1H-15N NOESY

Instrument

Bruker Avance - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	entity	[U-98% 13C; U-98% 15N]	1.2 mM
2	sodium chloride	natural abundance	50 mM
3	sodium phosphate	natural abundance	20 mM
4	sodium azide	natural abundance	5 mM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

5 APSY 4D-HACANH

Instrument

Bruker Avance - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	entity	[U-98% 13C; U-98% 15N]	1.2 mM
2	sodium chloride	natural abundance	50 mM
3	sodium phosphate	natural abundance	20 mM
4	sodium azide	natural abundance	5 mM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

6 APSY 5D-CBCACONH

Instrument

Bruker Avance - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	entity	[U-98% 13C; U-98% 15N]	1.2 mM
2	sodium chloride	natural abundance	50 mM
3	sodium phosphate	natural abundance	20 mM
4	sodium azide	natural abundance	5 mM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

7 APSY 5D-HACACONH

Instrument

Bruker Avance - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	entity	[U-98% 13C; U-98% 15N]	1.2 mM
2	sodium chloride	natural abundance	50 mM
3	sodium phosphate	natural abundance	20 mM
4	sodium azide	natural abundance	5 mM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_25760_2n6d.nef
Input source #2: Coordindates	2n6d.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	Warning

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

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

-------110-------120-------130-------140-------150-------160-------170--
PPTFKETNQLKTKLPENLSSKVKLLQLYSEASVALLKLNNPKDFQELNKQTKKNMTIDGKELTISPAYLLWD
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PPTFKETNQLKTKLPENLSSKVKLLQLYSEASVALLKLNNPKDFQELNKQTKKNMTIDGKELTISPAYLLWD

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	172	0	0	100.0

Content subtype: combined_25760_2n6d.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1831		96.5 (chain: A, length: 172)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	Warning	2345 (1)	noe	98.8 (chain: A, length: 172)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 172, Sequence coverage: 96.5%
- Total number of assignments
  - ¹H chemical shifts: 973
  - ¹³C chemical shifts: 679
  - ¹⁵N chemical shifts: 179
- Completeness of assignments
  - Entity_assemble_ID: A
- 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)
29	HIS	ND1	200.902
62	HIS	ND1	202.46
76	ARG	HH22	8.427
76	ARG	HH21	8.279
76	ARG	NH2	70.072

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	1072	971	90.6
¹³C chemical shifts	808	679	84.0
¹⁵N chemical shifts	180	176	97.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	337	328	97.3
¹³C chemical shifts	344	253	73.5
¹⁵N chemical shifts	159	156	98.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	735	643	87.5
¹³C chemical shifts	464	426	91.8
¹⁵N chemical shifts	21	20	95.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	111	105	94.6
¹³C chemical shifts	111	105	94.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	67	65	97.0
¹³C chemical shifts	65	61	93.8
¹⁵N chemical shifts	2	2	100.0

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 172, Sequence coverage: 98.8%
- Total number of restraints: 2345
- Weight of restraints: 1.0 (2345)
- Potential type of restraints: upper-bound-parabolic (2345)
- Range of distance target values: 2.4, 5.5 (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

Keywords Unknown Function

Search

Query history

Resources

Search for primary databases

Search for subsidiary databases

Display

Hits per page

Statistics

Query Changes will take effect after "OK" button is selected.

Maximum hits

Default conjunction operator

Omni-box

Search filter

Sequence search (BLAST)

E-value

Query sequence coverage

Miscellaneous

The number of previewed publications

Completeness of assigned chemical shift

Sequence chart about top aligned regions

Sequence chart about interacting regions

Hit context with highlight

Link destinations for BMRB, PDB and EMDB

Found 1 Document (1.097 seconds)

BMRB: 25760

Sample

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. GNPTAB, : 2 : 6 entities Detail

Interaction partners 1. GNPTAB, : 16 interactors Detail

Experiments performed 7 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 3 contents Detail