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Found 1 Document (0.788 seconds)

BMRB: 17501

2LA3

The NMR structure of the protein NP_344798.1 reveals a CCA-adding enzyme head domain

Authors

MOHANTY, B., SERRANO, P., GERALT, M., HORST, R., WUTHRICH, K.

Assembly

NP 344798.1

Entity

1. NP 344798.1 (polymer, Thiol state: all free), 191 monomers, 22807.51 Da Detail

GMNTVKNKQE ILEAFRESPD MMAILTIIRD LGLKDSWLAA GSVRNFIWNL LSDKSPFDHE TDIDVIFFDP DFSYEETLLL EKKLREDFPQ YQWELKNQVY MHQHSPHTAS YTSSRDAMSK YPERCTAVGL RLNEELDFEL YVPYGLEDIL NFQVRPTPHF LENEDRMELY QTRLSKKNWQ EKWKNLIFKN T

Formula weight

22807.51 Da

Source organism

Streptococcus pneumoniae TIGR4

Exptl. method

solution NMR

Refine. method

molecular dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 99.5 %, Completeness: 94.8 %, Completeness (bb): 94.8 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	94.8 % (2246 of 2370)	95.6 % (1187 of 1242)	92.7 % (855 of 922)	99.0 % (204 of 206)
Backbone	94.8 % (1069 of 1128)	96.8 % (366 of 378)	92.1 % (523 of 568)	98.9 % (180 of 182)
Sidechain	95.4 % (1362 of 1428)	95.0 % (821 of 864)	95.7 % (517 of 540)	100.0 % (24 of 24)
Aromatic	89.0 % (226 of 254)	89.8 % (114 of 127)	87.7 % (107 of 122)	100.0 % (5 of 5)
Methyl	98.9 % (184 of 186)	98.9 % (92 of 93)	98.9 % (92 of 93)

1. NP 344798.1

Show sample condition

Sample

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0, Details 50mM sodium chloride, 20mM sodium phosphate, 4.5mM sodium azide, 1.2mM [U-98% 13C; U-98% 15N] NP_344798.1

#	Name	Isotope labeling	Concentration
1	NP_344798.1	[U-98% 13C; U-98% 15N]	1.2 mM
2	sodium phosphate	natural abundance	20 mM
3	sodium chloride	natural abundance	50 mM
4	sodium azide	natural abundance	4.5 mM
5	H2O	natural abundance	95 %
6	D2O	natural abundance	5 %

LACS Plot; CA

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

Referencing offset: -0.06 ppm, Outliers: 2 Detail

LACS Plot; CB

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

Referencing offset: -0.06 ppm, Outliers: 2 Detail

LACS Plot; HA

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

Referencing offset: -0.04 ppm, Outliers: 1 Detail

LACS Plot; CO

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

Referencing offset: -0.4 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2LA3, Strand ID: A Detail

Release date

2011-03-24

Citation

NMR reveals structural rearrangements associated to substrate insertion in nucleotide-adding enzymes
MOHANTY, B., SERRANO, P., GERALT, M., HORST, R., WUTHRICH, K.
Protein Sci. (2016), 25, 917-925, PubMed 26749007 , DOI 10.1002/pro.2872 , Abstract

Related entities 1. NP 344798.1, : 1 entities Detail

Experiments performed 8 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0, Details 50mM sodium chloride, 20mM sodium phosphate, 4.5mM sodium azide, 1.2mM [U-98% 13C; U-98% 15N] NP_344798.1

#	Name	Isotope labeling	Concentration
1	NP_344798.1	[U-98% 13C; U-98% 15N]	1.2 mM
2	sodium phosphate	natural abundance	20 mM
3	sodium chloride	natural abundance	50 mM
4	sodium azide	natural abundance	4.5 mM
5	H2O	natural abundance	95 %
6	D2O	natural abundance	5 %

2 2D 1H-13C HSQC

Instrument

Bruker Avance - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	NP_344798.1	[U-98% 13C; U-98% 15N]	1.2 mM
2	sodium phosphate	natural abundance	20 mM
3	sodium chloride	natural abundance	50 mM
4	sodium azide	natural abundance	4.5 mM
5	H2O	natural abundance	95 %
6	D2O	natural abundance	5 %

3 4D APSY - HACANH

Instrument

Bruker Avance - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	NP_344798.1	[U-98% 13C; U-98% 15N]	1.2 mM
2	sodium phosphate	natural abundance	20 mM
3	sodium chloride	natural abundance	50 mM
4	sodium azide	natural abundance	4.5 mM
5	H2O	natural abundance	95 %
6	D2O	natural abundance	5 %

4 5D APSY - HACACONH

Instrument

Bruker Avance - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	NP_344798.1	[U-98% 13C; U-98% 15N]	1.2 mM
2	sodium phosphate	natural abundance	20 mM
3	sodium chloride	natural abundance	50 mM
4	sodium azide	natural abundance	4.5 mM
5	H2O	natural abundance	95 %
6	D2O	natural abundance	5 %

5 5D APSY - CBCACONH

Instrument

Bruker Avance - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	NP_344798.1	[U-98% 13C; U-98% 15N]	1.2 mM
2	sodium phosphate	natural abundance	20 mM
3	sodium chloride	natural abundance	50 mM
4	sodium azide	natural abundance	4.5 mM
5	H2O	natural abundance	95 %
6	D2O	natural abundance	5 %

6 15N resolved [1H,1H]-NOESY

Instrument

Bruker Avance - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	NP_344798.1	[U-98% 13C; U-98% 15N]	1.2 mM
2	sodium phosphate	natural abundance	20 mM
3	sodium chloride	natural abundance	50 mM
4	sodium azide	natural abundance	4.5 mM
5	H2O	natural abundance	95 %
6	D2O	natural abundance	5 %

7 13Cali resolved [1H,1H]-NOESY

Instrument

Bruker Avance - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	NP_344798.1	[U-98% 13C; U-98% 15N]	1.2 mM
2	sodium phosphate	natural abundance	20 mM
3	sodium chloride	natural abundance	50 mM
4	sodium azide	natural abundance	4.5 mM
5	H2O	natural abundance	95 %
6	D2O	natural abundance	5 %

8 13Caro resolved [1H,1H]-NOESY

Instrument

Bruker Avance - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	NP_344798.1	[U-98% 13C; U-98% 15N]	1.2 mM
2	sodium phosphate	natural abundance	20 mM
3	sodium chloride	natural abundance	50 mM
4	sodium azide	natural abundance	4.5 mM
5	H2O	natural abundance	95 %
6	D2O	natural abundance	5 %

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_17501_2la3.nef
Input source #2: Coordindates	2la3.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
GMNTVKNKQEILEAFRESPDMMAILTIIRDLGLKDSWLAAGSVRNFIWNLLSDKSPFDHETDIDVIFFDPDFSYEETLLLEKKLREDFPQYQWELKNQVY
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GMNTVKNKQEILEAFRESPDMMAILTIIRDLGLKDSWLAAGSVRNFIWNLLSDKSPFDHETDIDVIFFDPDFSYEETLLLEKKLREDFPQYQWELKNQVY

-------110-------120-------130-------140-------150-------160-------170-------180-------190-
MHQHSPHTASYTSSRDAMSKYPERCTAVGLRLNEELDFELYVPYGLEDILNFQVRPTPHFLENEDRMELYQTRLSKKNWQEKWKNLIFKNT
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MHQHSPHTASYTSSRDAMSKYPERCTAVGLRLNEELDFELYVPYGLEDILNFQVRPTPHFLENEDRMELYQTRLSKKNWQEKWKNLIFKNT

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	191	0	0	100.0

Content subtype: combined_17501_2la3.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	2239		99.0 (chain: A, length: 191)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	4499 (1)	noe	99.0 (chain: A, length: 191)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_3	Warning	799 (797)	.	100.0 (chain: A, length: 191)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 191, Sequence coverage: 99.0%
- Total number of assignments
  - ¹H chemical shifts: 1197
  - ¹³C chemical shifts: 834
  - ¹⁵N chemical shifts: 208
- 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

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	1242	1197	96.4
¹³C chemical shifts	922	834	90.5
¹⁵N chemical shifts	216	208	96.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	378	371	98.1
¹³C chemical shifts	382	318	83.2
¹⁵N chemical shifts	182	177	97.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	864	826	95.6
¹³C chemical shifts	540	516	95.6
¹⁵N chemical shifts	34	31	91.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	99	98	99.0
¹³C chemical shifts	99	98	99.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	127	114	89.8
¹³C chemical shifts	122	107	87.7
¹⁵N chemical shifts	5	5	100.0

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 191, Sequence coverage: 99.0%
- Total number of restraints: 4499
- Weight of restraints: 1.0 (4499)
- Potential type of restraints: upper-bound-parabolic (4499)
- 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

Dihedral angle restraints

Saveframe: DYANA/DIANA_dihedral_3
- Status: Warning
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 191, Sequence coverage: 100.0%
- Total number of restraints: 797
- Total number of restraints per polymer type: 797
- Weight of restraints: 1.0 (797)
- Potential type of restraints: square-well-parabolic (797)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords ATP binding, CCA-adding domain, CTP binding, DUF925, NP_344798.1, PJ06042C

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Found 1 Document (0.788 seconds)

BMRB: 17501

Sample

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. NP 344798.1, : 1 entities Detail

Experiments performed 8 experiments Detail

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NMR combined restraints 4 contents Detail